Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dynamics simulation”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2023

Investigating the time dependence of neutron-proton equilibration using molecular dynamics simulations

Neutron-proton equilibration has previously been studied experimentally in dynamically deformed nuclei in heavy ion collisions [Phys. Rev. Lett. 118, 062501 (2017); Phys. Rev. C 95, 044604 (2017)] using the NIMROD detector array at the Cyclotron Institute at Texas A&M University. Results indicated the composition of the two heaviest fragments originating from the excited projectile-like fragment evolved exponential with respect to their orientation angle to be more similar. Constrained Molecular Dynamics and Antisymmetrized Molecular Dynamics simulations were performed for different formulations of the density dependence of the asymmetry energy term of the nuclear equation of state. The simulations are compared to experimental results, which indicate a better agreement with a softer interaction in the nuclear equation of state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2011

Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

Wilson, Michael A.↗
DOE OSTI2015

Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

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

Sensitivity Analysis and Uncertainty Quantification for the LAMMPS Molecular Dynamics Simulation Code

We examine sensitivity analysis and uncertainty quantification for molecular dynamics simulation. Extreme (large or small) output values for the LAMMPS code often occur at the boundaries of input regions, and uncertainties in those boundary values are overlooked by common SA methods. Similarly, input values for which code outputs are consistent with calibration data can also occur near boundaries. Upon applying approaches in the literature for imprecise probabilities (IPs), much more realistic results are obtained than for the complacent application of standard SA and code calibration.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1989

A model for including thermal conduction in molecular dynamics simulations

A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

Wu, Yue↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

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

A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

RDX Compression, α→ γ Phase Transition, and Shock Hugoniot Calculations from Density-Functional-Theory-Based Molecular Dynamics Simulations

Prediction of the density and lattice compression properties of the α and γ phases of the hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) crystal and of the low-pressure α → γ phase transition upon pressure increase are general tests used to assess the accuracy of density-functional-theory- (DFT-) based computational methods and to identify the essential parameters that govern the behavior of this high-energy-density material under extreme conditions. The majority of previous DFT studies have analyzed such issues under static optimization conditions by neglecting the corresponding temperature effects. In this paper, we extend previous investigations and analyze the performance of dispersion-corrected density functional theory to predict the compression of RDX in the pressure range of 0–9 GPa and the corresponding α → γ phase transition under realistic temperature and pressure conditions. We demonstrate that, by using static dispersion-corrected density functional theory calculations, direct interconversion between the α and γ phases upon compression is not observed. This limitation can be addressed by using isobaric–isothermal molecular dynamic simulations in conjunction with DFT-D2-calculated potentials, an approach that is shown to provide an accurate description of both the crystallographic RDX lattice parameters and the dynamical effects associated with the α→ γ phase transformation. An even more comprehensive and demanding analysis was done by predicting the corresponding shock Hugoniot curve of RDX in the pressure range of 0–9 GPa. It was found that the theoretical results reproduce reasonably well the available experimental Hugoniot shock data for both the α and γ phases. Finally, the results obtained demonstrate that a satisfactory prediction of the shock properties in high-energy-density materials undergoing crystallographic and configurational transformations is possible through the combined use of molecular dynamics simulations in the isobaric–isothermal ensemble with dispersion-corrected density functional theory methods.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Molecular dynamics simulations of intergranular fracture in UO2 with nine empirical interatomic potentials

The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2014

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