Dynamics of the Indian-Ocean oxygen minimum zones

In the Indian Ocean, mid-depth oxygen minimum zones (OMZs) occur in the Arabian Sea and the Bay of Bengal. The lower part of the Arabian-Sea OMZ (ASOMZ; below 400 m) intensifies northward across the basin; in contrast, its upper part (above 400 m) is located in the central/eastern basin, well east of the most productive regions along the western boundary. The Bay-of-Bengal OMZ (BBOMZ), although strong, is weaker than the ASOMZ. To investigate the processes that maintain the Indian-Ocean OMZs, we obtain a suite of solutions to a coupled biological/physical model. Its physical component is a variable-density, 6 1/2-layer model, in which each layer corresponds to a distinct dynamical regime or water-mass type. Its biological component has six compartments: nutrients, phytoplankton, zooplankton, two size classes of detritus, and oxygen. Because the model grid is non-eddy resolving (0.5 degrees), the biological model also includes a parameterization of enhanced mixing based on the eddy kinetic energy derived from satellite observations. To explore further the impact of local processes on OMZs, we also obtain analytic solutions to a one-dimensional, simplified version of the biological model. Our control run is able to simulate basic features of the oxygen, nutrient, and phytoplankton fields throughout the Indian Ocean. The model OMZs result from a balance, or lack thereof, between a sink of oxygen by remineralization and subsurface oxygen sources due primarily to northward spreading of oxygenated water from the Southern Hemisphere, with a contribution from Persian-Gulf water in the northern Arabian Sea. The northward intensification of the lower ASOMZ results mostly from horizontal mixing since advection is weak in its depth range. The eastward shift of the upper ASOMZ is due primarily to enhanced advection and vertical eddy mixing in the western Arabian Sea, which spread oxygenated waters both horizontally and vertically. Advection carries small detritus from the western boundary into the central/eastern Arabian Sea, where it provides an additional source of remineralization that drives the ASOMZ to suboxic levels. The model BBOMZ is weaker than the ASOMZ because the Bay lacks a remote source of detritus from the western boundary. Although detritus has a prominent annual cycle, the model OMZs do not because there is not enough time for significant remineralization to occur.

Molecular dynamics simulations of PPI dendrimer-drug complexes

Dendrimeric nanoparticles are potential drug delivery devices which can enhance the solubility of hydrophobic drugs, thus increasing their bioavailability and sustained release action. A quantitative understanding of the dendrimer-drug interactions can give valuable insight into the solubility and release profile of hydrophobic drug molecules in various solvent conditions. Fully atomistic molecular dynamics (MD) simulations have been performed to study the interactions of G5 PPIEDA (G5 ethylenediamine cored poly(propylene imine)) dendrimer and two well known drugs (Famotidine and Indomethacin) at different pH conditions. The study suggested that at low pH the dendrimer-drug complexes are thermodynamically unstable as compared to neutral and high pH conditions. Calculated Potential of Mean Force (PMF) by umbrella sampling showed that the release of drugs from the dendrimer at low pH is spontaneous, median release at neutral pH and slow release at high pH. In addition, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculations were also performed at each umbrella sampling window to identify the various energy contributions. To understand the effect of dendrimer chemistry and topology on the solubility and release profile of drugs, this study is extended to explore the solubility and release profile of phenylbutazone drug complexed with G3 poly(amidoamine) and G4 diaminobutane cored PPI dendrimers. The results indicate that the pH-induced conformational changes in dendrimer, ionization states, dendrimer type and pK(a) of the guest molecules influence the free energy barrier and stability of complexation, and thus regulate drug loading, solubility and release.

Music and symbolic dynamics: the science behind an art

Music signals comprise of atomic notes drawn from a musical scale. The creation of musical sequences often involves splicing the notes in a constrained way resulting in aesthetically appealing patterns. We develop an approach for music signal representation based on symbolic dynamics by translating the lexicographic rules over a musical scale to constraints on a Markov chain. This source representation is useful for machine based music synthesis, in a way, similar to a musician producing original music. In order to mathematically quantify user listening experience, we study the correlation between the max-entropic rate of a musical scale and the subjective aesthetic component. We present our analysis with examples from the south Indian classical music system.

Out of equilibrium plasticity dynamics and the annealing of supersolidity in solid He-4

We present a numerical study of a continuum plasticity field coupled to a Ginzburg-Landau model for superfluidity. The results suggest that a supersolid fraction may appear as a long-lived transient during the time evolution of the plasticity field at higher temperatures where both dislocation climb and glide are allowed. Supersolidity, however, vanishes with annealing. As the temperature is decreased, dislocation climb is arrested and any residual supersolidity due to incomplete annealing remains frozen. Our results may provide a resolution of many perplexing issues concerning a variety of experiments on bulk solid He-4.

