Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBS) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. (C) 2011 Elsevier Masson SAS. All rights reserved.

Composite instantaneous comparators basis for design and their transient performance

Principles of design of composite instantaneous comparators (a combination of amplitude- and phase- comparison techniques) are laid out to provide directional, directional-reactance, nonoffset-resistance and conductance characteristices. The respective signals provided by the voltage transformer and the current transformer are directly used as relaying signals without resorting to any form of mixing. Phase shifts required, are obtained by using magnetic ferrite cores in a novel manner. Sampling units employing a combination of ferrite cores and semiconductor devices provide highly reliable designs. Special attention is paid to the choice of relaying signals, to eliminate the need for any synchronisation or modification and to avoid `image¿ characteristics. These factors have resulted in a considerable simplification of the practical circuitry. A thyristor AND circuit is employed in dual comparator units to provide the final tripping, and leads to a circuit which is much less sensitive to extraneous signals than a single-thyristor unit.

Dry tribology and nanomechanics of gaseous flame soot in comparison with carbon black and diesel soot

Ethylene gas is burnt and the carbon soot particles are thermophoretically collected using a home-built equipment where the fuel air injection and intervention into the 7.5-cm long flame are controlled using three small pneumatic cylinders and computer-driven controllers. The physical and mechanical properties and tribological performance of the collected soot are compared with those of carbon black and diesel soot. The crystalline structures of the nanometric particles generated in the flame, as revealed by high-resolution transmission electron studies, are shown to vary from the flame root to the exhaust. As the particle journeys upwards the flame, through a purely amorphous coagulated phase at the burner nozzle, it leads to a well-defined crystalline phase shell in the mid-flame zone and to a disordered phase consisting of randomly distributed short-range crystalline order at the exhaust. In the mid-flame region, a large shell of radial-columnar order surrounds a dense amorphous core. The hardness and wear resistance as well as friction coefficient of the soot extracted from this zone are low. The mechanical properties characteristics of this zone may be attributed to microcrystalline slip. Moving towards the exhaust, the slip is inhibited and there is an increase in hardness and friction compared to those in the mid-flame zone. This study of the comparison of flame soot to carbon black and diesel soot is further extended to suggest a rationale based on additional physico-chemical study using micro-Raman spectroscopy.

Performance evaluation of neural network algorithms for multisensor data fusion in an airborne track while scan radar

This paper deals with the solution to the problem of multisensor data fusion for a single target scenario as detected by an airborne track-while-scan radar. The details of a neural network implementation, various training algorithms based on standard backpropagation, and the results of training and testing the neural network are presented. The promising capabilities of RPROP algorithm for multisensor data fusion for various parameters are shown in comparison to other adaptive techniques

Performance evaluation of nonthermal plasma reactors for NO oxidation in diesel engine exhaust gas treatment

The discharge plasma-chemical hybrid process for NO/sub x/ removal from the due gas emissions is an extremely effective and economical approach in comparison with the conventional selective catalytic reduction system. In this paper we bring out a relative comparison of several discharge plasma reactors from the point of NO removal efficiency. The reactors were either energized by AC or by repetitive pulses. Ferroelectric pellets were used to study the effect of pellet assisted discharges on gas cleaning. Diesel engine exhaust, at different loads, is used to approximately simulate the due gas composition. Investigations were carried out at room temperature with respect to the variation of reaction products against the discharge power. Main emphasis is laid on the oxidation of NO to NO/sub 2/, without reducing NOx concentration (i.e., minimum reaction byproducts), with least power consumption. The produced NO/sub 2/ will be totally converted to N/sub 2/ and Na/sub 2/SO/sub 4/ using Na/sub 2/SO/sub 3/. The AC packed bed reactor and pelletless pulsed corona reactor showed better performance, with minimum reaction products for a given power, when the NO concentration was low (/spl sim/100 ppm). At high engine loads (NO>300 ppm) there was not much decrease in NO/sub x/ reduction and more or less all the reactors performed equally. The paper discusses these observations in detail.

