Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Monte Carlo simulation of ion conduction in silver based glassy electrolytes

A simplified structural model to study the ionic transport in silver based glasses has been formulated. The diffusion of silver ion under the influence of coulombic interactions of mobile cation and anions has been studied. Monte Carlo simulations of silver ion hopping in glass have suggested two different kinds of population of silver ions. We discuss the results of variation in diffusion constant with dopant (AgI) concentration using the diffusion path model. (C) 1997 Elsevier-Science S.A.

Simulation and modelling of orbital debris environment by equivalent breakups

It is well known that the increasing space activities pose a serious threat to future missions. This is mainly due to the presence of spent stages, rockets spacecraft and fragments which can lead to collisions. The calculation of the collision probability of future space vehicles with the orbital debris is necessary for estimating the risk. There is lack of adequately catalogued and openly available detailed information on the explosion characteristics of trackable and untrackable debris data. Such a situation compels one to develop suitable mathematical modelling of the explosion and the resultant debris environment. Based on a study of the available information regarding the fragmentation, subsequent evolution and observation, it turns out to be possible to develop such a mathematical model connecting the dynamical features of the fragmentation with the geometrical/orbital characteristics of the debris and representing the environment through the idea of equivalent breakup. (C) 1997 COSPAR.

Translational and rotational motion in molecular liquids: A computer simulation study of Lennard-Jones ellipsoids

In order to understand the translational and rotational motion in dense molecular liquids, detailed molecular dynamics simulations of Lennard-Jones ellipsoids have been carried out for three different values of the aspect ratio kappa. For ellipsoids with an aspect ratio equal to 2, the product of the translational diffusion coefficient (D-T) and the average orientational correlation time of the l-th rank harmonics (tau(lR)), converges to a nearly constant value at high density. Surprisingly, this density independent value of D-T tau(lR) is within 5% of the hydrodynamic prediction with the slip boundary condition. This is despite the fact that both D-T and tau(lR) themselves change nearly by an order of magnitude in the density range considered, and the rotational correlation function itself is strongly nonexponential. For small aspect ratios (kappa less than or equal to 1.5), the rotational correlation function remains largely Gaussian even at a very large density, while for a large aspect ratio (kappa greater than or equal to 3), the transition to the nematic liquid-crystalline phase precludes the hydrodynamic regime. Thus, the rotational dynamics of ellipsoids show great sensitivity to the aspect ratio. At low density, tau(lR) goes through a minimum value, indicating the role of interactions in enhancing the rate of orientational relaxation. (C) 1997 American Institute of Physics. [S0021-9606(97)50142-5].

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

Subquadratic quantum number dependence and other anomalies of vibrational dephasing in liquid nitrogen: Molecular dynamics simulation study from the triple point to the critical point and beyond

Vibrational phase relaxation near gas-liquid and liquid-solid phase coexistence has been studied by molecular dynamics simulations of N-N stretch in N-2. Experimentally observed pronounced insensitivity of phase relaxation from the triple point to beyond the boiling point is found to originate from a competition between density relaxation and resonant-energy transfer terms. The sharp rise in relaxation rate near the critical point (CP) can be attributed at least partly to the sharp, rise in vibration-rotation coupling contribution. Substantial subquadratic quantum number dependence of overtone dephasing rate is found near the CP and in supercritical fluids. [S0031-9007 (99)09318-7].

Autoignition in a non-premixed medium: DNS studies on the effects of three-dimensional turbulence

Direct numerical simulation (DNS) results of autoignition in anon-premixed medium under an isotropic, homogeneous, and decaying turbulence are presented. The initial mixture consists of segregated fuel parcels randomly distributed within warm air, and the entire medium is subjected to a three-dimensional turbulence. Chemical kinetics is modeled by a four-step reduced reaction mechanism for autoignition of n-heptane/air mixture. Thus, this work overcomes the principal limitations of a previous contribution of the authors on two-dimensional DNS of autoignition with a one-step reaction model. Specific attention is focused on the differences in the effects of two- and three-dimensional turbulence on autoignition characteristics. The three-dimensional results show that ignition spots are most likely to originate at locations jointly corresponding to the most reactive mixture fraction and low scalar dissipation rate. Further, these ignition spots are found to originate at locations corresponding to the core of local vortical structures, and after ignition, the burning gases move toward the vortex periphery Such a movement is explained as caused by the cyclostrophic imbalance developed when the local gas density is variable. These results lead to the conclusion that the local ignition-zone structure does not conform to the classical stretched flamelet description. Parametric studies show that the ignition delay time decreases with an increase in turbulence intensity. Hence, these three-dimensional simulation results resolve the discrepancy between trends in experimental data and predictions from DNSs of two-dimensional turbulence. This qualitative difference between DNS results from three- and two-dimensional simulations is discussed and attributed to the effect of vortex stretching that is present in the former, but not in the latter.