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo.

Grain growth and grain boundary dynamics in colloidal polycrystals

Grain boundary dynamics and grain growth play a pivotal role in the fabrication of functional polycrystalline materials. However, not much is known about the delicate interplay between various microscopic processes that drive grain boundary motion which eventually culminates in the desired grain morphology. Colloidal systems are ideally suited to bridge the gap between the microscopic and macroscopic processes underlying grain growth, since their dynamics can be followed in real space and real time with single-particle resolution. The present review aims at highlighting contributions from colloid experiments that have led to a holistic understanding of grain growth in polycrystalline materials.

Dynamics of the North American continent

The forces that cause deformation of western North America have been debated for decades. Recent studies, primarily based on analysis of crustal stresses in the western United States, have suggested that the deformation of the region is mainly controlled by gravitational potential energy (GPE) variations and boundary loads, with basal tractions due to mantle flow playing a relatively minor role. We address these issues by modelling the deviatoric stress field over western North America from a 3-D finite element mantle circulation model with lateral viscosity variations. Our approach takes into account the contribution from both topography and shallow lithosphere structure (GPE) as well as that from deeper mantle flow in one single model, as opposed to separate lithosphere and circulation models, as has been done so far. In addition to predicting the deviatoric stresses we also jointly fit the constraints of geoid, dynamic topography and plate motion both globally and over North America, in order to ensure that the forces that arise in our models are dynamically consistent. We examine the sensitivity of the dynamic models to different lateral viscosity variations. We find that circulation models that include upper mantle slabs yield a better fit to observed plate velocities. Our results indicate that a model of GPE variations coupled with mantle convection gives the best fit to the observational constraints. We argue that although GPE variations control a large part of the deformation of the western United States, deeper mantle tractions also play a significant role. The average deviatoric stress magnitudes in the western United States range 30-40 MPa. The cratonic region exhibits higher coupling to mantle flow than the rest of the continent. We find that a relatively strong San Andreas fault gives a better fit to the observational constraints, especially that of plate velocity in western North America.

Projecting low and extensive dimensional chaos from spatio-temporal dynamics

We review the spatio-temporal dynamical features of the Ananthakrishna model for the Portevin-Le Chatelier effect, a kind of plastic instability observed under constant strain rate deformation conditions. We then establish a qualitative correspondence between the spatio-temporal structures that evolve continuously in the instability domain and the nature of the irregularity of the scalar stress signal. Rest of the study is on quantifying the dynamical information contained in the stress signals about the spatio-temporal dynamics of the model. We show that at low applied strain rates, there is a one-to-one correspondence with the randomly nucleated isolated bursts of mobile dislocation density and the stress drops. We then show that the model equations are spatio-temporally chaotic by demonstrating the number of positive Lyapunov exponents and Lyapunov dimension scale with the system size at low and high strain rates. Using a modified algorithm for calculating correlation dimension density, we show that the stress-strain signals at low applied strain rates corresponding to spatially uncorrelated dislocation bands exhibit features of low dimensional chaos. This is made quantitative by demonstrating that the model equations can be approximately reduced to space independent model equations for the average dislocation densities, which is known to be low-dimensionally chaotic. However, the scaling regime for the correlation dimension shrinks with increasing applied strain rate due to increasing propensity for propagation of the dislocation bands. The stress signals in the partially propagating to fully propagating bands turn to have features of extensive chaos.

Solvation dynamics of tryptophan in water-dimethyl sulfoxide binary mixture: In search of molecular origin of composition dependent multiple anomalies

