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.

Glassy behavior in neural network models of associative memory

Neural network models of associative memory exhibit a large number of spurious attractors of the network dynamics which are not correlated with any memory state. These spurious attractors, analogous to "glassy" local minima of the energy or free energy of a system of particles, degrade the performance of the network by trapping trajectories starting from states that are not close to one of the memory states. Different methods for reducing the adverse effects of spurious attractors are examined with emphasis on the role of synaptic asymmetry. (C) 2002 Elsevier Science B.V. All rights reserved.

Neural network based optimal routing algorithm for communication networks

This paper presents the capability of the neural networks as a computational tool for solving constrained optimization problem, arising in routing algorithms for the present day communication networks. The application of neural networks in the optimum routing problem, in case of packet switched computer networks, where the goal is to minimize the average delays in the communication have been addressed. The effectiveness of neural network is shown by the results of simulation of a neural design to solve the shortest path problem. Simulation model of neural network is shown to be utilized in an optimum routing algorithm known as flow deviation algorithm. It is also shown that the model will enable the routing algorithm to be implemented in real time and also to be adaptive to changes in link costs and network topology. (C) 2002 Elsevier Science Ltd. All rights reserved.

Real-time kinetic analysis of hCG-monoclonal antibody interaction using radiolabeled hCG probe: presence of two forms of Ag-mAb complex as revealed by solid phase dissociation studies

Real-time kinetics of ligand-ligate interaction has predominantly been studied by either fluorescence or surface plasmon resonance based methods. Almost all such studies are based on association between the ligand and the ligate. This paper reports our analysis of dissociation data of monoclonal antibody-antigen (hCG) system using radio-iodinated hCG as a probe and nitrocellulose as a solid support to immobilize mAb. The data was analyzed quantitatively for a one-step and a two-step model. The data fits well into the two-step model. We also found that a fraction of what is bound is non-dissociable (tight-binding portion (TBP)). The TBP was neither an artifact of immobilization nor does it interfere with analysis. It was present when the reaction was carried out in homogeneous solution in liquid phase. The rate constants obtained from the two methods were comparable. The work reported here shows that real-time kinetics of other ligand-ligate interaction can be studied using nitrocellulose as a solid support. (C) 2002 Elsevier Science B.V. All rights reserved.

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.

Ellipsometry as a Sensitive Technique to Probe film -Substrate Interfaces: Al2O3 on Si(100)

An attempt has been made to study the film-substrate interface by using a sensitive, non- conventional tool. Because of the prospective use of gate oxide in MOSFET devices, we have chosen to study alumina films grown on silicon. Film-substrate interface of alumina grown by MOCVD on Si(100) was studied systematically using spectroscopic ellipsometry in the range 1.5-5.0 eV, supported by cross-sectional SEM, and SIMS. The (ε1,ε2) versus energy data obtained for films grown at 600°C, 700°C, and 750°C were modeled to fit a substrate/interface/film “sandwich”. The experimental results reveal (as may be expected) that the nature of the substrate -film interface depends strongly on the growth temperature. The simulated (ε1,ε2) patterns are in excellent agreement with observed ellipsometric data. The MOCVD precursors results the presence of carbon in the films. Theoretical simulation was able to account for the ellipsometry data by invoking the presence of “free” carbon in the alumina films.

Study of Brittle-to-ductile-transition in Pt-aluminide bond coat using micro-tensile testing method

The Brittle-to-ductile-transition-temperature (BDTT) of free-standing Pt-aluminide (PtAl) coating specimens, i.e. stand-alone coating specimens without any substrate, was determined by micro-tensile testing technique. The effect of Pt content, expressed in terms of the thickness of initial electro-deposited Pt layer, on the BDTT of the coating has been evaluated and an empirical correlation drawn. Increase in the electrodeposited Pt layer thickness from nil to 10 mu m was found to cause an increase in the BDTT of the coating by about 100 degrees C.

A System-C based Micro architectural Exploration Framework for Latency, Power and Performance Trade-offs of On-Chip Interconnection

We describe a System-C based framework we are developing, to explore the impact of various architectural and microarchitectural level parameters of the on-chip interconnection network elements on its power and performance. The framework enables one to choose from a variety of architectural options like topology, routing policy, etc., as well as allows experimentation with various microarchitectural options for the individual links like length, wire width, pitch, pipelining, supply voltage and frequency. The framework also supports a flexible traffic generation and communication model. We provide preliminary results of using this framework to study the power, latency and throughput of a 4x4 multi-core processing array using mesh, torus and folded torus, for two different communication patterns of dense and sparse linear algebra. The traffic consists of both Request-Response messages (mimicing cache accesses)and One-Way messages. We find that the average latency can be reduced by increasing the pipeline depth, as it enables higher link frequencies. We also find that there exists an optimum degree of pipelining which minimizes energy-delay product.

Micro stepping of Shape Memory Alloy based Poly Phase motor

In literature we find broadly two types of shape memory alloy based motors namely limited rotation motor and unlimited rotation motor. The unlimited rotation type SMA based motor reported in literature uses SMA springs for actuation. An attempt has been made in this paper to develop an unlimited rotation type balanced poly phase motor based on SMA wire in series with a spring in each phase. By isolating SMA actuation and spring action we are able achieve a constant force by the SMA wire through out its range of operation. The Poly phase motor can be used in stepping mode for generating incremental motion and servo mode for generating continuous motion. A method of achieving servo motion by micro stepping is presented. Micro stepping consists of controlling single-phase temperature with a position feedback. The motor has been modeled with a new approach to the SMA wire Hysterysis model. Motor is simulated for different responses and the results are compared with the experimental data.

Volume Change behaviour in Calcitic Soil influenced with Sulphuric Acid using Artificial Neural Networks

This paper elucidates the methodology of applying artificial neural network model (ANNM) to predict the percent swell of calcitic soil in sulphuric acid solutions, a complex phenomenon involving many parameters. Swell data required for modelling is experimentally obtained using conventional oedometer tests under nominal surcharge. The phases in ANN include optimal design of architecture, operation and training of architecture. The designed optimal neural model (3-5-1) is a fully connected three layer feed forward network with symmetric sigmoid activation function and trained by the back propagation algorithm to minimize a quadratic error criterion.The used model requires parameters such as duration of interaction, calcite mineral content and acid concentration for prediction of swell. The observed strong correlation coefficient (R2 = 0.9979) between the values determined by the experiment and predicted using the developed model demonstrates that the network can provide answers to complex problems in geotechnical engineering.