DoSA: Database of Structural Alignments

Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.

Spark plasma sintering may lead to phase instability and inferior mechanical properties: A case study with TiB2

In contrast to the widely reported beneficial aspects of spark plasma sintering in developing materials with better properties, we report here two interesting aspects recorded with difficult-to-sinter titanium diboride: (a) in situ formation of second phase (TiB) and (b) inferior hardness (by similar to 30%) and elastic modulus (by similar to 20%) for spark plasma sintered TiB2, with respect to hot pressed TiB2. The formation of TiB is discussed with reference to the enhanced reaction kinetics in the presence of pulsed electric field. (C) 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Influence of annealing on structural, morphological, compositional and surface properties of magnetron sputtered nickel-titanium thin films

Thin films of NiTi were deposited by DC magnetron sputtering from an equiatomic alloy target (Ni/Ti: 50/50 at.%). The films were deposited without intentional heating of the substrates. The thickness of the deposited films was approximately 2 mu m. The structure and morphology of NiTi films annealed at different temperatures were analyzed in order to understand the effect of annealing on physical properties of the films. The compositional investigations of fresh and annealed films were also evaluated by energy dispersive X-ray spectroscopy (EDS) and X-ray photo-electron spectroscopy (XPS) techniques. X-ray diffraction (XRD) studies showed that as-deposited films were amorphous in nature whereas annealed films were found to poly-crystalline with the presence of Austenite phase as the dominant phase. AFM investigations showed higher grain size and surface roughness values in the annealed films. In annealed films, the grain size and film roughness values were increased from 10 to 85 nm and 2-18 nm. Film composition measured by EDS were found to 52.5 atomic percent of Ni and 47.5 atomic percent of Ti. XPS investigations, demonstrated the presence of Ni content on the surface of the films, in fresh films, whereas annealed films did not show any nickel. From HR-XPS investigations, it can be concluded that annealed NiTi films have higher tendency to form metal oxide (titanium dioxide) layer on the surface of the films than fresh NiTi films. (C) 2013 Elsevier B. V. All rights reserved.

Estimation of Probabilistic Bounds on Phase CPI and Relevance in WCET Analysis

Estimating program worst case execution time(WCET) accurately and efficiently is a challenging task. Several programs exhibit phase behavior wherein cycles per instruction (CPI) varies in phases during execution. Recent work has suggested the use of phases in such programs to estimate WCET with minimal instrumentation. However the suggested model uses a function of mean CPI that has no probabilistic guarantees. We propose to use Chebyshev's inequality that can be applied to any arbitrary distribution of CPI samples, to probabilistically bound CPI of a phase. Applying Chebyshev's inequality to phases that exhibit high CPI variation leads to pessimistic upper bounds. We propose a mechanism that refines such phases into sub-phases based on program counter(PC) signatures collected using profiling and also allows the user to control variance of CPI within a sub-phase. We describe a WCET analyzer built on these lines and evaluate it with standard WCET and embedded benchmark suites on two different architectures for three chosen probabilities, p={0.9, 0.95 and 0.99}. For p= 0.99, refinement based on PC signatures alone, reduces average pessimism of WCET estimate by 36%(77%) on Arch1 (Arch2). Compared to Chronos, an open source static WCET analyzer, the average improvement in estimates obtained by refinement is 5%(125%) on Arch1 (Arch2). On limiting variance of CPI within a sub-phase to {50%, 10%, 5% and 1%} of its original value, average accuracy of WCET estimate improves further to {9%, 11%, 12% and 13%} respectively, on Arch1. On Arch2, average accuracy of WCET improves to 159% when CPI variance is limited to 50% of its original value and improvement is marginal beyond that point.

Role of the cloud adjustment time scale in simulation of the interannual variability of Indian summer monsoon

The simulation of precipitation in a general circulation model relying on relaxed mass flux cumulus parameterization scheme is sensitive to cloud adjustment time scale (CATS). In this study, the frequency of the dominant intra-seasonal mode and interannual variability of Indian summer monsoon rainfall (ISMR) simulated by an atmospheric general circulation model is shown to be sensitive to the CATS. It has been shown that a longer CATS of about 5 h simulates the spatial distribution of the ISMR better. El Nio Southern Oscillation-ISMR relationship is also sensitive to CATS. The equatorial Indian Ocean rainfall and ISMR coupling is sensitive to CATS. Our study suggests that a careful choice of CATS is necessary for adequate simulation of spatial pattern as well as interannual variation of Indian summer monsoon precipitation.

