DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Geotechnical Characterization of Some Indian Bentonites for their Use as Buffer Material in Geological Repository

The present study examines the geotechnical properties of Indian bentonite clays for their suitability as buffer material in deep geological repository for high-level nuclear wastes. The bentonite samples are characterized for index properties, compaction, hydraulic conductivity and swelling characteristics. Evaluation of geotechnical properties of the compacted bentonite-sand admixtures, from parts of NW India reveals swelling potentials and hydraulic conductivities in the range of 55 % - 108 % and 1.2 X 10 –10 cm/s to 5.42x 10 –11 cm/s respectively. Strong correlation was observed between ESP (exchangeable sodium percentage) and liquid limit/swell potential of tested specimens. Relatively less well-defined trends emerged between ESP and swell pressure/hydraulic conductivity. The Barmer-1 bentonite despite possessing relatively lower montmorillonite content of 68 %, developed higher Atterberg limit and swell potential, and exhibited comparable swelling pressure and hydraulic conductivity as other bentonites with higher montmorillonite contents (82 to 86 %). The desirable geotechnical properties of Barmer clay as a buffer material is attributed to its large ESP (63 %) and, EMDD (1.17 Mg/m3) attained at the experimental compactive stress(5 MPa).

Setting up Multilingual Information Repository: A case Study with EPrints.org Software

Today 80 % of the content on the Web is in English, which is spoken by only 8% of the World population and 5% of Indian population. There is wealth of useful content in the various languages of the world other than English, which can be made available on the Internet. But, to date, for various reasons most of it is not yet available on the Internet. India itself has 18 officially recognized languages and scores of dialects. Although the medium of instruction for most of the higher education and research in India is English, substantial amount of literature by way of novels, textbooks, scholarly information are being generated in the other languages in the country. Many of the e-governance initiatives are in the respective state languages. In the past, support for different languages by the operating systems and the software packages were not very encouraging. However, with the advent of Unicode technology, operating systems and software packages are supporting almost all the major languages of the world that have scripts. In the work reported in this paper, we have explained the configuration changes that are needed for Eprints.org software to store multilingual content and to create a multilingual user interface.

Random security scheme selection for mobile transactions

Security in a mobile communication environment is always a matter for concern, even after deploying many security techniques at device, network, and application levels. The end-to-end security for mobile applications can be made robust by developing dynamic schemes at application level which makes use of the existing security techniques varying in terms of space, time, and attacks complexities. In this paper we present a security techniques selection scheme for mobile transactions, called the Transactions-Based Security Scheme (TBSS). The TBSS uses intelligence to study, and analyzes the security implications of transactions under execution based on certain criterion such as user behaviors, transaction sensitivity levels, and credibility factors computed over the previous transactions by the users, network vulnerability, and device characteristics. The TBSS identifies a suitable level of security techniques from the repository, which consists of symmetric, and asymmetric types of security algorithms arranged in three complexity levels, covering various encryption/decryption techniques, digital signature schemes, andhashing techniques. From this identified level, one of the techniques is deployed randomly. The results shows that, there is a considerable reduction in security cost compared to static schemes, which employ pre-fixed security techniques to secure the transactions data.

CREMOFAC- a database of chromatin remodeling factors

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors.Results: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable.

Nucleation and growth of Al2O3/metal composites by oxidation of aluminum alloys

The nucleation and growth mechanisms during high temperature oxidation of liquid Al-3% Mg and Al-3% Mg-3% Si alloys were studied with the aim of enhancing our understanding of a new composite fabrication process. The typical oxidation sequence consists of an initial event of rapid but brief oxidation, followed by an incubation period of limited oxide growth after which bulk Al2O3/Al composite forms. A duplex oxide layer, MgO (upper) and MgAl2O4 (lower), forms on the alloy surface during initial oxidation and incubation. The spinel layer remains next to the liquid alloy during bulk oxide growth and is the eventual repository for most of the magnesium in the original alloy. Metal microchannels developed during incubation continuously supply alloy through the composite to the reaction interface. During the growth process, a layered structure exists at the upper extremity of the composite, consisting of MgO at the top surface, MgAl2O4 (probably discontinuous), Al alloy, and finally the bulk Al2O3 composite containing microchannels of the alloy. The bulk oxide growth mechanism appears to involve continuous formation and dissolution of the Mg-rich oxides at the surface, diffusion of oxygen through the underlying liquid metal, and epitaxial growth of Al2O3 on the existing composite body. The roles of Mg and Si in the composite growth process are discussed.

