Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Hydrophobins are small (similar to 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/ hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily P-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in a-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

Stochastic gauges in quantum dynamics for many-body simulations

Quantum dynamics simulations can be improved using novel quasiprobability distributions based on non-orthogonal Hermitian kernel operators. This introduces arbitrary functions (gauges) into the stochastic equations. which can be used to tailor them for improved calculations. A possible application to full quantum dynamic simulations of BEC's is presented. (C) 2001 Elsevier Science B.V. All rights reserved.

Gas-surface interactions in the thermal and sub-thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study the interaction of low-energy Ar atoms with the Ni(001) surface, Angular scattering distributions, in and out of the plane of incidence, are investigated as a function of incident energy, angles of incidence, crystallographic orientation of the incident beam and surface temperature. The results show a clear transition to the structure scattering regime at around 2 eV. However, at lower energies, two sub-regimes are revealed by the simulations, Far energies up to 250 meV, scattering is mainly diffuse, and significant trapping on the surface is observed, At energies above this level, lobular patterns start to form and trapping decreases with the increase in energy, Generally, there is a weak temperature dependence, but variations in the angle of incidence and/or changes in the crystallographic direction, generate significant changes in the scattering patterns.

Non-equilibrium energy and momentum accommodation coefficients of Ar atoms scattered from Ni(001) in the thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study energy and momentum transfer of low-energy Ar atoms scattered from the Ni(001) surface. The investigation concentrates on the dependence of these processes on incident energy, angles of incidence and surface temperature. Energy transfer exhibits a strong dependence on the surface temperature, at incident energies below 500 meV, and incident angles close to specular incidence. Above 500 meV, the surface temperature dependence vanishes, and a limiting value in the amount of energy transferred to the surface is attained. Momentum exchange is investigated in terms of tangential and normal components. Both components exhibit a weak surface temperature dependence, but they have opposite behaviours at all incidence angles. In each component, momentum can be lost or gained following the interaction with the surface. (C) 1997 Elsevier Science B.V.

Molecular dynamics characterization of n-octyl-beta-D-glucopyranoside micelle structure in aqueous solution

n-Octyl-beta-D-glueopyranoside (OG) is a non-ionic glycolipid, which is used widely in biotechnical and biochemical applications. All-atom molecular dynamics simulations from two different initial coordinates and velocities in explicit solvent have been performed to characterize the structural behaviour of an OG aggregate at equilibrium conditions. Geometric packing properties determined from the simulations and small angle neutron scattering experiment state that OG micelles are more likely to exist in a non-spherical shape, even at the concentration range near to the critical micelle concentration (0.025 M). Despite few large deviations in the principal moment of inertia ratios, the average micelle shape calculated from both simulations is a prolate ellipsoid. The deviations at these time scales are presumably the temporary shape change of a micelle. However, the size of the micelle and the accessible surface areas were constant during the simulations with the micelle surface being rough and partially elongated. Radial distribution functions computed for the hydroxyl oxygen atoms of an OG show sharper peaks at a minimum van der Waals contact distance than the acetal oxygen, ring oxygen, and anomeric carbon atoms. This result indicates that these atoms are pointed outwards at the hydrophilic/hydrophobic interface, form hydrogen bonds with the water molecules, and thus hydrate the micelle surface effectively. (c) 2005 Elsevier Inc. All rights reserved.

Using computational fluid dynamics in combating erosion-corrosion

Computational fluid dynamics was used to search for the links between the observed pattern of attack seen in a bauxite refinery's heat exchanger headers and the hydrodynamics inside the header. Validation of the computational fluid dynamics results was done by comparing then with flow parameters measured in a 1:5 scale model of the first pass header in the laboratory. Computational fluid dynamics simulations were used to establish hydrodynamic similarity between the 1:5 scale and full scale models of the first pass header. It was found that the erosion-corrosion damage seen at the tubesheet of the first pass header was a consequence of increased levels of turbulence at the tubesheet caused by a rapidly turning flow. A prismatic flow corrections device introduced in the past helped in rectifying the problem at the tubesheet but exaggerated the erosion-corrosion problem at the first pass header shell. A number of alternative flow correction devices were tested using computational fluid dynamics. Axial ribbing in the first pass header and an inlet flow diffuser have shown the best performance and were recommended for implementation. Computational fluid dynamics simulations have revealed a smooth orderly low turbulence flow pattern in the second, third and fourth pass as well as the exit headers where no erosion-corrosion was seen in practice. This study has confirmed that near-wall turbulence intensity, which can be successfully predicted by using computational fluid dynamics, is a good hydrodynamic predictor of erosion-corrosion damage in complex geometries. (c) 2006 Published by Elsevier Ltd.

