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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS1997

Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.

Norman, Michael L.↗
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↗
NASA NTRS2006

Non-linear controls influence functions in an aircraft dynamics simulator

In the development and testing of novel structural and controls concepts, such as morphing aircraft wings, appropriate models are needed for proper system characterization. In most instances, available system models do not provide the required additional degrees of freedom for morphing structures but may be modified to some extent to achieve a compatible system. The objective of this study is to apply wind tunnel data collected for an Unmanned Air Vehicle (UAV), that implements trailing edge morphing, to create a non-linear dynamics simulator, using well defined rigid body equations of motion, where the aircraft stability derivatives change with control deflection. An analysis of this wind tunnel data, using data extraction algorithms, was performed to determine the reference aerodynamic force and moment coefficients for the aircraft. Further, non-linear influence functions were obtained for each of the aircraft s control surfaces, including the sixteen trailing edge flap segments. These non-linear controls influence functions are applied to the aircraft dynamics to produce deflection-dependent aircraft stability derivatives in a non-linear dynamics simulator. Time domain analysis of the aircraft motion, trajectory, and state histories can be performed using these nonlinear dynamics and may be visualized using a 3-dimensional aircraft model. Linear system models can be extracted to facilitate frequency domain analysis of the system and for control law development. The results of this study are useful in similar projects where trailing edge morphing is employed and will be instrumental in the University of Maryland s continuing study of active wing load control.

Guerreiro, Nelson M.↗
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↗
DOE OSTI2017

Combined molecular and spin dynamics simulation of bcc iron with lattice vacancies

By using an atomistic model that treats both translational and spin degrees of freedom, we have performed combined molecular and spin dynamics simulations to study dynamic properties of BCC iron with varying vacancy concentrations. Atomic interactions are described by an empirical many-body potential while spin interactions are handled with a Heisenberg-like Hamiltonian with a coordinate dependent exchange interaction. By calculating the Fourier transform of spatial and temporal correlation functions, vibrational and magnetic excitations have been studied. The creation of vacancies in the material has shown splitting of the characteristic transverse spin-wave excitations, indicating the production of additional excitation modes. By merging two vacancies to form a nearest neighbor pair, we find that these modes become more distinct. Investigation of longitudinal spin-wave excitations reveals interactions between constituent components of the split transverse excitations.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Molecular dynamics simulations of hydrogen diffusion in aluminum

In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear how they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Calculations of Beam-Beam Effect and Luminosity for Crab Dynamics Simulations in JLEIC

Crab crossing is an integral part of the Jefferson Lab Electron-Ion Collider (JLEIC) design to achieve high luminosity while meeting the detection and physics pro-gram requirements. The crab crossing scheme provides a head-on beam-beam collision for beams with a nonzero crossing angle. Simulations of crabbing dynamics currently do not include beam-beam effects. We describe a framework for accurate simulation of beam-beam effects on crabbing dynamics by applying a numerical calculation of the Bassetti-Erskine analytic solution to symplectic particle tracking codes. The numerical calculation is benchmarked against the analytic solution by calculating the luminosity reduction for several colliding beam scenarios. Benchmarking results show good agreement be-tween the numerical calculation and analytic solution, paving the way for implementation of the beam-beam kick to Elegant tracking simulations.

Huang, He↗
DOE OSTI2015

Atomic packing and diffusion in Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy analyzed by ab initio molecular dynamics simulation

In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