Feature weighting for clustering by particle swarm optimization

Clustering has been the most popular method for data exploration. Clustering is partitioning the data set into sub-partitions based on some measures say the distance measure, each partition has its own significant information. There are a number of algorithms explored for this purpose, one such algorithm is the Particle Swarm Optimization(PSO) which is a population based heuristic search technique derived from swarm intelligence. In this paper we present an improved version of the Particle Swarm Optimization where, each feature of the data set is given significance accordingly by adding some random weights, which also minimizes the distortions in the dataset if any. The performance of the above proposed algorithm is evaluated using some benchmark datasets from Machine Learning Repository. The experimental results shows that our proposed methodology performs significantly better than the previously performed experiments.

Modified particle swarm optimization for pattern clustering

Data clustering is a common technique for statistical data analysis, which is used in many fields, including machine learning and data mining. Clustering is grouping of a data set or more precisely, the partitioning of a data set into subsets (clusters), so that the data in each subset (ideally) share some common trait according to some defined distance measure. In this paper we present the genetically improved version of particle swarm optimization algorithm which is a population based heuristic search technique derived from the analysis of the particle swarm intelligence and the concepts of genetic algorithms (GA). The algorithm combines the concepts of PSO such as velocity and position update rules together with the concepts of GA such as selection, crossover and mutation. The performance of the above proposed algorithm is evaluated using some benchmark datasets from Machine Learning Repository. The performance of our method is better than k-means and PSO algorithm.

Hydro-mechanical characterization of Barmer 1 bentonite from Rajasthan, India

The conceptual model for deep geological disposal of high level nuclear waste (HLW) is based on multiple barrier system consisting of natural and engineered barriers. Buffer/backfill material is regarded as the most important engineered barrier in HLW repositories. Due to large swelling ability, cation adsorption capacity, and low permeability bentonite is considered as suitable buffer material in HLW repositories. Japan has identified Kunigel VI bentonite, South Korea - Kyungju bentonite, China - GMZ bentonite, Belgium - FoCa clay, Sweden - MX-80 bentonite, Spain - FEBEX bentonite and Canada - Avonseal bentonite as candidate bentonite buffer for deep geological repository program. An earlier study on Indian bentonites by one of the authors suggested that bentonite from Barmer district of Rajasthan (termed Barmer 1 bentonite), India is suited for use as buffer material in deep geological repositories. However, the hydro-mechanical properties of the Barmer 1 bentonite are unavailable. This paper characterizes Barmer 1 bentonite for hydro-mechanical properties, such as, swell pressure, saturated permeability, soil water characteristic curve (SWCC) and unconfined compression strength at different dry densities. The properties of Barmer 1 bentonite were compared with bentonite buffers reported in literature and equations for designing swell pressure and saturated permeability coefficient of bentonite buffers were arrived at. (C) 2013 Elsevier B.V. All rights reserved.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

Characterization of silver-kaolinite (AgK): an adsorbent for long-lived I-129 species

Bentonite is a preferred buffer and backfill material for deep geological disposal of high-level nuclear waste (HLW). Bentonite does not retain anions by virtue of its negatively charged basal surface. Imparting anion retention ability to bentonite is important to enable the expansive clay to retain long-lived I-129 (iodine-129; half-life = 16 million years) species that may escape from the HLW geological repository. Silver-kaolinite (AgK) material is prepared as an additive to improve the iodide retention capacity of bentonite. The AgK is prepared by heating kaolinite-silver nitrate mix at 400 degrees C to study the kaolinite influence on the transition metal ion when reacting at its dehydroxylation temperature. Thermo gravimetric-Evolved Gas Detection analysis, X-ray diffraction analysis, X-ray photo electron spectroscopy and electron probe micro analysis indicated that silver occurs as AgO/Ag2O surface coating on thermally reacting kaolinite with silver nitrate at 400 degrees C.

A Novel Approach for Multispectral Satellite Image Classification Based on the Bat Algorithm

Among the multiple advantages and applications of remote sensing, one of the most important uses is to solve the problem of crop classification, i.e., differentiating between various crop types. Satellite images are a reliable source for investigating the temporal changes in crop cultivated areas. In this letter, we propose a novel bat algorithm (BA)-based clustering approach for solving crop type classification problems using a multispectral satellite image. The proposed partitional clustering algorithm is used to extract information in the form of optimal cluster centers from training samples. The extracted cluster centers are then validated on test samples. A real-time multispectral satellite image and one benchmark data set from the University of California, Irvine (UCI) repository are used to demonstrate the robustness of the proposed algorithm. The performance of the BA is compared with two other nature-inspired metaheuristic techniques, namely, genetic algorithm and particle swarm optimization. The performance is also compared with the existing hybrid approach such as the BA with K-means. From the results obtained, it can be concluded that the BA can be successfully applied to solve crop type classification problems.