Molecular theory of solvation and solvation dynamics of a classical ion in a dipolar liquid

A microscopic theory of equilibrium solvation and solvation dynamics of a classical, polar, solute molecule in dipolar solvent is presented. Density functional theory is used to explicitly calculate the polarization structure around a solvated ion. The calculated solvent polarization structure is different from the continuum model prediction in several respects. The value of the polarization at the surface of the ion is less than the continuum value. The solvent polarization also exhibits small oscillations in space near the ion. We show that, under certain approximations, our linear equilibrium theory reduces to the nonlocal electrostatic theory, with the dielectric function (c(k)) of the liquid now wave vector (k) dependent. It is further shown that the nonlocal electrostatic estimate of solvation energy, with a microscopic c(k), is close to the estimate of linearized equilibrium theories of polar liquids. The study of solvation dynamics is based on a generalized Smoluchowski equation with a mean-field force term to take into account the effects of intermolecular interactions. This study incorporates the local distortion of the solvent structure near the ion and also the effects of the translational modes of the solvent molecules.The latter contribution, if significant, can considerably accelerate the relaxation of solvent polarization and can even give rise to a long time decay that agrees with the continuum model prediction. The significance of these results is discussed.

A simple classical approach for the melting temperature of inert-gas nanoparticles

Like the metal and semiconductor nanoparticles, the melting temperature of free inert-gas nanoparticles decreases with decreasing size. The variation is linear with the inverse of the particle size for large nanoparticles and deviates from the linearity for small nanoparticles. The decrease in the melting temperature is slower for free nanoparticles with non-wetting surfaces, while the decrease is faster for nanoparticles with wetting surfaces. Though the depression of the melting temperature has been reported for inert-gas nanoparticles in porous glasses, superheating has also been observed when the nanoparticles are embedded in some matrices. By using a simple classical approach, the influence of size, geometry and the matrix on the melting temperature of nanoparticles is understood quantitatively and shown to be applicable for other materials. It is also shown that the classical approach can be applied to understand the size-dependent freezing temperature of nanoparticles.

Estimating Frequencies of Minority Nevirapine-Resistant Strains in Chronically HIV-1-Infected Individuals Naive to Nevirapine by Using Stochastic Simulations and a Mathematical Model

Nevirapine forms the mainstay of our efforts to curtail the pediatric AIDS epidemic through prevention of mother-to-child transmission of HIV-1. A key limitation, however, is the rapid selection of HIV-1 strains resistant to nevirapine following the administration of a single dose. This rapid selection of resistance suggests that nevirapine-resistant strains preexist in HIV-1 patients and may adversely affect outcomes of treatment. The frequencies of nevirapine-resistant strains in vivo, however, remain poorly estimated, possibly because they exist as a minority below current assay detection limits. Here, we employ stochastic simulations and a mathematical model to estimate the frequencies of strains carrying different combinations of the common nevirapine resistance mutations K103N, V106A, Y181C, Y188C, and G190A in chronically infected HIV-1 patients naive to nevirapine. We estimate the relative fitness of mutant strains from an independent analysis of previous competitive growth assays. We predict that single mutants are likely to preexist in patients at frequencies (similar to 0.01% to 0.001%) near or below current assay detection limits (>0.01%), emphasizing the need for more-sensitive assays. The existence of double mutants is subject to large stochastic variations. Triple and higher mutants are predicted not to exist. Our estimates are robust to variations in the recombination rate, cellular superinfection frequency, and the effective population size. Thus, with 10(7) to 10(8) infected cells in HIV-1 patients, even when undetected, nevirapine-resistant genomes may exist in substantial numbers and compromise efforts to prevent mother-to-child transmission of HIV-1, accelerate the failure of subsequent antiretroviral treatments, and facilitate the transmission of drug resistance.