The N-terminal region containing the zinc finger domain of tobacco streak virus coat protein is essential for the formation of virus-like particles

Tobacco streak virus (TSV), a member of the genus Ilarvirus (family Bromoviridae), has a tripartite genome and forms quasi-isometric virions. All three viral capsids, encapsidating RNA 1, RNA 2 or RNA 3 and subgenomic RNA 4, are constituted of a single species of coat protein (CP). Formation of virus-like particles (VLPs) could be observed when the TSV CP gene was cloned and the recombinant CP (rCP) was expressed in E. coli. TSV VLPs were found to be stabilized by Zn2+ ions and could be disassembled in the presence of 500 mM CaCl2. Mutational analysis corroborated previous studies that showed that an N-terminal arginine-rich motif was crucial for RNA binding; however, the results presented here demonstrate that the presence of RNA is not a prerequisite for assembly of TSV VLPs. Instead, the N-terminal region containing the zinc finger domain preceding the arginine-rich motif is essential for assembly of these VLPs.

Exfoliated graphite/titanium dioxide nanocomposites for photodegradation of eosin yellow

An improved photocatalyst consisting of a nanocomposite of exfoliated graphite and titanium dioxide (EG-TiO2) was prepared. SEM and TEM micrographs showed that the spherical TiO2 nanoparticles were evenly distributed on the surface of the EG sheets. A four times photocatalytic enhancement was observed for this floating nanocomposite compared to TiO2 and EG alone for the degradation of eosin yellow. For all the materials, the reactions followed first order kinetics where for EG-TiO2, the rate constant was much higher than for EG and TiO2 under visible light irradiation. The enhanced photocatalytic activity of EG-TiO2 was ascribed to the capability of graphitic layers to accept and transport electrons from the excited TiO2, promoting charge separation. This indicates that carbon, a cheap and abundant material, can be a good candidate as an electron attracting reservoir for photocatalytic organic pollutant degradation. (C) 2014 Elsevier B.V. All rights reserved.

AN APPROACH FOR EVALUATION OF USE OF GEOCELLS IN FLEXIBLE PAVEMENTS

The design methodology for flexible pavements needs to address the mechanisms of pavement failure, loading intensities and also develop suitable approaches for evaluation of pavement performance. In the recent years, the use of geocells to improve pavement performance has been receiving considerable attention. This paper studies the influence of geocells on the required thickness of pavements by placing it below the granular layers (base and sub-base) and above the subgrade. The reduction in thickness here refers to the reduction in the thickness of the GSB (Granular Sub-base) layer, with a possibility of altogether getting rid of it. To facilitate the analysis, a simple linear elastic approach is used, considering six of the sections as given in the Indian Roads Congress (IRC) code. All the analysis was done using the pavement analysis package KENPAVE. The results show that the use of geocells enables a reduction in pavement thickness.

The generalized Onsager model for a binary gas mixture

The Onsager model for the secondary flow field in a high-speed rotating cylinder is extended to incorporate the difference in mass of the two species in a binary gas mixture. The base flow is an isothermal solid-body rotation in which there is a balance between the radial pressure gradient and the centrifugal force density for each species. Explicit expressions for the radial variation of the pressure, mass/mole fractions, and from these the radial variation of the viscosity, thermal conductivity and diffusion coefficient, are derived, and these are used in the computation of the secondary flow. For the secondary flow, the mass, momentum and energy equations in axisymmetric coordinates are expanded in an asymptotic series in a parameter epsilon = (Delta m/m(av)), where Delta m is the difference in the molecular masses of the two species, and the average molecular mass m(av) is defined as m(av) = (rho(w1)m(1) + rho(w2)m(2))/rho(w), where rho(w1) and rho(w2) are the mass densities of the two species at the wall, and rho(w) = rho(w1) + rho(w2). The equation for the master potential and the boundary conditions are derived correct to O(epsilon(2)). The leading-order equation for the master potential contains a self-adjoint sixth-order operator in the radial direction, which is different from the generalized Onsager model (Pradhan & Kumaran, J. Fluid Mech., vol. 686, 2011, pp. 109-159), since the species mass difference is included in the computation of the density, viscosity and thermal conductivity in the base state. This is solved, subject to boundary conditions, to obtain the leading approximation for the secondary flow, followed by a solution of the diffusion equation for the leading correction to the species mole fractions. The O(epsilon) and O(epsilon(2)) equations contain inhomogeneous terms that depend on the lower-order solutions, and these are solved in a hierarchical manner to obtain the O(epsilon) and O(epsilon(2)) corrections to the master potential. A similar hierarchical procedure is used for the Carrier-Maslen model for the end-cap secondary flow. The results of the Onsager hierarchy, up to O(epsilon(2)), are compared with the results of direct simulation Monte Carlo simulations for a binary hard-sphere gas mixture for secondary flow due to a wall temperature gradient, inflow/outflow of gas along the axis, as well as mass and momentum sources in the flow. There is excellent agreement between the solutions for the secondary flow correct to O(epsilon(2)) and the simulations, to within 15 %, even at a Reynolds number as low as 100, and length/diameter ratio as low as 2, for a low stratification parameter A of 0.707, and when the secondary flow velocity is as high as 0.2 times the maximum base flow velocity, and the ratio 2 Delta m/(m(1) + m(2)) is as high as 0.5. Here, the Reynolds number Re = rho(w)Omega R-2/mu, the stratification parameter A = root m Omega R-2(2)/(2k(B)T), R and Omega are the cylinder radius and angular velocity, m is the molecular mass, rho(w) is the wall density, mu is the viscosity and T is the temperature. The leading-order solutions do capture the qualitative trends, but are not in quantitative agreement.

