Relation Between the Diffusivity, Viscosity, and Ionic Radius of LiCl in Water, Methanol, and Ethylene Glycol: A Molecular Dynamics Simulation

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several; structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent solvent interaction is important in EG while solute solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes we show that there is a relation between the void and neck radius on e one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (lambda(0)) of TMA(+), while in water in EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in lambda(0) as a function ionic radius is seen for Br- in water EG but for the larger ClO4- ion in methanol. The relation between the void and neck distribution and the variation in lambda(0) with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer. (C) 2014 AIP Publishing LLC.

Influence of a Counterion on the Ion Atmosphere of an Anion: A Molecular Dynamics Study of LiX and CsX (X = F-, Cl-, I-) in Methanol

We report molecular dynamics (MD) simulations to explore the influence of a counterion on the structure and dynamics of cationic and anionic solvation shells for various ions in methanol at 298 K. We show that the variation in ionic size of either the cation or the anion in an ion pair influences the solvation structure of the other ion as well as the diffusivity in an electrolyte solution of methanol. The extent of ionic association between the cation and its counteranion of different ionic sizes has been investigated by analyzing the radial distribution functions (RDFs) and the orientation of methanol molecules in the first solvation shell (FSS) of ions. It is shown that the methanol in the FSS of the anion as well the cation exhibit quite different radial and orientational structures as compared to methanol which lie in the FSS of either the anion or the cation but not both. We find that the coordination number (CN) of F-, Cr-, and I- ions decreases with increasing size of the anion which is contrary to the trend reported for the anions in H2O. The mean residence time (MRT) of methanol molecules in the FSS of ions has been calculated using the stable states picture (SSP) approach. It is seen that the ion-counterion interaction has a considerable influence on the MRT of methanol molecules in the FSS of ions. We also discuss the stability order of the ion-counterion using the potentials of mean force (PMFs) for ion pairs with ions of different sizes. The PMF plots reveal that the Li+-F- pair (small-small) is highly stable and the Li+-I- pair is least stable (small-large) in electrolyte solutions.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Self-organized criticality in dynamics without branching

We demonstrate the phenomenon of self-organized criticality (SOC) in a simple random walk model described by a random walk of a myopic ant, i.e., a walker who can see only nearest neighbors. The ant acts on the underlying lattice aiming at uniform digging, i.e., reduction of the height profile of the surface but is unaffected by the underlying lattice. In one, two, and three dimensions we have explored this model and have obtained power laws in the time intervals between consecutive events of "digging." Being a simple random walk, the power laws in space translate to power laws in time. We also study the finite size scaling of asymptotic scale invariant process as well as dynamic scaling in this system. This model differs qualitatively from the cascade models of SOC.

Shock propagation in gas dynamics: explicit form of higher order compatibility conditions

With the use of tensor analysis and the method of singular surfaces, an infinite system of equations can be derived to study the propagation of curved shocks of arbitrary strength in gas dynamics. The first three of these have been explicitly given here. This system is further reduced to one involving scalars only. The choice of dependent variables in the infinite system is quite important, it leads to coefficients free from singularities for all values of the shock strength.

Experiments on a plume with off-source heating: Implications for cloud fluid dynamics

We report here on a series of laboratory experiments on plumes, undertaken with the object of simulating the effect of the heat release that occurs in clouds on condensation of water vapor. The experimental technique used for this purpose relies on ohmic heating generated in an electrically conducting plume fluid subjected to a suitable alternating voltage across specified axial stations in the plume flow [Bhat et al., 1989]. The present series of experiments achieves a value of the Richardson number that is toward the lower end of the range that characteristics cumulus clouds. It is found that the buoyancy enhancement due to heating disrupts the eddy structures in the flow and reduces the dilution owing to entrainment of ambient fluid that would otherwise have occurred in the central region of the plume. Heating also reduces the spread rate of the plume, but as it accelerates the flow as well, the overall specific mass flux in the plume does not show a very significant change at the heat input employed in the experiment. However, there is some indication that the entrainment rate (proportional to the streamwise derivative of the mass flux) is slightly higher immediately after heat injection and slightly lower farther downstream. The measurements support a previous proposal for a cloud scenario [Bhat and Narasimha, 1996] and demonstrate how fresh insights into certain aspects of the fluid dynamics of clouds may be derived from the experimental techniques employed here.

Cell Dynamics of Model Proteins

We design rapidly folding sequences by assigning the strongest couplings to the contacts present in a target native state in a two dimensional model of heteropolymers. The pathways to folding and their dependence on the temperature are illustrated via a mapping of the dynamics into motion within the space of the maximally compact cells.

Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Self-Absorption and Focusing Effects in Carrier Relaxation Dynamics under Depletion Conditions

The effect of a one-dimensional field (1) on the self-absorption characteristics and (2) when we have a finite numerical aperture for the objective lens that focuses the laser beam on the solid are considered here. Self-absorption, in particular its manifestation as an inner filter for the emitted signal, has been observed in luminescence experiments. Models for this effect exist and have been analyzed, but only in the absence of space charge. Using our previous results on minority carrier relaxation in the presence of a field, we obtain expressions incorporating inner filter effects. Focusing of a light beam on the sample, by an objective lens, results in a three-dimensional source and consequently a three-dimensional continuity equation to be solved for the minority carrier concentration. Assuming a one-dimensional electric field and employing Fourier-Bessel transforms, we recast the problem of carrier relaxation and solve the same via an identity that relates it to solutions obtained in the absence of focusing effects. The inner filter effect as well as focusing introduces new time scales in the problem of carrier relaxation. The interplay between the electric field and the parameters which characterize these effects and the consequent modulation of the intensity and time scales of carrier decay signals are analyzed and discussed.

