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.

Precise measurement of hyperfine intervals using avoided crossing of dressed states

We demonstrate a technique for precisely measuring hyperfine intervals in alkali atoms. The atoms form a three-level system in the presence of a strong control laser and a weak probe laser. The dressed states created by the control laser show significant linewidth reduction. We have developed a technique for Doppler-free spectroscopy that enables the separation between the dressed states to be measured with high accuracy even in room temperature atoms. The states go through an avoided crossing as the detuning of the control laser is changed from positive to negative. By studying the separation as a function of detuning, the center of the level-crossing diagram is determined with high precision, which yields the hyperfine interval. Using room temperature Rb vapor, we obtain a precision of 44 kHz. This is a significant improvement over the current precision of similar to1 MHz.

A cascaded discharge plasma-adsorbent technique for engine exhaust treatment

A cascaded system of electrical discharges (non-thermal plasma) and adsorption process was investigated for the removal of oxides of Nitrogen (NOx) and total hydrocarbons (THC) from an actual diesel engine exhaust. The non-thermal plasma and adsorption processes were separately studied first and then the cascaded process was studied. In this study, different types of adsorbents were used. The NOx removal efficiency was higher with plasma-associated adsorption (cascaded) process compared to the individual processes and the removal efficiency was found almost invariant in time. When associated by plasma, among the adsorbents studied, activated charcoal and MS-13X were more effective for NOx and THC removal respectively. The experiments were conducted at no load and at 50% load conditions. The plasma reactor was kept at room temperature throughout the experiment, while the temperature of the adsorbent reactor was varied. A relative comparison of adsorbents was discussed at the end.

Synthesis and metallic probe induced conductance of Au tipped ultranarrow PbS rods

Au tipped ultranarrow PbS nanorods are synthesized. DFT electronic structure calculations and transport studies show that Au probes modify the nature and energies of PbS nanorod orbitals creating efficient electron conduction channels for enhanced conductance even at low applied bias.

Interface states of laser ablated BaTiO3 and Ba0.9Ca0.1TiO3 thin films in MFS structure determined by DLTS and C – V technique

BaTiO3 and Ba0.9Ca0.1TiO3 thin films were deposited on the p – type Si substrate by pulsed excimer laser ablation technique. The Capacitance – Voltage (C-V) measurement measured at 1 MHz exhibited a clockwise rotating hysteresis loop with a wide memory window for the Metal – Ferroelectric – Semiconductor (MFS) capacitor confirming the ferroelectric nature. The low frequency C – V measurements exhibited the response of the minority carriers in the inversion region while at 1 MHz the C – V is of a high frequency type with minimum capacitance in the inversion region. The interface states of both the MFS structures were calculated from the Castagne – Vaipaille method (High – low frequency C – V curve). Deep Level Transient Spectroscopy (DLTS) was used to analyze the interface traps and capture cross section present in the MFS capacitor. There were distinct peaks present in the DLTS spectrum and these peaks were attributed to the presence of the discrete interface states present at the semiconductor – ferroelectric interface. The distribution of calculated interface states were mapped with the silicon energy band gap for both the undoped and Ca doped BaTiO3 thin films using both the C – V and DLTS method. The interface states of the Ca doped BaTiO3 thin films were found to be higher than the pure BaTiO3 thin films.

Dynamics of bound dyes in a nonpolymeric aqueous gel derived from a tripodal bile salt

Rotational dynamics of polarity sensitive fluorescent dyes (ANS and DPH) in a nonpolymertic aqueous gel derived from tripodal cholamide I was studied using ultrafast time-resolved fluorescence technique. Results were compared with that of naturally occurring di- and trihydroxy bile salts. ANS in the gel showed two rotational correlation time (phi) components, 13.2 ns (bound to the hydrophobic region of the gel) and 1.0 ns (free aqueous ANS), whereas DPH showed only one component (4.8 ns). In the sol state, faster rotational motion was observed, both for ANS and DPH. Our data revealed that dyes get encapsulated more tightly in the gel network when compared to the micellar aggregates. ANS has more restrained rotation compared to DPH. This was attributed to the interaction of the sulfonate group of ANS with water molecules and hydrophilic parts of the gelator molecule. No restricted rotation was observed for DPH in the gel state unlike when it is in the gel phase of lipid bilayer.

Studies of the wetting characteristics of liquid iron on dense alumina by the X-ray sessile drop technique

In the present work, the reaction between a molten iron drop and dense alumina was studied using the X-ray sessile-drop method under different oxygen partial pressures in the gas atmosphere. The changes in contact angles between the iron drop and the alumina substrate were followed as functions of temperature and varying partial pressures of oxygen in the temperature range 1823 to 1873 K both in static and dynamic modes. The results of the contact angle measurements with pure iron in contact with dense alumina in extremely well-purified argon as well as under different oxygen partial pressures in the gas atmosphere showed good agreement with earlier measurements reported in the literature. In the dynamic mode, when argon was replaced by a CO-CO2-Ar mixture with a well-defined PO, in the gas, the contact angle showed an initial decrease followed by a period of nearly constant contact angle. At the end of this period, the length of which was a function of the P-O2 imposed, a further steep decrease in the contact angle was noticed. An intermediate layer of FeAl2O4 was detected in the scanning electron microscope (SEM) analysis of the reacted substrates. An interesting observation in the present experiments is that the iron drop moved away from the site of the reaction once the product layer covered the interface. The results are analyzed on the basis of the various forces acting on the drop.

