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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two crossovers at molecular level are discussed.

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

Structural and chemical orders in N i 64.5 Z r 35.5 metallic glass by molecular dynamics simulation

The atomic structure of Ni 64.5 Zr 35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni 64.5 Zr 35.5 , i.e., Mixed- Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICOCube and Twined-Cube clusters exhibit the characteristics of the crystalline B2 phase. In conclusion, our simulation results suggest that the weak glass-forming ability (GFA) of Ni 64.5 Zr 35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Executive Summary: Special Section on Credible Computational Fluid Dynamics Simulations

This summary presents the motivation for the Special Section on the credibility of computational fluid dynamics (CFD) simulations, its objective, its background and context, its content, and its major conclusions. Verification and validation (V&V) are the processes for establishing the credibility of CFD simulations. Validation assesses whether correct things are performed and verification assesses whether they are performed correctly. Various aspects of V&V are discussed. Progress is made in verification of simulation models. Considerable effort is still needed for developing a systematic validation method that can assess the credibility of simulated reality.

Mehta, Unmeel B.↗
DOE OSTI2015

Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations

The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1996

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

Han, Jie↗
DOE OSTI2016

Counter-ion binding and mobility in the presence of hydrophobic polyions – combining molecular dynamics simulations and NMR

Counter-ion binding and mobility in aqueous solutions of partially hydrophobic ionene oligoions is studied here by a combination of all-atomic molecular dynamics (MD) simulations and NMR ({sup 19}F and {sup 81}Br nuclei) measurements. We present results for 12, 12–ionenes in the presence of different halide ions (F{sup −}, Cl{sup −}, Br{sup −} and I{sup −}), as well as their mixtures; the latter allowing us to probe counter-ion selectivity of these oligoions. We consolidate both structural and dynamic information, in particular simulated radial distribution functions and average residence times of counter-ions in the vicinity of ionenes and NMR data in the form of counter-ion chemical shift and self-diffusion coefficients. On one hand, previously reported enthalpy of dilution and mixing measurements show a reverse counter-ion sequence for 12, 12–ionenes with respect to their less hydrophobic 3, 3– and 6, 6– analogues. On the other hand, the current MD and NMR data, reflecting the counter-ion binding tendencies to the ionene chain, give evidence for the same ordering as that observed by MD for 3, 3–ionenes. This is not seen as a contradiction and can be rationalized on the basis of increasing chain hydrophobicity, which has different consequences for enthalpy and ion-binding. The latter is reflecting free energy changes and as such includes both enthalpic and entropic contributions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

DNA self-assembly is a highly programmable method to construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study the structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments involving different motif designs, structural optimization, or new synthesis methods, while their mechanics are not yet fully understood. The complex properties of DNA crystals are difficult to study via experiments alone, and numerical simulation can complement and aid the experiments. The coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We found that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

DNA crystal↗
DOE OSTI2021

Stoichiometric tuning of lattice flexibility and Na diffusion in NaAlSiO 4 : quasielastic neutron scattering experiment and ab initio molecular dynamics simulations

We have performed quasielastic neutron scattering (QENS) experiments up to 1243 K and ab initio molecular dynamics (AIMD) simulations to investigate the Na diffusion in various phases of NaAlSiO4 (NASO), namely, low-carnegieite (L-NASO; trigonal), high-carnegieite (H-NASO; cubic) and nepheline (N-NASO; hexagonal) phases. The QENS measurements reveal Na ions localized diffusion behavior in L-NASO and N-NASO, but long-range diffusion behavior in H-NASO. Furthermore, the AIMD simulation supplemented the QENS measurements and showed that excess Na ions in H-NASO enhance the host network flexibility and activate the AlO 4 /SiO 4 tetrahedra rotational modes. These framework modes enable the long-range diffusion of Na across a pathway of interstitial sites. The simulations also show Na diffusion in Na-deficient N-NASO through vacant Na sites along the hexagonal c-axis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here in this paper, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations

The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm{sup 3} along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Early Stage of Oxidation on Titanium Surface by Reactive Molecular Dynamics Simulation

Understanding of metal oxidation is very critical to corrosion control, catalysis synthesis, and advanced materials engineering. Metal oxidation is a very complex phenomenon, with many different processes which are coupled and involved from the onset of reaction. In this work, the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics (MD) simulations using a reactive force field (ReaxFF). We show that oxygen transport is the dominant process during the initial oxidation. Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titanium (0001) surface and further prevented oxidation in the deeper layers. As a result, the mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Molecular dynamics simulation of joining process of Ag-Au nanowires and mechanical properties of the hybrid nanojoint

The nanojoining process of Ag-Au hybrid nanowires at 800K was comprehensively studied by virtue of molecular dynamics (MD) simulation. Three kinds of configurations including end-to-end, T-like and X-like were built in the simulation aiming to understand the nanojoining mechanism. The detailed dynamic evolution of atoms, crystal structure transformation and defects development during the nanojoining processes were performed. The results indicate that there are two stages in the nanojoining process of Ag-Au nanowires which are atom diffusion and new bonds formation. Temperature is a key parameter affecting both stages ascribed to the energy supply and the optimum temperature for Ag-Au nanojoint with diameter of 4.08 nm has been discussed. The mechanical properties of the nanojoint were examined with simulation of tensile test on the end-to-end joint. It was revealed that the nanojoint was strong enough to resist fracture at the joining area.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).

