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.

Structures and molecular-dynamics studies of three active-site mutants of bovine pancreatic phospholipase A(2)

Phospholipase A(2) hydrolyzes phospholipids at the sn-2 position to cleave the fatty-acid ester bond of L-glycerophospholipids. The catalytic dyad (Asp99 and His48) along with a nucleophilic water molecule is responsible for enzyme hydrolysis. Furthermore, the residue Asp49 in the calcium-binding loop is essential for controlling the binding of the calcium ion and the catalytic action of phospholipase A2. To elucidate the structural role of His48 and Asp49, the crystal structures of three active-site single mutants H48N, D49N and D49K have been determined at 1.9 angstrom resolution. Although the catalytically important calcium ion is present in the H48N mutant, the crystal structure shows that proton transfer is not possible from the catalytic water to the mutated residue. In the case of the Asp49 mutants, no calcium ion was found in the active site. However, the tertiary structures of the three active-site mutants are similar to that of the trigonal recombinant enzyme. Molecular-dynamics simulation studies provide a good explanation for the crystallographic results.

Dynamics of ''internal'' interannual variability of the Indian summer monsoon in a GCM

1] The poor predictability of the Indian summer monsoon ( ISM) appears to be due to the fact that a large fraction of interannual variability (IAV) is governed by unpredictable "internal'' low frequency variations. Mechanisms responsible for the internal IAV of the monsoon have not been clearly identified. Here, an attempt has been made to gain insight regarding the origin of internal IAV of the seasonal ( June - September, JJAS) mean rainfall from "internal'' IAV of the ISM simulated by an atmospheric general circulation model (AGCM) driven by fixed annual cycle of sea surface temperature (SST). The underlying hypothesis that monsoon ISOs are responsible for internal IAV of the ISM is tested. The spatial and temporal characteristics of simulated summer intraseasonal oscillations ( ISOs) are found to be in good agreement with those observed. A long integration with the AGCM forced with observed SST, shows that ISO activity over the Asian monsoon region is not modulated by the observed SST variations. The internal IAV of ISM, therefore, appears to be decoupled from external IAV. Hence, insight gained from this study may be useful in understanding the observed internal IAV of ISM. The spatial structure of the ISOs has a significant projection on the spatial structure of the seasonal mean and a common spatial mode governs both intraseasonal and interannual variability. Statistical average of ISO anomalies over the season ( seasonal ISO bias) strengthens or weakens the seasonal mean. It is shown that interannual anomalies of seasonal mean are closely related to the seasonal mean of intraseasonal anomalies and explain about 50% of the IAV of the seasonal mean. The seasonal mean ISO bias arises partly due to the broad-band nature of the ISO spectrum allowing the time series to be aperiodic over the season and partly due to a non-linear process where the amplitude of ISO activity is proportional to the seasonal bias of ISO anomalies. The later relation is a manifestation of the binomial character of rainfall time series. The remaining 50% of the IAV may arise due to land-surface processes, interaction between high frequency variability and ISOs, etc.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics

The way in which basal tractions, associated with mantle convection, couples with the lithosphere is a fundamental problem in geodynamics. A successful lithosphere-mantle coupling model for the Earth will satisfy observations of plate motions, intraplate stresses, and the plate boundary zone deformation. We solve the depth integrated three-dimensional force balance equations in a global finite element model that takes into account effects of both topography and shallow lithosphere structure as well as tractions originating from deeper mantle convection. The contribution from topography and lithosphere structure is estimated by calculating gravitational potential energy differences. The basal tractions are derived from a fully dynamic flow model with both radial and lateral viscosity variations. We simultaneously fit stresses and plate motions in order to delineate a best-fit lithosphere-mantle coupling model. We use both the World Stress Map and the Global Strain Rate Model to constrain the models. We find that a strongly coupled model with a stiff lithosphere and 3-4 orders of lateral viscosity variations in the lithosphere are best able to match the observational constraints. Our predicted deviatoric stresses, which are dominated by contribution from mantle tractions, range between 20-70 MPa. The best-fitting coupled models predict strain rates that are consistent with observations. That is, the intraplate areas are nearly rigid whereas plate boundaries and some other continental deformation zones display high strain rates. Comparison of mantle tractions and surface velocities indicate that in most areas tractions are driving, although in a few regions, including western North America, tractions are resistive. Citation: Ghosh, A., W. E. Holt, and L. M. Wen (2013), Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics.

Current kinematics and dynamics of Africa and the East African Rift System

Although the East African Rift System (EARS) is an archetype continental rift, the forces driving its evolution remain debated. Some contend buoyancy forces arising from gravitational potential energy (GPE) gradients within the lithosphere drive rifting. Others argue for a major role of the diverging mantle flow associated with the African Superplume. Here we quantify the forces driving present-day continental rifting in East Africa by (1) solving the depth averaged 3-D force balance equations for 3-D deviatoric stress associated with GPE, (2) inverting for a stress field boundary condition that we interpret as originating from large-scale mantle tractions, (3) calculating dynamic velocities due to lithospheric buoyancy forces, lateral viscosity variations, and velocity boundary conditions, and (4) calculating dynamic velocities that result from the stress response of horizontal mantle tractions acting on a viscous lithosphere in Africa and surroundings. We find deviatoric stress associated with lithospheric GPE gradients are similar to 8-20 MPa in EARS, and the minimum deviatoric stress resulting from basal shear is similar to 1.6 MPa along the EARS. Our dynamic velocity calculations confirm that a force contribution from GPE gradients alone is sufficient to drive Nubia-Somalia divergence and that additional forcing from horizontal mantle tractions overestimates surface kinematics. Stresses from GPE gradients appear sufficient to sustain present-day rifting in East Africa; however, they are lower than the vertically integrated strength of the lithosphere along most of the EARS. This indicates additional processes are required to initiate rupture of continental lithosphere, but once it is initiated, lithospheric buoyancy forces are enough to maintain rifting.

Joint modeling of lithosphere and mantle dynamics: Evaluation of constraints from global tomography models

With the advances in technology, seismological theory, and data acquisition, a number of high-resolution seismic tomography models have been published. However, discrepancies between tomography models often arise from different theoretical treatments of seismic wave propagation, different inversion strategies, and different data sets. Using a fixed velocity-to-density scaling and a fixed radial viscosity profile, we compute global mantle flow models associated with the different tomography models and test the impact of these for explaining surface geophysical observations (geoid, dynamic topography, stress, and strain rates). We use the joint modeling of lithosphere and mantle dynamics approach of Ghosh and Holt (2012) to compute the full lithosphere stresses, except that we use HC for the mantle circulation model, which accounts for the primary flow-coupling features associated with density-driven mantle flow. Our results show that the seismic tomography models of S40RTS and SAW642AN provide a better match with surface observables on a global scale than other models tested. Both of these tomography models have important similarities, including upwellings located in Pacific, Eastern Africa, Iceland, and mid-ocean ridges in the Atlantic and Indian Ocean and downwelling flows mainly located beneath the Andes, the Middle East, and central and Southeast Asia.

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.

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.