The effect of host glass on optical absorption and fluorescence of Nd3+ in xNa(2)O-(30-x)K2O-70B(2)O(3) glasses

The effect of host glass composition on the optical absorption and fluorescence spectra of Nd3+ has been studied in mixed alkali borate glasses of the type xNa(2)O-(30-x)K2O-69.5B(2)O(3)-0.5Nd(2)O(3) (X = 5,10,15,20 and 25). Various spectroscopic parameters such as Racah (E-1, E-2 and E-3), spin-orbit (xi(4f)) and configuration interaction (alpha, beta) parameters have been calculated. The Judd-Ofelt intensity parameters (Omega(lambda)) have been calculated and the radiative transition probabilities (A(rad)), radiative lifetimes (tau(r)), branching ratios (beta) and integrated absorption cross sections (Sigma) have been obtained for certain excited states of the Nd3+, ion and are discussed with respect to x. From the fluorescence spectra, the effective fluorescence line widths (Deltalambda(eff)) and stimulated emission cross sections (sigma(p)) have been obtained for the three transitions F-4(3/2) --> I-4(9/2), F-4(3/2) --> I-4(11/2) and F-4(3/2) --> I-4(13/2) of Nd3+. The stimulated emission cross section (sigma(p)) values are found to be in the range (2.0-4.8) x 10(-2)0 cm(2) and they are large enough to indicate that the mixed alkali borate glasses could be potential laser host materials.

Turbulent flow computations using upwind RANS technique for a flat plate and an airfoil

Reynolds Averaged Navier Stokes (RANS) equations are solved using third order upwind biased Roe's scheme for the inviscid fluxes and second order central difference scheme for the viscous fluxes. The Baldwin & Lomax turbulence model is employed for Reynolds stresses. The governing equations are solved using finite-volume implicit scheme in body fitted curvilinear coordinate O-grid system. Computations axe reported for a flat plate apart from RAE 2822 and NACA 0012 airfoils. Results for the flat plate at M = 0.3, R-c = 4.0 x 10(6) compare favourably with the analytical solution. Results for the two airfoils are compared with experiment. There is a good agreement in C-p distribution between experiment and computation for both the airfoils. Comparison of C-f distribution with experiment for RAE 2822 airfoil is reasonable.

Fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using Stern-Volmer plots

Fluorescence quenching of biologically active carboxamide namely (E)-2-(4-chlorobenzylideneamino)-N-(2-chlorophenyl)-4,5,6,7-tetrahydrobe nzo[b]thiophene-3-carboxamide [ECNCTTC] by aniline and carbon tetrachloride (CCl(4)) quenchers in different solvents using steady state method and time resolved method using only one solvent has been carried out at room temperature to understand the role of quenching mechanisms. The Stern-Volmer plot has been found to be linear for all the solvents studied. The probability of quenching per encounter p (p') was determined in all the solvents and was found to be less than unity. Further, from the studies of rate parameters and life time measurements in n-heptane and cyclohexane with aniline and carbon tetrachloride as quenchers have been shown that, the phenomenon of quenching is generally governed by the well-known Stern-Volmer (S-V) plot. The activation energy E(a) (or E(a)') of quenching was determined using the literature values of activation energy of diffusion E(d) and the experimentally determined values of p (or p'). It has been found that, the activation energy E(a) (E(a)') is greater than the activation energy for diffusion E(d) in all solvents. Hence, from the magnitudes of E(a) (or E(a)') as well as p (or p') infer that, the quenching mechanism is not solely due to the material diffusion, but there is also contribution from the activation energy. (C) 2011 Elsevier B.V. All rights reserved.

Contrained linear spectral unmixing technique for regional land cover mapping using MODIS data

Over the last few decades, there has been a significant land cover (LC) change across the globe due to the increasing demand of the burgeoning population and urban sprawl. In order to take account of the change, there is a need for accurate and up- to-date LC maps. Mapping and monitoring of LC in India is being carried out at national level using multi-temporal IRS AWiFS data. Multispectral data such as IKONOS, Landsat- TM/ETM+, IRS-1C/D LISS-III/IV, AWiFS and SPOT-5, etc. have adequate spatial resolution (~ 1m to 56m) for LC mapping to generate 1:50,000 maps. However, for developing countries and those with large geographical extent, seasonal LC mapping is prohibitive with data from commercial sensors of limited spatial coverage. Superspectral data from the MODIS sensor are freely available, have better temporal (8 day composites) and spectral information. MODIS pixels typically contain a mixture of various LC types (due to coarse spatial resolution of 250, 500 and 1000 m), especially in more fragmented landscapes. In this context, linear spectral unmixing would be useful for mapping patchy land covers, such as those that characterise much of the Indian subcontinent. This work evaluates the existing unmixing technique for LC mapping using MODIS data, using end- members that are extracted through Pixel Purity Index (PPI), Scatter plot and N-dimensional visualisation. The abundance maps were generated for agriculture, built up, forest, plantations, waste land/others and water bodies. The assessment of the results using ground truth and a LISS-III classified map shows 86% overall accuracy, suggesting the potential for broad-scale applicability of the technique with superspectral data for natural resource planning and inventory applications.