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.

On the spurious increase in particle volume fraction during coarsening simulations

The problem of spurious increase in volume fraction of second-phase particles during computer simulations of coarsening is examined. The origin of this problem is traced to the use of too long a time step (used for numerical integration of growth rates with respect to time) which leads to small particles with large negative growth rates shrinking to negative radii at the end of the time step. Such a shrinkage to negative sizes has the effect of pumping solute into the system. It is therefore suggested that the length of the time step be chosen in accordance with the size of the smallest particle present in the system. It is shown that spurious increase in particle Volume has a significant effect on the particle size distributions in the scaling regime (making them broader and more skewed in the Lifshitz-Slyozov-Wagner model). Its effect on coarsening kinetics, however, is found to be small.

Modeling of angiogenin-3 '-NMP complex

Angiogenin belongs to the Ribonuclease superfamily and has a weak enzymatic activity that is crucial for its biological function of stimulating blood vessel growth. Structural studies on ligand bound Angiogenin will go a long way in understanding the mechanism of the protein as well as help in designing drugs against it. In this study we present the first available structure of nucleotide ligand bound Angiogenin obtained by computer modeling. The importance of this study in itself notwithstanding, is a precursor to modeling a full dinucleotide substrate onto Angiogenin. Bovine Angiogenin, the structure of which has been solved at a high resolution, was earlier subjected to Molecular Dynamics simulations for a nanosecond. The MD structures offer better starting points for docking as they offer lesser obstruction than the crystal structure to ligand binding. The MD structure with the least serious short contacts was modeled to obtain a steric free Angiogenin - 3' mononucleotide complex structure. The structures were energetically minimized and subjected to a brief spell of Molecular Dynamics. The results of the simulation show that all the li,ligand-Angiogenin interactions and hydrogen bonds are retained, redeeming the structure and docking procedure. Further, following ligand - protein interactions in the case of the ligands 3'-CMP and 3'-UMP we were able to speculate on how Angiogenin, a predominantly prymidine specific ribonuclease prefers Cytosine to Uracil in the first base position.

Numerical simulations of fracture initiation in ductile solids under mode I, dynamic loading

In this paper, an overview of some recent computational studies by the authors on ductile crack initiation under mode I, dynamic loading is presented. In these studies, a large deformation finite element procedure is employed along with the viscoplastic version of the Gurson constitutive model that accounts for the micro-mechanical processes of void nucleation, growth and coalescence. A three-point bend fracture specimen subjected to impact, and a single edge notched specimen loaded by a tensile stress pulse are analysed. Several loading rates are simulated by varying the impact speed or the rise time and magnitude of the stress pulse. A simple model involving a semi-circular notch with a pre-nucleated circular hole situated ahead of it is considered. The growth of the hole and its interaction with the notch tip, which leads to plastic strain and porosity localization in the ligament connecting them, is simulated. The role of strain-rate dependence on ductile crack initiation at high loading rates, and the specimen geometry effect on the variation of dynamic fracture toughness with loading rate are Investigated.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

Full Sphere Axisymmetric Simulations of the Solar Dynamo

We explore a full sphere (2D axisymmetric) kinematic solar dynamo model based on the Babcock-Leighton idea that the poloidal field is generated in the surface layers from the decay of tilted bipolar solar active regions. This model incorporates the helioseismically deduced solar rotation profile and an algorithm for buoyancy motivated from simulations of flux tube dynamics. A prescribed deep meridional circulation plays an important role in the advection of magnetic flux. We specifically address the parity issue and show that – contrary to some recent claims – the Babcock-Leighton dynamo can reproduce solar-like dipolar parity if certain reasonable conditions are satisfied in the solar interior, the most important requirement being that the poloidal field of the two hemispheres be efficiently coupled across the equator.

Size-dependent and strain rate effects in quantum dot nanostructures with molecular dynamic simulations

Size and strain rate effects are among several factors which play an important role in determining the response of nanostructures, such as their deformations, to the mechanical loadings. The mechanical deformations in nanostructure systems at finite temperatures are intrinsically dynamic processes. Most of the recent works in this context have been focused on nanowires [1, 2], but very little attention has been paid to such low dimensional nanostructures as quantum dots (QDs). In this contribution, molecular dynamics (MD) simulations with an embedded atom potential method(EAM) are carried out to analyse the size and strain rate effects in the silicon (Si) QDs, as an example. We consider various geometries of QDs such as spherical, cylindrical and cubic. We choose Si QDs as an example due to their major applications in solar cells and biosensing. The analysis has also been focused on the variation in the deformation mechanisms with the size and strain rate for Si QD embedded in a matrix of SiO2 [3] (other cases include SiN and SiC matrices).It is observed that the mechanical properties are the functions of the QD size, shape and strain rate as it is in the case for nanowires [2]. We also present the comparative study resulted from the application of different EAM potentials in particular, the Stillinger-Weber (SW) potential, the Tersoff potentials and the environment-dependent interatomic potential (EDIP) [1]. Finally, based on the stabilized structural properties we compute electronic bandstructures of our nanostructures using an envelope function approach and its finite element implementation.

Correction for Bias in Downscaling GCM Simulations for Hydrologic Impact Assessment

In a statistical downscaling model, it is important to remove the bias of General Circulations Model (GCM) outputs resulting from various assumptions about the geophysical processes. One conventional method for correcting such bias is standardisation, which is used prior to statistical downscaling to reduce systematic bias in the mean and variances of GCM predictors relative to the observations or National Centre for Environmental Prediction/ National Centre for Atmospheric Research (NCEP/NCAR) reanalysis data. A major drawback of standardisation is that it may reduce the bias in the mean and variance of the predictor variable but it is much harder to accommodate the bias in large-scale patterns of atmospheric circulation in GCMs (e.g. shifts in the dominant storm track relative to observed data) or unrealistic inter-variable relationships. While predicting hydrologic scenarios, such uncorrected bias should be taken care of; otherwise it will propagate in the computations for subsequent years. A statistical method based on equi-probability transformation is applied in this study after downscaling, to remove the bias from the predicted hydrologic variable relative to the observed hydrologic variable for a baseline period. The model is applied in prediction of monsoon stream flow of Mahanadi River in India, from GCM generated large scale climatological data.

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.

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.