Laboratory simulations show diabatic heating drives cumulus-cloud evolution and entrainment

Clouds are the largest source of uncertainty in climate science, and remain a weak link in modeling tropical circulation. A major challenge is to establish connections between particulate microphysics and macroscale turbulent dynamics in cumulus clouds. Here we address the issue from the latter standpoint. First we show how to create bench-scale flows that reproduce a variety of cumulus-cloud forms (including two genera and three species), and track complete cloud life cycles-e.g., from a ``cauliflower'' congestus to a dissipating fractus. The flow model used is a transient plume with volumetric diabatic heating scaled dynamically to simulate latent-heat release from phase changes in clouds. Laser-based diagnostics of steady plumes reveal Riehl-Malkus type protected cores. They also show that, unlike the constancy implied by early self-similar plume models, the diabatic heating raises the Taylor entrainment coefficient just above cloud base, depressing it at higher levels. This behavior is consistent with cloud-dilution rates found in recent numerical simulations of steady deep convection, and with aircraft-based observations of homogeneous mixing in clouds. In-cloud diabatic heating thus emerges as the key driver in cloud development, and could well provide a major link between microphysics and cloud- scale dynamics.

Structural Rigidity of Paranemic Crossover and Juxtapose DNA Nanostructures

Crossover motifs are integral components for designing DNA-based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date there is no quantitative information about structural rigidity and the mechanical strength of parallel crossover DNA motifs. We have used fully atomistic molecular dynamics simulations in explicit solvent to get the force-extension curve of parallel DNA nanostructures to characterize their mechanical rigidity. In the presence of monovalent Na(+) ions, we find that the stretch modulus (gamma(1)) of the paranemic crossover and its topoisomer JX DNA structure is significantly higher (similar to 30%) compared to normal B-DNA of the same sequence and length. However, this is in contrast to the original expectation that these motifs are almost twice as rigid compared to the double-stranded B-DNA. When the DNA motif is surrounded by a solvent with Mg(2+) counterions, we find an enhanced rigidity compared to Na(+) environment due to the electrostatic screening effects arising from the divalent nature of Mg(2+) ions. To our knowledge, this is the first direct determination of the mechanical strength of these crossover motifs, which can be useful for the design of suitable DNA for DNA-based nanostructures and nanomechanical devices with improved structural rigidity.

Explicit filtering LES for turbulent non-premixed combustion

Two models for large eddy simulation of turbulent reacting flow in homogeneous turbulence were studied. The sub-grid stress arising out of non-linearities of the Navier-Stokes equations were modeled using an explicit filtering approach. A filtered mass density function (FMDF) approach was used for closure of the sub-grid scalar fluctuations. A posteriori calculations, when compared with the results from the direct numerical simulation, indicate that the explicit filtering is adequate in representing the effect of sub-grid stress on the filtered velocity field in the absence of reaction. Discrepancies arise when reactions occur, but the FMDF approach suffices to account for sub-grid scale fluctuations of the reacting scalars, accurately.

A Hybrid Energy-insensitive Explicit Guidance Scheme for Long Range Flight Vehicles with Solid Motors

Combining the newly developed nonlinear model predictive static programming technique with null range direction concept, a novel explicit energy-insensitive guidance design method is presented in this paper for long range flight vehicles, which leads to a closed form solution of the necessary guidance command update. Owing to the closed form nature, it does not lead to computational difficulties and the proposed optimal guidance algorithm can be implemented online. The guidance law is verified in a solid motor propelled long range flight vehicle, for which coming up with an effective guidance law is more difficult as compared to a liquid engine propelled vehicle (mainly because of the absence of thrust cutoff facility). Assuming the starting point of the second stage to be a deterministic point beyond the atmosphere, the scheme guides the vehicle properly so that it completes the mission within a tight error bound. The simulation results demonstrate its ability to intercept the target, even with an uncertainty of greater than 10% in burnout time.

