iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Fabrication and evaluation of 450 F electrochemical redox supercapacitors using inexpensive and high-performance, polyaniline coated, stainless-steel electrodes

Redox supercapacitors using polyaniline (PANI) coated. stainless-steel (SS) electrodes have been assembled and characterized. PANI has been deposited on SS substrate by a potentiodynamic method from an acidic electrolyte which contains aniline monomer. By employing stacks of electrodes, each with a geometrical area of 24 cm(2), in acidic perchlorate electrolyte, a capacitance value of about 450 F has been obtained over a long cycle-life. Characterization studies have been carried out by galvanostatic charge-discharge cycling of the capacitors singly, as well as in series and parallel configurations. Various electrical parameters have been evaluated. Use of the capacitors in parallel with a battery for pulse-power loads. and also working of a toy fan connected to the charged capacitors have been demonstrated. A specific capacitance value of about 1300 F g(-1) of PANI has been obtained at a discharge power of about 0.5 kW kg(-1). This value is several times higher than those reported in the literature for PANI and is, perhaps, the highest value known for a capacitor material. The inexpensive SS substrate and the high-capacitance PANI are favorable factors for commercial exploitation. (C) 2002 Elsevier Science B.V. All rights reserved.

Machine-tool selection and operation allocation in FMS: solving a fuzzy goal-programming model using a genetic algorithm

The decision-making process for machine-tool selection and operation allocation in a flexible manufacturing system (FMS) usually involves multiple conflicting objectives. Thus, a fuzzy goal-programming model can be effectively applied to this decision problem. The paper addresses application of a fuzzy goal-programming concept to model the problem of machine-tool selection and operation allocation with explicit considerations given to objectives of minimizing the total cost of machining operation, material handling and set-up. The constraints pertaining to the capacity of machines, tool magazine and tool life are included in the model. A genetic algorithm (GA)-based approach is adopted to optimize this fuzzy goal-programming model. An illustrative example is provided and some results of computational experiments are reported.

Tool for Identification of Duplicate Records Downloaded from Multiple Cd-Roms. A Case Study with Spirs Based Databases

As research becomes more and more interdisciplinary, literature search from CD-ROM databases is often carried out on more than one CD-ROM database. This results in retrieving duplicate records due to same literature being covered (indexed) in more than one database. The retrieval software does not identify such duplicate records. Three different programs have been written to accomplish the task of identifying the duplicate records. These programs are executed from a shell script to minimize manual intervention. The various fields that have been used (extracted) to identify the duplicate records include the article title, year, volume number, issue number and pagination. The shell script when executed prompts for input file that may contain duplicate records. The programs identify the duplicate records and write them to a new file.

Implementing WWWISIS for Providing Web Access to Bibliographic Databases

CDS/ISIS, an advanced non-numerical information storage and retrieval software was developed by UNESCO. With the emergence of WWW technology, most of the information activities are becoming Web-centric. Libraries and information providers are taking advantage of these Internet developments to provide access to their resources/information on the Web. A number of tools are now available for publishing CDS/ISIS databases on the Internet. One such tool is the WWWISIS Web gateway software, developed by BIREME, Brazil. This paper illustrates porting of sample records from a bibliographic database into CDS/ISIS, and then publishing this database on the Internet using WWWISIS.

Performance of monolithic and TiB2 reinforced MoSi2 in dry sliding contact with steel

MoSi2 and its composite with TiB2 (10 and 20 wt.%) particulates were synthesized by the hot pressing technique. Dry sliding wear experiments were done on these samples by pin-on-disc method on an EN-24 steel disc. It was observed that the densification and the reinforcement of the matrix are beneficial in reducing the friction and wear Of MoSi2. The tribofilm that was formed during sliding contained both the disc and the pin material. (C) 2002 Elsevier Science B.V. All rights reserved.

Potentiodynamically deposited polyaniline on stainless steel - Inexpensive, high-performance electrodes for electrochemical supercapacitors

Polyaniline (PANI) has been studied as an active material for electrochemical capacitors. Polymerization of aniline to PANI has been carried out potentiodynamically on a stainless steel (SS) substrate, instead of Pt-based substrates generally employed for this application. The PANI/SS electrodes have been evaluated by assembling symmetrical capacitors in NaClO(4) + HClO(4) mixed electrolyte and subjecting them to galvanostatic charge/discharge cycles between 0 and 0.75 V. The effect of substrate has been assessed by comparing the capacitance of PANI/SS and PANI/Pt electrodes. The capacitance of PANI/SS electrode is higher than that of PANI/Pt electrode by several times. The effect of sweep rate of potentiodynamic deposition of PANI/SS on capacitance has been investigated. At a power density of 0.5 kW kg(-1), a capacitance value of 815 F g(-1) of PANI is obtained for the deposition sweep rate of 200 mV s(-1). Increase in thickness of PANI on the SS substrate results in an increase in capacitance of PANI. This value of capacitance is the highest ever reported for any electrochemical capacitor material. Thus, in addition to a favorable economic aspect involved in using SS instead of Pt or Pt-based substrate, the advantage of higher capacitance of PANI has also been achieved. (C) 2002 The Electrochemical Society.