Elasto-Electrostatic Analysis of Circular Microplates Used in Capacitive Micromachined Ultrasonic Transducers

The active structural component of a capacitive micromachined ultrasonic transducer (CMUT) is the top plate which vibrates under the influence of a time-varying electrostatic force thereby producing ultrasound waves of the desired frequency in the surrounding medium. Analysis of MEMS devices which rely on electrostatic actuation is complicated due to the fact that the structural deformations alter the electrostatic forces, which redistribute and modify the applied loads. Hence, it becomes imperative to consider the electrostatics-structure coupling aspect in the design of these devices. This paper presents an approximate analytical solution for the static deflection of a thin, clamped circular plate caused by electrostatic forces which are inherently nonlinear. Traditionally, finite element simulations using some commercial software such as ANSYS are employed to determine the structural deflections caused by electrostatic forces. Since the structural deformation alters the electrostatic field, a coupled-field simulation is required wherein the electrostatic mesh is continuously updated to coincide with the deflection of the structure. Such simulations are extremely time consuming, in addition to being nontransparent and somewhat hard to implement. We employ the classical thin-plate theory which is adequate when the ratio of the diameter to thickness of the plate is very large, a situation commonly prevalent in many MEMS devices, especially the CMUTs. We solve the thin-plate electrostatic-elastic equation using the Galerkin-weighted residual technique, under the assumption that the deflections are small in comparison to the thickness of the plate. The evaluation of the electrostatic force between the two plates is simplified due to the fact that the electrostatic gap is much smaller than the lateral dimensions of the device. The results obtained are compared to those found from ANSYS simulations and an excellent agreement is observed between the two. The pull-in voltage predicted by our model is close to the value predicted by ANSYS simulations.

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Activation barriers for d.c. conductivity in ionic glasses: Classical calculations using the small-cluster approximation

A small-cluster approximation has been used to calculate the activation barriers for the d.c. conductivity in ionic glasses. The main emphasis of this approach is on the importance of the hitherto ignored polarization energy contribution to the total activation energy. For the first time it has been demonstrated that the d.c. conductivity activation energy can be calculated by considering ionic migration to a neighbouring vacancy in a smali cluster of ions consisting of face-sharing anion polyhedra. The activation energies from the model calculations have been compared with the experimental values in the case of highly modified lithium thioborate glasses.

Dense granular flow down an inclined plane A comparison between the hard particle model and soft particle simulations

The granular flow down an inclined plane is simulated using the discrete element (DE) technique to examine the extent to which the dynamics of an unconfined dense granular flow can be well described by a hard particle model First, we examine the average coordination number for the particles in the flow down an inclined plane using the DE technique using the linear contact model with and without friction, and the Hertzian contact model with friction The simulations show that the average coordination number decreases below 1 for values of the spring stiffness corresponding to real materials, such as sand and glass, even when the angle of inclination is only 10 larger than the angle of repose Additional measures of correlations in the system, such as the fraction of particles with multibody contact, the force ratio (average ratio of the magnitudes of the largest and the second largest force on a particle), and the angle between the two largest forces on the particle, show no evidence of force chains or other correlated motions in the system An analysis of the bond-orientational order parameter indicates that the flow is in the random state, as in event-driven (ED) simulations V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] The results of the two simulation techniques for the Bagnold coefficients (ratio of stress and square of the strain rate) and the granular temperature (mean square of the fluctuating velocity) are compared with the theory V Kumaran, J Fluid Mech 632, 107 (2009), J Fluid Mech 632, 145 (2009)] and are found to be in quantitative agreement In addition, we also conduct a comparison of the collision frequency and the distribution of the precollisional relative velocities of particles in contact The strong correlation effects exhibited by these two quantities in event-driven simulations V Kumaran, J Fluid Mech 632, 145 (2009)] are also found in the DE simulations (C) 2010 American Institute of Physics doi 10 1063/1 3504660]

Direct numerical simulations of statistically steady, homogeneous, isotropic fluid turbulence with polymer additives

We carry out a direct numerical simulation (DNS) study that reveals the effects of polymers on statistically steady, forced, homogeneous, and isotropic fluid turbulence. We find clear manifestations of dissipation-reduction phenomena: on the addition of polymers to the turbulent fluid, we obtain a reduction in the energy dissipation rate; a significant modification of the fluid-energy spectrum, especially in the deep-dissipation range; and signatures of the suppression of small-scale structures, including a decrease in small-scale vorticity filaments. We also compare our results with recent experiments and earlier DNS studies of decaying fluid turbulence with polymer additives.