Spectrum sensing using distributed sequential detection via noisy reporting MAC

This paper considers cooperative spectrum sensing algorithms for Cognitive Radios which focus on reducing the number of samples to make a reliable detection. We propose algorithms based on decentralized sequential hypothesis testing in which the Cognitive Radios sequentially collect the observations, make local decisions and send them to the fusion center for further processing to make a final decision on spectrum usage. The reporting channel between the Cognitive Radios and the fusion center is assumed more realistically as a Multiple Access Channel (MAC) with receiver noise. Furthermore the communication for reporting is limited, thereby reducing the communication cost. We start with an algorithm where the fusion center uses an SPRT-like (Sequential Probability Ratio Test) procedure and theoretically analyze its performance. Asymptotically, its performance is close to the optimal centralized test without fusion center noise. We further modify this algorithm to improve its performance at practical operating points. Later we generalize these algorithms to handle uncertainties in SNR and fading. (C) 2014 Elsevier B.V. All rights reserved.

Optimal Linear Glauber Model

Contrary to the actual nonlinear Glauber model, the linear Glauber model (LGM) is exactly solvable, although the detailed balance condition is not generally satisfied. This motivates us to address the issue of writing the transition rate () in a best possible linear form such that the mean squared error in satisfying the detailed balance condition is least. The advantage of this work is that, by studying the LGM analytically, we will be able to anticipate how the kinetic properties of an arbitrary Ising system depend on the temperature and the coupling constants. The analytical expressions for the optimal values of the parameters involved in the linear are obtained using a simple Moore-Penrose pseudoinverse matrix. This approach is quite general, in principle applicable to any system and can reproduce the exact results for one dimensional Ising system. In the continuum limit, we get a linear time-dependent Ginzburg-Landau equation from the Glauber's microscopic model of non-conservative dynamics. We analyze the critical and dynamic properties of the model, and show that most of the important results obtained in different studies can be reproduced by our new mathematical approach. We will also show in this paper that the effect of magnetic field can easily be studied within our approach; in particular, we show that the inverse of relaxation time changes quadratically with (weak) magnetic field and that the fluctuation-dissipation theorem is valid for our model.

Use of permeable reactive barrier to mitigate groundwater nitrate contamination from on-site sanitation

Nearly 50% of India's population depends on variants of pit-toilet systems for human waste disposal. Nitrate contamination of groundwater by pit-toilet leachate is a major environmental concern in the country as it sources a major proportion (50-80%) of potable water from aquifers. Therefore, minimizing nitrate contamination of groundwater due to leachate infiltration from pit-toilet systems is essential. Batch and column experiments demonstrated the capability of bentonite-enhanced sand (BES) specimens to reduce nitrate concentrations in synthetic solutions (initial NO3-N concentration = 22.7 mg/L, C/N = 3) by about 85-90% in 10 to 24 hour by a heterotrophic denitrification process. Based on the laboratory results, it is recommended that use of a BES-permeable reactive barrier layer at the base of pit-toilets will facilitate heterotrophic denitrification and mitigate nitrate contamination of the underlying aquifer.

Numerical study of solidification of A356 aluminum alloy flowing on an oblique plate with experimental validation

Molten A356 aluminum alloy flowing on an oblique plate is water cooled from underneath. The melt partially solidifies on plate wall with continuous formation of columnar dendrites. These dendrites are continuously sheared off into equiaxed/fragmented grains and carried away with the melt by producing semisolid slurry collected at plate exit. Melt pouring temperature provides required solidification whereas plate inclination enables necessary shear for producing slurry of desired solid fraction. A numerical model concerning transport equations of mass, momentum, energy and species is developed for predicting velocity, temperature, macrosegregation and solid fraction. The model uses FVM with phase change algorithm, VOF and variable viscosity. The model introduces solid phase movement with gravity effect as well. Effects of melt pouring temperature and plate inclination on hydrodynamic and thermo-solutal behaviors are studied subsequently. Slurry solid fractions at plate exit are 27%, 22%, 16%, and 10% for pouring temperatures of 620 degrees C, 625 degrees C, 630 degrees C, and 635 degrees C, respectively. And, are 27%, 25%, 22%, and 18% for plate inclinations of 30, 45, 60, and 75, respectively. Melt pouring temperature of 625 degrees C with plate inclination of 60 generates appropriate quality of slurry and is the optimum. Both numerical and experimental results are in good agreement with each other. (C) 2015 Taiwan Institute of Chemical Engineers. Published by Elsevier B.V. All rights reserved.