A family of Runge-Kutta based explicit methods for rotational dynamics

The present paper develops a family of explicit algorithms for rotational dynamics and presents their comparison with several existing methods. For rotational motion the configuration space is a non-linear manifold, not a Euclidean vector space. As a consequence the rotation vector and its time derivatives correspond to different tangent spaces of rotation manifold at different time instants. This renders the usual integration algorithms for Euclidean space inapplicable for rotation. In the present algorithms this problem is circumvented by relating the equation of motion to a particular tangent space. It has been accomplished with the help of already existing relation between rotation increments which belongs to two different tangent spaces. The suggested method could in principle make any integration algorithm on Euclidean space, applicable to rotation. However, the present paper is restricted only within explicit Runge-Kutta enabled to handle rotation. The algorithms developed here are explicit and hence computationally cheaper than implicit methods. Moreover, they appear to have much higher local accuracy and hence accurate in predicting any constants of motion for reasonably longer time. The numerical results for solutions as well as constants of motion, indicate superior performance by most of our algorithms, when compared to some of the currently known algorithms, namely ALGO-C1, STW, LIEMID[EA], MCG, SUBCYC-M.

Redundancy resolution using a tractrix and its application to real-time simulations of hyper-redundant manipulators, snakes and tying of knots

To realistically simulate the motion of flexible objects such as ropes, strings, snakes, or human hair,one strategy is to discretise the object into a large number of small rigid links connected by rotary or spherical joints. The discretised system is highly redundant and the rotations at the joints (or the motion of the other links) for a desired Cartesian motion of the end of a link cannot be solved uniquely. In this paper, we propose a novel strategy to resolve the redundancy in such hyper-redundant systems.We make use of the classical tractrix curve and its attractive features. For a desired Cartesian motion of the `head'of a link, the `tail' of the link is moved according to a tractrix,and recursively all links of the discretised objects are moved along different tractrix curves. We show that the use of a tractrix curve leads to a more `natural' motion of the entire object since the motion is distributed uniformly along the entire object with the displacements tending to diminish from the `head' to the `tail'. We also show that the computation of the motion of the links can be done in real time since it involves evaluation of simple algebraic, trigonometric and hyperbolic functions. The strategy is illustrated by simulations of a snake, tying of knots with a rope and a solution of the inverse kinematics of a planar hyper-redundant manipulator.

Tryptophan-water interaction in Monellin:Hydration patterns from molecular dynamics simulations

Femtosecond spectroscopy carried out earlier on Monellin and some other systems has given insights into the hydration dynamics of the proteins. In the present work, molecular dynamics simulations have been performed on Monellin to study the hydration dynamics. A method has been described to follow up the molecular events of the protein–water interactions in detail. The time constants of the survival correlation function match well with the reported experimental values. This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general.

Single Cavity Trapped Vortex Combustor Simulations

The present work describes steady and unsteady computation of reacting flow in a Trapped Vortex Combustor. The primary motivation of this study is to develop this concept into a working combustor in modern gas turbines. The present work is an effort towards development of an experimental model test rig for further understanding dynamics of a single cavity trapped vortex combustor. The steady computations with and without combustion have been done for L/D of 0.8, 1 and 1.2; also unsteady non-reacting flow simulation has been done for L/D of 1. Fuel used for the present study is methane and Eddy-Dissipation model has been used for combustion-turbulence interactions. For L/D of 0.8, combustion efficiency is maximum and pattern factor is minimum. Also, primary vortex in the cavity is more stable and symmetric for L/D of 0.8. From unsteady non-reacting flow simulations, it is found that there is no vortex shedding from the cavity but there are oscillations in the span-wise direction of the combustor.

Efficient Key Management and Distribution for MANET

Ad hoc networks are being used in applications ranging from disaster recovery to distributed collaborative entertainment applications. Ad hoc networks have become one of the most attractive solution for rapid deployment of interconnecting large number of mobile personal devices. The user community of mobile personal devices are demanding a variety of value added multimedia entertainment services. The popularity of peer group is increasing and one or some members of the peer group need to send data to some or all members of the peer group. The increasing demand for group oriented value added services is driving for efficient multicast service over ad hoc networks. Access control mechanisms need to be deployed to provide guarantee that the unauthorized users cannot access the multicast content. In this paper, we present a topology aware key management and distribution scheme for secure overlay multicast over MANET to address node mobility related issues for multicast key management. We use overlay approach for key distribution and our objective is to keep communication overhead low for key management and distribution. We also incorporate reliability using explicit acknowledgments with the key distribution scheme. Through simulations we show that the proposed key management scheme has low communication overhead for rekeying and improves the reliability of key distribution.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.