Parallel Tempering Simulations of Liquid-Phase Adsorption of n-Alkane Mixtures in Zeolite LTA-5A

Adsorption of n-alkane mixtures in the zeolite LTA-5A under liquid-phase conditions has been studied using grand canonical Monte Carlo (GCMC) simulations combined with parallel tempering. Normal GCMC techniques fail for some of these systems due to the preference of linear molecules to coil within a single cage in the zeolite. The narrow zeolite windows severerly restrict interactions of the molecules, making it difficult to simulate cooperative rearrangements necessary to explore configuration space. Because of these reasons, normal GCMC simulations results show poor reproducibility in some cases. These problems were overcome with parallel tempering techniques. Even with parallel tempering, these are very challenging systems for molecular simulation. Similar problems may arise for other zeolites such as CHA, AFX, ERI, KFI, and RHO having cages connected by narrow windows. The simulations capture the complex selectivity behavior observed in experiments such as selectivity inversion and azeotrope formation.

E. C. G. Sudarshan and Symmetry in Classical Dynamics, Optics and Quantum Mechanics

We review work initiated and inspired by Sudarshan in relativistic dynamics, beam optics, partial coherence theory, Wigner distribution methods, multimode quantum optical squeezing, and geometric phases. The 1963 No Interaction Theorem using Dirac's instant form and particle World Line Conditions is recalled. Later attempts to overcome this result exploiting constrained Hamiltonian theory, reformulation of the World Line Conditions and extending Dirac's formalism, are reviewed. Dirac's front form leads to a formulation of Fourier Optics for the Maxwell field, determining the actions of First Order Systems (corresponding to matrices of Sp(2,R) and Sp(4,R)) on polarization in a consistent manner. These groups also help characterize properties and propagation of partially coherent Gaussian Schell Model beams, leading to invariant quality parameters and the new Twist phase. The higher dimensional groups Sp(2n,R) appear in the theory of Wigner distributions and in quantum optics. Elegant criteria for a Gaussian phase space function to be a Wigner distribution, expressions for multimode uncertainty principles and squeezing are described. In geometric phase theory we highlight the use of invariance properties that lead to a kinematical formulation and the important role of Bargmann invariants. Special features of these phases arising from unitary Lie group representations, and a new formulation based on the idea of Null Phase Curves, are presented.

Molecular Dynamics Simulations of Orientational Relaxation in Dipolar Lattice: Lack of Diffusive Decay for Second and Higher Rank Correlation Functions

Extensive molecular dynamics simulations have been carried out to calculate the orientational correlation functions Cl(t), G(t) = [4n/(21 + l)]Ci=-l (Y*lm(sZ(0)) Ylm(Q(t))) (where Y,,(Q) are the spherical harmonics) of point dipoles in a cubic lattice. The decay of Cl(t) is found to be strikingly different from higher l-correlation functions-the latter do not exhibit diffusive dynamics even in the long time. Both the cumulant expansion expression of Lynden-Bell and the conventional memory function equation provide very good description of the Cl(t) in the short time but fail to reproduce the observed slow, long time decay of c1 (t) .

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Finite element simulations of ductile rupture in a constrained metal foil

A numerical study of the ductile rupture in a metal foil constrained between two stiff ceramic blocks is performed. The finite element analysis is carried out under the conditions of mode I, plane strain, small-scale yielding. The rate-independent version of the Gurson model that accounts for the ductile failure mechanisms of microvoid nucleation, growth and coalescence is employed to represent the behavior of the metal foil. Different distributions of void nucleating sites in the metal foil are considered for triggering the initiation of discrete voids. The results clearly show that far-field triaxiality-induced cavitation is the dominant failure mode when the spacing of the void nucleating sites is large. On the contrary, void coalescence near the notch tip is found to be the operative failure mechanism when closely spaced void nucleating sites are considered.