Yashonath Subramanian

A molecular dynamics study of ambient and high pressure phases of silica: Structure and enthalpy variation with molar volume

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, α-PbO2-type, and pyrite-type - for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase.

Effect of pressure on the ionic conductivity of Li+ and Cl- ions in water.

A molecular dynamics simulation study of aqueous solution of LiCl is reported as a function of pressure. Experimental measurements of conductivity of Li(+) ion as a function of pressure shows an increase in conductivity with pressure. Our simulations are able to reproduce the observed trend in conductivity. A number of relevant properties have been computed in order to understand the reasons for the increase in conductivity with pressure. These include radial distribution function, void and neck distributions, hydration or coordination numbers, diffusivity, velocity autocorrelation functions, angles between ion-oxygen and dipole of water as well as OH vector, mean residence time for water in the hydration shell, etc. These show that the increase in pressure acts as a structure breaker. The decay of the self part of the intermediate scattering function at small wave number k shows a bi-exponential decay at 1 bar which changes to single exponential decay at higher pressures. The k dependence of the ratio of the self part of the full width at half maximum of the dynamic structure factor to 2Dk(2) exhibits trends which suggest that the void structure of water is playing a role. These support the view that the changes in void and neck distributions in water can account for changes in conductivity or diffusivity of Li(+) with pressure. These results can be understood in terms of the levitation effect.

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 Carlo (CBMC) simulations ofn-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 ofn-butane and other longern-alkanes such asn-hexane andn-heptane when they are confined in different zeolites are presented. The changes in the conformational properties ofn-butane andn-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of thegauche population as compared to the pure unconfined fluid.

GPGPU-based parallel computation: application to molecular dynamics problems

Parallel and distributed computing techniques have been applied to solve problems that have long running times. Molecular dynamics (MD) is used extensively in physics, chemistry, material sciences and biology to study statistical mechanical properties of systems. MD simulators are known to have extremely long running times, especially as the number of particles being simulated increase. Researchers have used PVM and MPI techniques to speed up MD computations and have achieved 5X to 10X speed up using clusters of computers. Recently NVIDIA and other Graphics Processing Unit (GPU) manufacturers have made available GPU cards for general purpose computing besides rendering graphics. We present a novel idea of solving the MD simulation problem in parallel using General Purpose Graphics Processing Unit (GPGPU) cards. MD problems are particularly amenable to data parallelization. Exploiting this property of the problem and the parallel constructs of GPGPU libraries, we present a parallel MD algorithm, which has a peak speedup of 200X for large problem sizes. Our work can be generalized to parallelize the now popular MapReduce programming paradigm.

High Interfacial Barriers at Narrow Carbon Nanotube–Water Interfaces

Water displays anomalous fast diffusion in narrow carbon nanotubes (CNTs), a behavior that has been reproduced in both experimental and simulation studies. However, little is reported on the effect of bulk water-CNT interfaces, which is critical to exploiting the fast transport of water across narrow carbon nanotubes in actual applications. Using molecular dynamics simulations, we investigate here the effect of such interfaces on the transport of water across arm-chair CNTs of different diameters. Our results demonstrate that diffusion of water is significantly retarded in narrow CNTs due to bulk regions near the pore entrance. The slowdown of dynamics can be attributed to the presence of large energy barriers at bulk water-CNT interfaces. The presence of such intense barriers at the bulk-CNT interface arises due to the entropy contrast between the bulk and confined regions, with water molecules undergoing high translational and rotational entropy gain on entering from the bulk to the CNT interior. The intensity of such energy barriers decreases with increase in CNT diameter. These results are very important for emerging technological applications of CNTs and other nanoscale materials, such as in nanofluidics, water purification, nanofiltration, and desalination, as well as for biological transport processes.

Diffusion processes in a poly-crystalline zeolitic material: A molecular dynamics study

Extensive molecular dynamics simulations of xenon in two classes of zeolite crystal systems, one consisting of purely intra-crystalline space and the other with both intra- and inter-crystalline space are reported. The latter mimics a typical poly-crystalline sample of zeolite. Comparison of results from these two systems provides insights into the structure and dynamics in the presence of inter-crystalline space. The temperature, as well as the distance between the crystallites, has been varied. The density distribution and diffusivities calculated inside the poly-crystalline system show that the interfacial region between the crystal and the inter-crystalline region acts as a bottleneck for diffusion through the system. At lower temperatures, the particles are trapped at the interface due to the pronounced energy minima present in that region. With the increase in temperature, the particles are able to overcome this barrier frequently, and the transport across the inter-crystalline region is increased. A ballistic or superdiffusive motion is seen in the inter-crystalline region along all the axes except along the axis which has the inter-crystalline space. The transition time for ballistic to diffusive motion increases with the increase in the length of the inter-crystalline space. Velocity auto- and cross correlation functions exhibit strong oscillations and exchange of kinetic energy along directions perpendicular to the direction of the inter-crystalline space. These results explain why uptake and PFG-NMR measurements exhibit lower values for diffusivity for the same system when compared to Quasi-Elastic Neutron Scattering. Thus, using molecular dynamics simulations, we were able to correlate the difference of diffusivity values measured using various experimental methods where these inter-crystalline regions are common.

A molecular dynamics calculation of solid phase of malonic acid: role of hydrogen-bond chains and the elastic constants

Recent studies suggest that hydrogen bonds, in particular, hydrogen bond chains play an important role in determining the properties of a substance. We report an investigation into the triclinic phase of crystalline malonic acid. One of two intermolecular interaction potentials proposed here is seen to predict the lattice parameters as well as the enthalpy of the triclinic phase in good agreement with experimental data. Structural and dynamic properties are reported. Also reported are the lifetime of the hydrogen bond and hydrogen bond chains of length l along [011] direction where l = 1 to 5. From the temperature dependence of the lifetime we have obtained the activation energies of the chains. We also report the elements of elastic constant tensor. The results show that the presence of the hydrogen bond chain along [011] direction leads to higher value for elastic tensor

Hexane Isomers in Faujasite: Anomalous Diffusion and Kinetic Separation

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