Vortex dynamics at rf frequencies in Bi2Sr2CaCu2O8 single crystals

We have studied the low magnetic field high temperature region of the H-T phase diagram of Bi2Sr2CaCu2O8 single crystals using the technique of non-resonant rf response at a frequency of 20 MHz. With H(rf)parallel to a, H parallel to c, the isothermal magnetic field scans below T-c show that the frequency f(H) of the tank circuit decreases continuously with increase in H before saturating at H similar to H-D(T). Such a decrease in f(H) reflects increasing rf penetration into the weakly screened region between CuO bilayers. The saturation of f(H) at its lowest value for H similar to H-D(T) indicates complete rf penetration land hence the disappearance of field dependence) due to the vanishing of the screening rf currents I-rf(c) in those regions or equivalently when the phase coherence between adjacent superconducting layers vanishes. Therefore H,(T) represents the decoupling of the adjacent superconducting bilayers, and hence also a 3D to 2D decoupling transition of the vortex structure. Simultaneous monitoring of the field dependent rf power dissipation P(H) shows a maximum in dP/dH at H-D(T). The observed H-D(T) line in many crystals is in excellent agreement with the (l/t-1) behavior proposed for decoupling.

Dynamics of a dilute sheared inelastic fluid. I. Hydrodynamic modes and velocity correlation functions

The hydrodynamic modes and the velocity autocorrelation functions for a dilute sheared inelastic fluid are analyzed using an expansion in the parameter epsilon=(1-e)(1/2), where e is the coefficient of restitution. It is shown that the hydrodynamic modes for a sheared inelastic fluid are very different from those for an elastic fluid in the long-wave limit, since energy is not a conserved variable when the wavelength of perturbations is larger than the ``conduction length.'' In an inelastic fluid under shear, there are three coupled modes, the mass and the momenta in the plane of shear, which have a decay rate proportional to k(2/3) in the limit k -> 0, if the wave vector has a component along the flow direction. When the wave vector is aligned along the gradient-vorticity plane, we find that the scaling of the growth rate is similar to that for an elastic fluid. The Fourier transforms of the velocity autocorrelation functions are calculated for a steady shear flow correct to leading order in an expansion in epsilon. The time dependence of the autocorrelation function in the long-time limit is obtained by estimating the integral of the Fourier transform over wave number space. It is found that the autocorrelation functions for the velocity in the flow and gradient directions decay proportional to t(-5/2) in two dimensions and t(-15/4) in three dimensions. In the vorticity direction, the decay of the autocorrelation function is proportional to t(-3) in two dimensions and t(-7/2) in three dimensions.

Dynamics of a dilute sheared inelastic fluid. II. The effect of correlations

The effect of correlations on the viscosity of a dilute sheared inelastic fluid is analyzed using the ring-kinetic equation for the two-particle correlation function. The leading-order contribution to the stress in an expansion in epsilon=(1-e)(1/2) is calculated, and it is shown that the leading-order viscosity is identical to that obtained from the Green-Kubo formula, provided the stress autocorrelation function in a sheared steady state is used in the Green-Kubo formula. A systemmatic extension of this to higher orders is also formulated, and the higher-order contributions to the stress from the ring-kinetic equation are determined in terms of the terms in the Chapman-Enskog solution for the Boltzmann equation. The series is resummed analytically to obtain a renormalized stress equation. The most dominant contributions to the two-particle correlation function are products of the eigenvectors of the conserved hydrodynamic modes of the two correlated particles. In Part I, it was shown that the long-time tails of the velocity autocorrelation function are not present in a sheared fluid. Using those results, we show that correlations do not cause a divergence in the transport coefficients; the viscosity is not divergent in two dimensions, and the Burnett coefficients are not divergent in three dimensions. The equations for three-particle and higher correlations are analyzed diagrammatically. It is found that the contributions due to the three-particle and higher correlation functions to the renormalized viscosity are smaller than those due to the two-particle distribution function in the limit epsilon -> 0. This implies that the most dominant correlation effects are due to the two-particle correlations.

Anomalous thermal dynamics of Bragg gratings inscribed in germanosilicate optical fiber

An interesting, periodic appearance of a new peak has been observed in the reflected spectrum of a Fiber Bragg Grating (FBG) inscribed in a germanosilicate fiber during thermal treatment. The new peak occurs on the longer wavelength side of the spectrum during heating and on the shorter wavelength side during cooling, following an identical reverse dynamics. Comparison with a commercial grating with 99.9% reflectivity shows a similar decay dynamics. It is proposed that the distortion due to simultaneous erasure and thermal expansion of the index modulation profile may be responsible for the observed anomaly. The reported results help us in understanding the thermal behavior of FBGs and provide additional insights into the mechanisms responsible for the photosensitivity in germanosilicate fibers.

Intermittent Dynamics, Stochastic Resonance and Dynamical Heterogeneity in Supercooled Liquid Water

Here we find through computer simulations and theoretical analysis that the low temperature thermodynamic anomalies of liquid water arises from the intermittent fluctuation between its high density and low density forms, consisting largely of 5-coordinated and 4-coordinated water molecules, respectively. The fluctuations exhibit strong dynamic heterogeneity (defined by the four point time correlation function), accompanied by a divergence like growth of the dynamic correlation length, of the type encountered in fragile supercooled liquids. The intermittency has been explained by invoking a two state model often employed to understand stochastic resonance, with the relevant periodic perturbation provided here by the fluctuation of the total volume of the system.