A model for tool-use traditions in primates: implications for the coevolution of culture and cognition

Inspired by the demonstration that tool-use variants among wild chimpanzees and orangutans qualify as traditions (or cultures), we developed a formal model to predict the incidence of these acquired specializations among wild primates and to examine the evolution of their underlying abilities. We assumed that the acquisition of the skill by an individual in a social unit is crucially controlled by three main factors, namely probability of innovation, probability of socially biased learning, and the prevailing social conditions (sociability, or number of potential experts at close proximity). The model reconfirms the restriction of customary tool use in wild primates to the most intelligent radiation, great apes; the greater incidence of tool use in more sociable populations of orangutans and chimpanzees; and tendencies toward tool manufacture among the most sociable monkeys. However, it also indicates that sociable gregariousness is far more likely to produce the maintenance of invented skills in a population than solitary life, where the mother is the only accessible expert. We therefore used the model to explore the evolution of the three key parameters. The most likely evolutionary scenario is that where complex skills contribute to fitness, sociability and/or the capacity for socially biased learning increase, whereas innovative abilities (i.e., intelligence) follow indirectly. We suggest that the evolution of high intelligence will often be a byproduct of selection on abilities for socially biased learning that are needed to acquire important skills, and hence that high intelligence should be most common in sociable rather than solitary organisms. Evidence for increased sociability during hominin evolution is consistent with this new hypothesis. (C) 2003 Elsevier Science Ltd. All rights reserved.

Crucible Steel in South India-Preliminary Investigations on Crucibles from Some Newly Identified Sites

European accounts from the 17th century onwards have referred to the repute and manufacture of “wootz’, a traditional crucible steel made especially in parts of southern India in the former provinces of Golconda, Mysore and Salem. Pliny's Natural History mentions the import of iron and steel from the Seres which have been thought to refer to the ancient southern Indian kingdom of the Cheras. As yet the scale of excavations and surface surveys is too limited to link the literary accounts to archaeometallurgical evidence, although pioneering exploratory investigations have been made by scholars, especially on the pre-industrial production sites of Konasamudram and Gatihosahalli discussed in 18th-19th century European accounts. In 1991–2 during preliminary surveys of ancient base metal mining sites, Srinivasan came across unreported dumps with crucible fragments at Mel-Siruvalur in Tamil Nadu, and Tintini and Machnur in Karnataka and she collected surface specimens from these sites as well as from the known site of Gatihosahalli. She was also given crucible fragments by the Tamil University, Tanjavur, from an excavated megalithic site at Kodumanal, dated to ca 2nd c. Bc, mentioned in Tamil Sangam literature (ca 3rd c. BC-3rd c. AD), and very near Karur, the ancient capital of the Sangam Cheras. Analyses of crucible fragments from the surface collection at Mel-Siruvalur showed several iron prills with a uniform pearlitic structure of high-carbon hypereutectoid steel (∼1–1.5% C) suggesting that the end product was uniformly a high-carbon steel of a structure consistent with those of high-carbon steels used successfully to experimentally replicate the watered steel patterns on ‘Damascus’ swords. Investigations indicate that the process was of carburisation of molten low carbon iron (m.p. 1400° C) in crucibles packed with carbonaceous matter. The fabric of crucibles from all the above mentioned sites appears similar. Preliminary investigations on these crucibles are thus reported to establish their relationship to crucible production of carbon steel and to thereby extend the known horizons of this technology further.

Lubricity of an oil in water emulsion in metal cutting: The effect of hydrophilic/lypophilic balance of emulsifiers

A steel disc is cut using a single point tool. The coefficient of friction of the nascent cut surface is measured by a spherical steel pin situated in close proximity of the point of cutting. The tool, disc and the friction pin are immersed in an oil in water emulsion bath during the experiment. The purpose of the experiments conducted here is to record the effect of hydrophilic/lypophilic balance (HLB) of the emulsifier on the lubricity experienced in the cutting operation. The more lypophilic emulsifiers were found to give greater lubricity than what is recorded when the emulsifier is more hydrophilic. XPS and FTIR spectroscopy are used to explore the tribofilm generated on the nascent cut surface to indicate a possible rationale for the effect. (C) 2011 Elsevier B.V. All rights reserved.

Lubricant Degradation and Related Wear of a Steel Pin in Lubricated Sliding Against a Steel Disc

In lubricated sliding contacts, components wear out and the lubricating oil ages with time. The present work explores the interactive influence between lubricant aging and component wear. The flat face of a steel pin is slid against a rotating steel disk under near isothermal conditions while the contact is immersed in a reservoir of lubricant (hexadecane). The chemical changes in the oil with time are measured by vibrational spectroscopy and gas chromatography. The corresponding chemistry of the pin surface is recorded using X-ray photoelectron spectroscopy while the morphology of the worn pins; surface and subsurface, are observed using a combination of focused ion beam milling and scanning electron 5 microscopy. When compared to thermal auto-oxidation of the lubricant alone, steel on steel friction and wear are found to accentuate the decomposition of oil and to reduce the beneficial impact of antioxidants. The catalytic action of nascent iron, an outcome of pin wear and disk wear, is shown to contribute to this detrimental effect. Over long periods of sliding, the decomposition products of lubricant aging on their own, as well as in conjunction with their products of reaction with iron, generate a thick tribofilm that is highly protective in terms of friction and wear.

Validation of processing maps for a 15Cr-15Ni-2.2Mo-0.3Ti austenitic stainless steel using hot forging and rolling tests

The processing maps are being developed for use in optimising hot workability and controlling the microstructure of the product. The present investigation deals with the examination to assess the prediction of the processing maps for a 15Cr-15Ni-2.2Mo-0.3Ti austenitic stainless steel using forging and rolling tests at different temperatures in the range of 600-1200 degreesC. The tensile properties of these deformed products were evaluated at room temperature. The influence of the processing conditions, i.e. strain rate and temperature on the tensile properties of the deformed product were analysed to identify the optimum processing parameters. The results have shown good agreement between the regimes exhibited by the map and the properties of the rolled or forged product. The optimum parameters for processing of this steel were identified as rolling or press forging at temperatures above 1050 degreesC to obtain optimum product properties. (C) 2002 Elsevier Science B.V. All rights reserved.