Flush air data system calibration using numerical simulation

The use of computational fluid dynamics simulations for calibrating a flush air data system is described, In particular, the flush air data system of the HYFLEX hypersonic vehicle is used as a case study. The HYFLEX air data system consists of nine pressure ports located flush with the vehicle nose surface, connected to onboard pressure transducers, After appropriate processing, surface pressure measurements can he converted into useful air data parameters. The processing algorithm requires an accurate pressure model, which relates air data parameters to the measured pressures. In the past, such pressure models have been calibrated using combinations of flight data, ground-based experimental results, and numerical simulation. We perform a calibration of the HYFLEX flush air data system using computational fluid dynamics simulations exclusively, The simulations are used to build an empirical pressure model that accurately describes the HYFLEX nose pressure distribution ol cr a range of flight conditions. We believe that computational fluid dynamics provides a quick and inexpensive way to calibrate the air data system and is applicable to a broad range of flight conditions, When tested with HYFLEX flight data, the calibrated system is found to work well. It predicts vehicle angle of attack and angle of sideslip to accuracy levels that generally satisfy flight control requirements. Dynamic pressure is predicted to within the resolution of the onboard inertial measurement unit. We find that wind-tunnel experiments and flight data are not necessary to accurately calibrate the HYFLEX flush air data system for hypersonic flight.

Method for determining the shear stress in cylindrical systems

We develop a method for determining the elements of the pressure tensor at a radius r in a cylindrically symmetric system, analogous to the so-called method of planes used in planar systems [B. D. Todd, Denis J. Evans, and Peter J. Daivis, Phys. Rev. E 52, 1627 (1995)]. We demonstrate its application in determining the radial shear stress dependence during molecular dynamics simulations of the forced flow of methane in cylindrical silica mesopores. Such expressions are useful for the examination of constitutive relations in the context of transport in confined systems.

Wall mediated transport in confined spaces: Exact theory for low density

We present a theory for the transport of molecules adsorbed in slit and cylindrical nanopores at low density, considering the axial momentum gain of molecules oscillating between diffuse wall reflections. Good agreement with molecular dynamics simulations is obtained over a wide range of pore sizes, including the regime of single-file diffusion where fluid-fluid interactions are shown to have a negligible effect on the collective transport coefficient. We show that dispersive fluid-wall interactions considerably attenuate transport compared to classical hard sphere theory.

Tractable molecular theory of transport of Lennard-Jones fluids in nanopores

We present here a tractable theory of transport of simple fluids in cylindrical nanopores, which is applicable over a wide range of densities and pore sizes. In the Henry law low-density region the theory considers the trajectories of molecules oscillating between diffuse wall collisions, while at higher densities beyond this region the contribution from viscous flow becomes significant and is included through our recent approach utilizing a local average density model. The model is validated by means of equilibrium as well nonequilibrium molecular dynamics simulations of supercritical methane transport in cylindrical silica pores over a wide range of temperature, density, and pore size. The model for the Henry law region is exact and found to yield an excellent match with simulations at all conditions, including the single-file region of very small pore size where it is shown to provide the density-independent collective transport coefficient. It is also shown that in the absence of dispersive interactions the model reduces to the classical Knudsen result, but in the presence of such interactions the latter model drastically overpredicts the transport coefficient. For larger micropores beyond the single-file region the transport coefficient is reduced at high density because of intermolecular interactions and hindrance to particle crossings leading to a large decrease in surface slip that is not well represented by the model. However, for mesopores the transport coefficient increases monotonically with density, over the range studied, and is very well predicted by the theory, though at very high density the contribution from surface slip is slightly overpredicted. It is also seen that the concept of activated diffusion, commonly associated with diffusion in small pores, is fundamentally invalid for smooth pores, and the apparent activation energy is not simply related to the minimum pore potential or the adsorption energy as generally assumed. (C) 2004 American Institute of Physics.

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation. (C) 2004 American Institute of Physics.

Adsorbate transport in nanopores

We present a tractable theory of transport of simple fluids in cylindrical nanopores, considering trajectories of molecules between diffuse wall collisions at low-density, and including viscous flow contributions at higher densities. The model is validated through molecular dynamics simulations of supercritical methane transport, over a wide range of conditions. We find excellent agreement between model and simulation at low to medium densities. However, at high densities the model tends to over-predict the transport behaviour, due to a large decrease in surface slip that is not well represented by the model. It is also seen that the concept of activated diffusion, commonly associated with diffusion in small pores, is fundamentally invalid for smooth pores.

Enhancement of hydrogen physisorption on single-walled carbon nanotubes resulting from defects created by carbon bombardment

The defect effect on hydrogen adsorption on single-walled carbon nanotubes (SWNTs) has been studied by using extensive molecular dynamics simulations and density functional theory (DFT) calculations. It indicates that the defects created on the exterior wall of the SWNTs by bombarding the tube wall with carbon atoms and C-2 dimers at a collision energy of 20 eV can enhance the hydrogen adsorption potential of the SWNTs substantially. The average adsorption energy for a H-2 molecule adsorbed on the exterior wall of a defected (10,10) SWNT is similar to 150 meV, while that for a H-2 molecule adsorbed on the exterior wall of a perfect (10,10) SWNT is similar to 104 meV. The H-2 sticking coefficient is very sensitive to temperature, and has a maximum value around 70 to 90 K. The electron density contours, the local density of states, and the electron transfers obtained from the DFT calculations clearly indicate that the H-2 molecules are all physisorbed on the SWNTs. At temperatures above 200 K, most of the H-2 molecules adsorbed on the perfect SWNT are soon desorbed, but the H-2 molecules can still remain on the defected SWNTs at 300 K. The detailed processes of H-2 molecules adsorbing on and desorbing from the (10,10) SWNTs are demonstrated.