Kubicki, J. D.↗
NASA NTRS1989

Test and validation for robot arm control dynamics simulation

The Flight Telerobotic Servicer (FTS) program will require an ability to develop, in a cost effective manner, many simulation models for design, analysis, performance evaluation, and crew training. Computational speed and the degree of modeling fidelity associated with each simulation must be commensurate with problem objectives. To demonstrate evolving state-of-the-art general purpose multibody modeling capabilities, to validate these by laboratory testing, and to expose their modeling shortcomings, two focus problems at the opposite ends of the simulation spectrum are defined: (1) Coarse Acquisition Control Dynamics. Create a real time man-in-the-control-loop simulator. Provide animated graphical display of robot arm dynamics and tactile feedback sufficient for cueing the operator. Interface simulator software with human operated tactile feedback controller; i.e., the Kraft mini-master. (2) Fine, Precision Mode Control Dynamics. Create a high speed, high fidelity simulation model for the design, analysis, and performance evaluation of autonomous 7 degree-of-freedom (DOF) trajectory control algorithms. This model must contain detail dynamic models for all significant dynamics elements within the robot arm, such as joint drive mechanisms.

Yae, K. Harold↗
DOE OSTI2016

Post-processing interstitialcy diffusion from molecular dynamics simulations

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Molecular Dynamics Simulations of the Adsorption of Phthalate Esters on Smectite Clay Surfaces

The partitioning of organic contaminants between water and solid surfaces is a key process controlling their fate and transport in natural environments. A novel methodology was developed to predict the adsorption of organic contaminants by smectite clay minerals (high specific surface area adsorbents abundant in natural soils) using molecular dynamics (MD) simulations. The methodology models a stack of flexible Ca- montmorillonite lamellae in direct contact with a bulk aqueous reservoir and uses the metadynamics technique to facilitate the exploration of the free energy landscape. The methodology was tested and validated in the case of six phthalate esters, widely used chemical plasticizers with endocrine disrupting properties. Simulation predictions reveal strong phthalate adsorption, especially for the larger and more hydrophobic phthalates. Predicted partition coefficients (K d values) are consistent with collected batch experimental data. Adsorption was observed on both the exterior basal surfaces and within the interlayer nanopore, with phthalate molecules predominately adopting a flat orientation on the clay surface. Intercalation was also detected in complementary X-ray diffraction (XRD) experiments. A strong inverse relationship between extent of adsorption and clay surface charge density was observed, as phthalate molecules preferentially occupied the more hydrophobic uncharged patches on each surface. Detailed analysis of the free energy of adsorption revealed that phthalate affinity for the clay surface results from a small favorable van der Waals contribution and a large favorable entropic contribution. Overall, this research demonstrates the substantial affinity of smectite clays for phthalate esters and establishes a computational methodology capable of predicting the water-clay partition coefficients of organic contaminants, a key parameter in environmental fate and transport models.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Extrapolation of thermal conductivity in non-equilibrium molecular dynamics simulations to bulk scale

Predictions of the bulk scale thermal conductivity of solids using non-equilibrium molecular dynamics (MD) simulations have relied on the linear extrapolation of the thermal resistivity versus the reciprocal of the system length in the simulations. Several studies have reported deviation of the extrapolation from linearity near the micro-scale, raising a concern of its applicability to large systems. To investigate this issue, present work conducted extensive MD simulations of silicon with two different potentials (EDIP and Tersoff-II) for unprecedented length scales up to 10.3 μm and simulation times up to 530 ns. For large systems ≥0.35 μm in size the non-linearity of the extrapolation of the reciprocal of the thermal conductivity is mostly due to ignoring the dependence of the thermal conductivity on temperature. To account for such dependence, the present analysis fixes the temperature range for determining the gradient for calculating the thermal conductivity values. However, short systems ≤0.23 μm in size show significant non-linearity in the calculated thermal conductivity values using a temperature window of 500 ± 10 K from the simulations results with the EDIP potential. Since these system sizes are shorter than the mean phonon free path in EDIP (~0.22 μm), the nonlinearity may be attributed to phonon transport. For the MD simulations with the Tersoff-II potential there is no significant non-linearity in the calculated thermal conductivity values for systems ranging in size from 0.05 to 5.4 μm.

42 ENGINEERING↗