Efficient parallel algorithms for solvent accessible surface areaof proteins

We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA is computed by finding the exposed surface areas of the spheres obtained by increasing the van der Waals radii of the atoms with the van der Waals radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is only O(n), where n is the number of atoms in the protein molecule. For computing sphere intersections, we present hash-based algorithms that run in O(n) expected sequential time and O(n/p) expected parallel time and sort-based algorithms that run in worst-case O(n log n) sequential time and O(n log n/p) parallel time. These are significant improvements over previously known algorithms which take O(n²) time sequentially and O(n²/p) time in parallel. We present a Monte Carlo algorithm for computing the solvent accessible surface area. The basic idea is to generate points uniformly at random on the surface of spheres obtained by increasing the van der Waals radii of the atoms with the van der Waals radius of the solvent molecule and to test the points for accessibility. We also provide error bounds as a function of the sample size. Experimental verification of the algorithms is carried out using an IBM SP-2     

Glass fibre reinforced composites of triglycidyl-p-aminophenol

Glass fibre reinforced epoxy composites were fabricated from the matrix resins diglycidyl ether of bisphenol A (DGEBA) and triglycidyl-p-aminophenol (TGAP) using diethylene triamine as curing agent. The epoxy laminates were evaluated for their mechanical properties, dielectrical properties and chemical resistance. Significant improvement in fiexural strength but a slight deterioration in dielectrical properties were observed on incorporation of an epoxy fortifier into the resin system before fabricating the composites.     

A numerical study of pulsatile blood flow in an eccentric catheterized artery using a fast algorithm

The pulsatile blood flow in an eccentric catheterized artery is studied numerically by making use of an extended version of the fast algorithm of Borges and Daripa [J. Comp. Phys., 2001]. The mathematical model involves the usual assumptions that the arterial segment is straight, the arterial wall is rigid and impermeable, blood is an incompressible Newtonian fluid, and the flow is fully developed. The flow rate (flux) is considered as a periodic function of time (prescribed). The axial pressure gradient and velocity distribution in the eccentric catheterized artery are obtained as solutions of the problem. Through the computed results on axial pressure gradient, the increases in mean pressure gradient and frictional resistance in the artery due to catheterization are estimated. These estimates can be used to correct the error involved in the measured pressure gradients using catheters.     

Extended Use of Linear Graph Theory for Analysis of Pipe Networks

Linear graph theory used for pipe network analysis is to make the method systematic. A numerical method that uses linear graph theory is presented for the steady-state analysis of flow and pressure in a pipe network including its hydraulic components (pumps, valves, junctions, etc.). The proposed method differs from other linear graph methods in terms of the linear graph and the selection of its tree. The solution algorithm uses a function that depends on a power law to update the pipe flows in successive iterations. The exponents of this function are chosen to obtain a fast convergence rate even for large errors in the assumption of initial pipe flows. The convergence rate of the proposed method is validated using an error function and is compared to those of other methods. Some typical networks are analyzed to check the reliability of the proposed method. The results demonstrate the superior conditioning of the proposed method.     

Impact of open dumping of municipal solid waste on soil properties in mountainous region

This paper presents the effect of open dumping of municipal solid waste (MSW) on soil characteristics in the mountainous region of Himachal Pradesh, India. The solid waste of dumpsite contains various complex characteristics with organic fractions of the highest proportions. As leachate percolates into the soil, it migrates contaminants into the soil and affects soil stability and strength. The study includes the geotechnical investigation of dump soil characteristics and its comparison with the natural soil samples taken from outside the proximity of dumpsites. The geochemical analysis of dumpsite soil samples was also carried out by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Visual inspection revealed that the MSW consists of high fraction of organics, followed by paper. The soil samples were collected from five trial pits in the dumpsites at depths of 0.5 m, 1 m and 1.5 m. Then the collected soil samples were subjected to specific gravity test, grain size analysis, Atterberg's limit test, compaction test, direct shear test, California bearing ratio (CBR) test and permeability analysis. The study indicated that the dumpsite soils from four study regions show decreasing trends in the values of maximum dry density (MDD), specific gravity, cohesion and CBR, and increasing permeability as compared to the natural soil. The results show that the geotechnical properties of the soils at all four study locations have been severely hampered due to contamination induced by open dumping of waste.     

Development of Biodegradable Nanocarriers Loaded with a Monoclonal Antibody

Treatments utilizing monoclonal antibody therapeutics against intracellular protein-protein interactions in cancer cells have been hampered by several factors, including poor intracellular uptake and rapid lysosomal degradation. Our current work examines the feasibility of encapsulating monoclonal antibodies within poly(lactic-co-glycolic acid) (PLGA) nanoparticles using a water/oil/water double emulsion solvent evaporation technique. This method can be used to prepare protective polymeric nanoparticles for transporting functional antibodies to the cytoplasmic compartment of cancer cells. Nanoparticles were formulated and then characterized using a number of physical and biological parameters. The average nanoparticle size ranged from 221 to 252 nm with a low polydispersity index. Encapsulation efficiency of 16%–22% and antibody loading of 0.3%–1.12% were observed. The antibody molecules were released from the nanoparticles in a sustained manner and upon release maintained functionality. Our studies achieved successful formulation of antibody loaded polymeric nanoparticles, thus indicating that a PLGA-based antibody nanoformulation is a promising intracellular delivery vehicle for a large number of new intracellular antibody targets in cancer cells.     

Studies on EVA‐Based Wax Fuel for Launch Vehicle Applications

A fuel for the hybrid rocket system was developed. The attempts made to improve the mechanical properties of wax by adding EVA (ethylene vinyl acetate) are illustrated. It was observed that the mechanical properties obtained by adding EVA to wax were dependent on the process of curing the fuel specimen. A proprietary method of curing the fuel specimen was established. The percentage elongation obtained with 20 % EVA and 80 % of wax was around 17 %, which was much higher than the values obtained with pure wax (4 %). It was observed from the study that the higher the percentage of EVA content in wax was, the better the mechanical properties were. Regression rate studies with EVA and wax combination were carried out. It was observed that the regression rate decreased upon addition of EVA in wax. This reduction was compensated by using a bluff body at the head end. The regression rate obtained with 20 % EVA and 80 % wax even with the use of bluff body is lower than that obtained with pure wax, but is around 3.5 times the regression rate obtained with polymeric fuels.     

Utilizing Semantic Knowledge for Access Control in Pervasive and Ubiquitous Systems

Controlling access in pervasive environments is crucial and a significant challenge because users and devices can connect from anywhere which results in users and resources becoming available at any point of time and location depending on the situation. Access control policies for this type of environment are required to conform to high-level business notions. In pervasive environments, these high-level notions refer to contexts of the situation which can change unpredictably and must be interpreted semantically to maintain proper access control. Therefore, it is necessary to have a formal representation that represents semantics of the contexts, reflects the change of the situation, and can be shared and understood by a policy system. This paper addresses these issues by introducing a context management system that uses a semantic web approach as an underlying mechanism to model and represent semantics of the contexts. The system stores current contexts in a semantic knowledge base which is used by a semantic access control system in order to form access control policies and evaluate policies at run time. The approach is validated through a proof of concept implementation that includes performance results of the context management system as it responds to a change of the situation.     

A slow wave structure and its application in bandpass filter design

This paper presents a new slow wave open-loop resonator filters with reduced size and improved stopband characteristics. A comprehensive treatment of different kind of coupling in this structure is demonstrated. Two and four resonator band pass filters at center frequency 2.15 and 2.30 GHz with different bandwidth are designed. The simulated results are verified with the help of two different software packages (IE3D and Sonnet Lite).