Excited state structure and dynamics of p-benzoquinone and bromanil from time-resolved resonance Raman spectra and simulation

p-Benzoquinone and its halogen substituted derivatives are known to have differing reactivities in the triplet excited state. While bromanil catalyzes the reduction of octaethylporphyrin most efficiently among the halogenated p-benzoquinones, the reaction does not take place in presence of the unsubstituted p-benzoquinone (T. Nakano and Y. Mori, Bull. Chem. Soc. Jpn., 67, 2627 (1994)). Understanding of such differences requires a detailed knowledge of the triplet state structures, normal mode compositions and excited state dynamics. In this paper, we apply a recently presented scheme (M. Puranik, S. Umapathy, J. G. Snijders, and J. Chandrasekhar, J. Chem, Phys., 115, 6106 (2001)) that combines parameters from experiment and computation in a wave packet dynamics simulation to the triplet states of p-benzoquinone and bromanil. The absorption and resonance Raman spectra of both the molecules have been simulated. The normal mode compositions and mode specific excited state displacements have been presented and compared. Time-dependent evolution of the absorption and Raman overlaps for all the observed modes has been discussed in detail. In p-benzoquinone, the initial dynamics is along the C=C stretching and C-H bending modes whereas in bromanil nearly equal displacements are observed along all the stretching coordinates.

Simulation and experimental study on compositional evolution of Li-Co in LiCoO(2) thin films during sputter deposition

The compositional evolution in sputter deposited LiCoO(2) thin films is influenced by process parameters involved during deposition. The electrochemical performance of these films strongly depends on their microstructure, preferential orientation and stoichiometry. The transport process of sputtered Li and Co atoms from the LiCoO(2) target to the substrate, through Ar plasma in a planar magnetron configuration, was investigated based on the Monte Carlo technique. The effect of sputtering gas pressure and the substrate-target distance (d(st)) on Li/Co ratio, as well as, energy and angular distribution of sputtered atoms on the substrate were examined. Stable Li/Co ratios have been obtained at 5 Pa pressure and d(st) in the range 5 11 cm. The kinetic energy and incident angular distribution of Li and Co atoms reaching the substrate have been found to be dependent on sputtering pressure. Simulations were extended to predict compositional variations in films prepared at various process conditions. These results were compared with the composition of films determined experimentally using x-ray photoelectron spectroscopy (XPS). Li/Co ratio calculated using XPS was in moderate agreement with that of the simulated value. The measured film thickness followed the same trend as predicted by simulation. These studies are shown to be useful in understanding the complexities in multicomponent sputtering. (C) 2011 American Institute of Physics. doi:10.1063/1.3597829]

Large eddy simulation of a premixed flame with approximate deconvolution modeling

Approximate deconvolution modeling is a very recent approach to large eddy simulation of turbulent flows. It has been applied to compressible flows with success. Here, a premixed flame which forms in the wake of a flameholder has been selected to examine the subgrid-scale modeling of reaction rate by this new method because a previous plane two-dimensional simulation of this wake flame, using a wrinkling function and artificial flame thickening, had revealed discrepancies when compared with experiment. The present simulation is of the temporal evolution of a round wakelike flow at two Reynolds numbers, Re = 2000 and 10,000, based on wake defect velocity and wake diameter. A Fourier-spectral code has been used. The reaction is single-step and irreversible, and the rate follows an Arrhenius law. The reference simulation at the lower Reynolds number is fully resolved. At Re = 10,000, subgrid-scale contributions are significant. It was found that subgrid-scale modeling in the present simulation agrees more closely with unresolved subgrid-scale effects observed in experiment. Specifically, the highest contributions appeared in thin folded regions created by vortex convection. The wrinkling function approach had not selected subgrid-scale effects in these regions.