Experimental and simulation studies have uncovered at least two anomalous concentration regimes in water-dimethyl sulfoxide (DMSO) binary mixture whose precise origin has remained a subject of debate. In order to facilitate time domain experimental investigation of the dynamics of such binary mixtures, we explore strength or extent of influence of these anomalies in dipolar solvation dynamics by carrying out long molecular dynamics simulations over a wide range of DMSO concentration. The solvation time correlation function so calculated indeed displays strong composition dependent anomalies, reflected in pronounced non-exponential kinetics and non-monotonous composition dependence of the average solvation time constant. In particular, we find remarkable slow-down in the solvation dynamics around 10%-20% and 35%-50% mole percentage. We investigate microscopic origin of these two anomalies. The population distribution analyses of different structural morphology elucidate that these two slowing down are reflections of intriguing structural transformations in water-DMSO mixture. The structural transformations themselves can be explained in terms of a change in the relative coordination number of DMSO and water molecules, from 1DMSO:2H(2)O to 1H(2)O:1DMSO and 1H(2)O:2DMSO complex formation. Thus, while the emergence of first slow down (at 15% DMSO mole percentage) is due to the percolation among DMSO molecules supported by the water molecules (whose percolating network remains largely unaffected), the 2nd anomaly (centered on 40%-50%) is due to the formation of the network structure where the unit of 1DMSO:1H(2)O and 2DMSO:1H(2)O dominates to give rise to rich dynamical features. Through an analysis of partial solvation dynamics an interesting negative cross-correlation between water and DMSO is observed that makes an important contribution to relaxation at intermediate to longer times.

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.

Dynamics of prolate spheroidal mass distributions with varying eccentricity

In this paper we calculate the potential for a prolate spheroidal distribution as in a dark matter halo with a radially varying eccentricity. This is obtained by summing up the shell-by-shell contributions of isodensity surfaces, which are taken to be concentric and with a common polar axis and with an axis ratio that varies with radius. Interestingly, the constancy of potential inside a shell is shown to be a good approximation even when the isodensity contours are dissimilar spheroids, as long as the radial variation in eccentricity is small as seen in realistic systems. We consider three cases where the isodensity contours are more prolate at large radii, or are less prolate or have a constant eccentricity. Other relevant physical quantities like the rotation velocity, the net orbital and vertical frequency due to the halo and an exponential disc of finite thickness embedded in it are obtained. We apply this to the kinematical origin of Galactic warp, and show that a prolate-shaped halo is not conducive to making long-lived warps - contrary to what has been proposed in the literature. The results for a prolate mass distribution with a variable axis ratio obtained are general, and can be applied to other astrophysical systems, such as prolate bars, for a more realistic treatment.

Dynamics and fracture of ligaments from a droplet on a vibrating surface

A droplet residing on a vibrating surface and in the pressure antinode of an asymmetric standing wave can spread radially outward and atomize. In this work, proper orthogonal decomposition through high speed imaging is shown to predict the likelihood of atomization for various viscous fluids based on prior information in the droplet spreading phase. Capillary instabilities are seen to affect ligament rupture. Viscous dissipation plays an important role in determining the wavelength of the most unstable mode during the inception phase of the ligaments. However, the highest ligament capillary number achieved was less than 1, and the influence of viscosity in the ligament growth and breakup phases is quite minimal. It is inferred from the data that the growth of a typical ligament is governed by a balance between the inertial force obtained from the inception phase and capillary forces. By including the effect of acoustic pressure field around the droplet, the dynamics of the ligament growth phase is revealed and the ligament growth profiles for different fluids are shown to collapse on a straight line using a new characteristic time scale.

Dynamics of a flexible splitter plate in the wake of a circular cylinder

Rigid splitter plates in the wake of bluff bodies are known to suppress the primary vortex shedding. In the present work, we experimentally study the problem of a flexible splitter plate in the wake of a circular cylinder. In this case, the splitter plate is free to continuously deform along its length due to the fluid forces acting on it; the flexural rigidity (EI) of the plate being an important parameter. Direct visualizations of the splitter plate motions, for very low values of flexural rigidity (EI), indicate periodic traveling wave type deformations of the splitter plate with maximum tip amplitudes of the order of I cylinder diameter. As the Reynolds number based on cylinder diameter is varied, two regimes of periodic splitter plate motions are found that are referred to as mode I and mode II, with a regime of aperiodic motions between them. The frequency of plate motions in both periodic modes is found to be close to the plane cylinder Strouhal number of about 0.2, while the average frequencies in the non-periodic regime are substantially lower. The measured normalized phase speed of the traveling wave for both periodic modes is also close to the convection speed of vortices in the plane cylinder wake. As the flexural rigidity of the plate (EI) is increased, the response of the plate was found to shift to the right when plotted with flow speed or Re. To better capture the effect of varying EI, we define and use a non-dimensional bending stiffness, K*, similar to the ones used in the flag flutter problem, K*=EI/(0.5 rho(UL3)-L-2), where U is the free-stream velocity and L is the splitter plate length. Amplitude data for different EI cases when plotted against this parameter appear to collapse on to a single curve for a given splitter plate length. Measurements of the splitter plate motions for varying splitter plate lengths indicate that plates that are substantially larger than the formation length of the plane cylinder wake have similar responses, while shorter plates show significant differences.