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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
DOE OSTI2018

Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces

Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, the film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.

bubble attachment↗
DOE OSTI2018

Nonadiabatic dynamics simulations of photoexcited urocanic acid

Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Here, the initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations.

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

Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Temperature dependence of the solid-liquid interface free energy of Ni and Al from molecular dynamics simulation of nucleation

The temperature dependence of the solid-liquid interfacial free energy, γ, is investigated for Al and Ni at the undercooled temperature regime based on a recently developed persistent-embryo method. The atomistic description of the nucleus shape is obtained from molecular dynamics simulations. The computed γ shows a linear dependence on the temperature. The values of γ extrapolated to the melting temperature agree well with previous data obtained by the capillary fluctuation method. Here, using the temperature dependence of γ, we estimate the nucleation free energy barrier in a wide temperature range from the classical nucleation theory. The obtained data agree very well with the results from the brute-force molecular dynamics simulations.

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

Anisotropy of the solid–liquid interface properties of the Ni–Zr B33 phase from molecular dynamics simulation

Solid–liquid interface (SLI) properties of the Ni–Zr B33 phase were determined from molecular dynamics simulations. In order to perform these measurements, a new semi-empirical potential for Ni–Zr alloy was developed that well reproduces the material properties required to model SLIs in the Ni 50.0 Zr 50.0 alloy. In particular, the developed potential is shown to provide that the solid phase emerging from the liquid Ni 50.0 Zr 50.0 alloy is B33 (apart from a small fraction of point defects), in agreement with the experimental phase diagram. The SLI properties obtained using the developed potential exhibit an extraordinary degree of anisotropy. It is observed that anisotropies in both the interfacial free energy and mobility are an order of magnitude larger than those measured to date in any other metallic compound. Moreover, the [0 1 0] interface is shown to play a significant role in the observed anisotropy. Our data suggest that the [0 1 0] interface simultaneously corresponds to the lowest mobility, the lowest free energy and the highest stiffness of all inclinations in B33 Ni–Zr. This finding can be understood by taking into account a rather complicated crystal structure in this crystallographic direction.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Molecular dynamics simulation of bicrystalline metal surface treatment

The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

New electric force and charge exchange modules in discrete element model enables particle dynamics simulation in electric field

Discrete element modeling (DEM) is an important technique for particle dynamics simulation. The field of metal additive manufacturing often utilizes DEM to simulate the rheological behaviors of powder. Standard contact and short-range interactions are sufficient in most cases but insufficient to describe the particle dynamics with the influence of an electric field. Modeling such a system requires additional physics to describe the particle–field interactions. The relevant physics has been experimentally understood but is not yet available in DEM. Here, we develop a charge exchange and an electric force module. The electric force module governs particle response to the electric field, while the charge exchange module enables particles to acquire proper charge during contact with charged geometries. We validate the modules against analytical calculations and high-speed videos of electrostatic powder deposition experiments. Notably, the model struggles to capture the initial particle levitation. We later deploy a modified electric field, as supported by static electric field simulation, to better approximate the electric field penetration into the powder layer. This modification improves the model’s capability of simulating realistic particle levitation. The results highlight the challenges of modeling particle behaviors in the electric field while demonstrating the feasibility of obtaining quantitative results, which are difficult to measure experimentally.

charge exchange↗
DOE OSTI2022

Extracting Inelastic Scattering Cross Sections for Finite and Aperiodic Materials from Electronic Dynamics Simulations

Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. Here, in this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

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

Molecular Rotational Dynamics in Mixed CH 4 –CO 2 Hydrates: Insights from Molecular Dynamics Simulations

The impact of guest molecule composition on the rotational dynamics in CH 4 , CO 2 , and mixed CH 4 –CO 2 gas hydrates is investigated with classical molecular dynamics simulations. Rotational autocorrelation functions are calculated for the guest and host molecules in each hydrate composition from simulation trajectories at 10, 40, 190, and 270 K. Analysis of these functions for each molecule is further decomposed into cage type for each CH 4 and CO 2 guest and cage face for the H 2 O host. CH 4 becomes more constrained, and CO 2 gains freedom in the mixed guest systems. Mixing guest species in gas hydrates alters the intermolecular interaction environment, impacting the rotational motion of the guest molecules. This effect is also seen in the host lattice H 2 O molecules, as evidence of molecular rotations is seen in the CO 2 hydrate at 270 K during longer simulations.

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

Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Molecular dynamics simulation of gold cluster growth during sputter deposition

We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Molecular dynamics simulations of field emission from a planar nanodiode

High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Resolving pseudosymmetry in γ-TiAl using cross-correlation electron backscatter diffraction with dynamically simulated reference patterns

Pseudosymmetry is a phenomenon that occurs when grains with different lattice parameters produce nearly identical diffraction patterns such that conventional electron backscatter diffraction (EBSD) techniques are unable to unambiguously differentiate the lattice orientations. This commonly occurs in materials with near-unity tetragonality, such as γ-TiAl. The current study uses cross-correlation EBSD to resolve pseudosymmetry in γ-TiAl. Three dynamically simulated reference patterns are generated for each point in the scan, one for each of the three potential pseudosymmetric orientations, which are subsequently correlated with the original pattern using six different methods in order to identify the correct orientation. The methods are first applied to a scan of dynamically simulated patterns, which is used to evaluate the sensitivity of the method to pattern resolution, pattern noise and pattern center error. It was determined that all six methods were 100% successful up to about 13 µm of pattern center error and pattern resolutions of about 80 × 80 pixels, and hence the methods were applied to an experimental sample of lamellar γ-TiAl. A hybrid combination of two of the methods was shown to successfully select the correct pseudosymmetry for about 96% of the points in the scan, improving upon the 70% accuracy of the Hough-based methods for the current study and 90% accuracy for previous studies resolving pseudosymmetry in lamellar γ-TiAl.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

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

Rotational Brownian Dynamics simulations of clathrin cage formation

The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

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

On Parallelizing Single Dynamic Simulation Using HPC Techniques and APIs of Commercial Software

Time-domain simulations are heavily used in today’s planning and operation practices to assess power system transient stability and post-transient voltage/frequency profiles following severe contingencies to comply with industry standards. Because of the increased modeling complexity, it is several times slower than real time for state-of-the-art commercial packages to complete a dynamic simulation for a large-scale model. With the growing stochastic behavior introduced by emerging technologies, power industry has seen a growing need for performing security assessment in real time. This paper presents a parallel implementation framework to speed up a single dynamic simulation by leveraging the existing stability model library in commercial tools through their application programming interfaces (APIs). Several high performance computing (HPC) techniques are explored such as parallelizing the calculation of generator current injection, identifying fast linear solvers for network solution, and parallelizing data outputs when interacting with APIs in the commercial package, TSAT. The proposed method has been tested on a WECC planning base case with detailed synchronous generator models and exhibits outstanding scalable performance with sufficient accuracy.

Diao, Ruisheng↗