Modelling, simulation, and graphical user interface for industrial gas carburising process

A mathematical model has been developed for the gas carburising (diffusion) process using finite volume method. The computer simulation has been carried out for an industrial gas carburising process. The model's predictions are in good agreement with industrial experimental data and with data collected from the literature. A study of various mass transfer and diffusion coefficients has been carried out in order to suggest which correlations should be used for the gas carburising process. The model has been interfaced in a Windows environment using a graphical user interface. In this way, the model is extremely user friendly. The sensitivity analysis of various parameters such as initial carbon concentration in the specimen, carbon potential of the atmosphere, temperature of the process, etc. has been carried out using the model.

Simulation of the infrared spectra of thioacetamide by the extended molecular mechanics method

The infrared spectrum of the matrix-isolated species of thioacetamide has been simulated using the extended molecular mechanics method. The equilibrium structure, vibrational frequencies, dipole moment and infrared absorption intensities of thioacetamide have been calculated in good agreement with the experiment. The vibrational frequencies and infrared absorption intensities for the isotopic molecules (CH2CSNH2)-C-13, (CH3CSNH2)-N-15 and (CH2CSND2)-C-13 have also been calculated consistent with the experiment. The infrared spectra of the matrix isolated species of N- and C- deuterated isotopomers of thioacetamide, CH3CSND2 and CD3CSNH2 have also been simulated in satisfactory agreement with the experimental spectra.

Study of translational and rotational mobility and orientational preference of ethane in one-dimensional channels

Structural and dynamical properties of ethane in one-dimensional channels of AlPO4-5 and carbon nanotube have been investigated at dilute concentration with the help of molecular dynamics simulation. Density distributions and orientational structure of ethane have been analyzed. Repulsive interactions seem to play an important role when ethane is located in the narrow part of the AlPO4-5 channel. In AlPO4-5, parallel orientation is predominant over perpendicular orientation except when ethane is located in the broader part of the channel. Unlike in the case of single-file diffusion, our results in carbon nanotube show that at dilute concentrations the mean squared displacement, mu(2)(t) approximate to t(alpha), alpha = 1.8. The autocorrelation function for the z-component of angular velocity of ethane in space-fixed frame of reference shows a pronounced negative correlation. This is attributed to the restriction in the movement of ethane along the x- and y- directions. It is seen that the ratio of reorientational correlation times does not follow the Debye model for confined ethane but it is closer to the predictions of the Debye model for bulk ethane.

An economical method for direct numerical simulation studies of transitional round jets

A pseudo-spectral method based on Fourier expansions in a Cartesian coordinate system is shown to be an economical method for direct numerical simulation studies of transitional round jets, Several characteristics of the solutions are presented to establish the validity of the solutions in spite of the unnatural choices. We show that neither periodicity, nor the use of a Cartesian system have adversely affected the simulations, Instead, there are benefits in terms of ease of computing and lack of the usual restrictions due to grid structure near the jet axis. By computing the simultaneous evolution of passive scalers, the process of reaction in round jet burners, between a fuel-laden jet and an ambient oxidizer, was also simulated. Some typical solutions are shown and then the results of analysis of these data are summarized. (C) 2001 Elsevier Science Ltd, All rights reserved.

Direct numerical simulation of turbulent spots

A group of high-order finite-difference schemes for incompressible flow was implemented to simulate the evolution of turbulent spots in channel flows. The long-time accuracy of these schemes was tested by comparing the evolution of small disturbances to a plane channel flow against the growth rate predicted by linear theory. When the perturbation is the unstable eigenfunction at a Reynolds number of 7500, the solution grows only if there are a comparatively large number of (equispaced) grid points across the channel. Fifth-order upwind biasing of convection terms is found to be worse than second-order central differencing. But, for a decaying mode at a Reynolds number of 1000, about a fourth of the points suffice to obtain the correct decay rate. We show that this is due to the comparatively high gradients in the unstable eigenfunction near the walls. So, high-wave-number dissipation of the high-order upwind biasing degrades the solution especially. But for a well-resolved calculation, the weak dissipation does not degrade solutions even over the very long times (O(100)) computed in these tests. Some new solutions of spot evolution in Couette flows with pressure gradients are presented. The approach to self-similarity at long times can be seen readily in contour plots.