Morphology dependent electrochemical performance of sputter deposited Sn thin films

This study deals with tailoring of the surface morphology, microstructure, and electrochemical properties of Sn thin films deposited by magnetron sputtering with different deposition rates. Scanning electron microscopy and atomic force microscopy are used to characterize the film surface morphology. Electrochemical properties of Sn thin film are measured and compared by cyclic voltammetry and charge-discharge cycle data at a constant current density. Sn thin film fabricated with a higher deposition rate exhibited an initial discharge capacity of 798 mAh g(-1) but reduced to 94 mAh g(-1) at 30th cycle. Film deposited with lower deposition rate delivered 770 mAh g(-1) during 1st cycle with improved capacity retention of 521 mAh g(-1) on 30th cycle. Comparison of electrochemical performances of these films has revealed important distinctions, which are associated with the surface morphology and hence on rate of deposition. (C) 2012 Elsevier Ltd. All rights reserved.

Performance and variability trade-off with gate-to-source/drain overlap length

The impact of gate-to-source/drain overlap length on performance and variability of 65 nm CMOS is presented. The device and circuit variability is investigated as a function of three significant process parameters, namely gate length, gate oxide thickness, and halo dose. The comparison is made with three different values of gate-to-source/drain overlap length namely 5 nm, 0 nm, and -5 nm and at two different leakage currents of 10 nA and 100 nA. The Worst-Case-Analysis approach is used to study the inverter delay fluctuations at the process corners. The drive current of the device for device robustness and stage delay of an inverter for circuit robustness are taken as performance metrics. The design trade-off between performance and variability is demonstrated both at the device level and circuit level. It is shown that larger overlap length leads to better performance, while smaller overlap length results in better variability. Performance trades with variability as overlap length is varied. An optimal value of overlap length of 0 nm is recommended at 65 nm gate length, for a reasonable combination of performance and variability.

Degradation studies of organic acids in commercially packed fruit juices: A reverse phase high performance liquid chromatographic approach

Organic acids are important constituents of fruit juices. They render tartness, flavour and specific taste to fruit juices. Shelf life and stability of fruit juices are important factors, which determine their nutritional quality and freshness. In this view, the effect of storage on the concentration of organic acids in commercially packed fruit juices is studied by reverse phase high performance liquid chromatography (RP-HPLC). Ten packed fruit juices from two different brands are stored at 30 C for 24, 48 and 72 hours. A reverse phase high performance liquid chromatographic method is used to determine the concentration of oxalic, tartaric, malic, ascorbic and citric acid in the fruit juices during storage. The chromatographic analysis of organic acids is carried out using mobile phase 0.5% (w/v) ammonium dihydrogen orthophosphate buffer (pH 2.8) on C18 column with UV-Vis detector. The results show that the concentration of organic acids generally decreases in juices under study with the increase in storage time. All the fruit juices belonging to tropicana brand underwent less organic acid degradation in comparison to juices of real brand. Orange fruit juice is found to be least stable among the juices under study, after the span of 72 hours. Amongst all the organic acids under investigation minimum stability is shown by ascorbic acid followed by malic and citric acid.

Antenna Selection in Interference-Constrained Underlay Cognitive Radios: SEP-Optimal Rule and Performance Benchmarking

In the underlay mode of cognitive radio, secondary users are allowed to transmit when the primary is transmitting, but under tight interference constraints that protect the primary. However, these constraints limit the secondary system performance. Antenna selection (AS)-based multiple antenna techniques, which exploit spatial diversity with less hardware, help improve secondary system performance. We develop a novel and optimal transmit AS rule that minimizes the symbol error probability (SEP) of an average interference-constrained multiple-input-single-output secondary system that operates in the underlay mode. We show that the optimal rule is a non-linear function of the power gain of the channel from the secondary transmit antenna to the primary receiver and from the secondary transmit antenna to the secondary receive antenna. We also propose a simpler, tractable variant of the optimal rule that performs as well as the optimal rule. We then analyze its SEP with L transmit antennas, and extensively benchmark it with several heuristic selection rules proposed in the literature. We also enhance these rules in order to provide a fair comparison, and derive new expressions for their SEPs. The results bring out new inter-relationships between the various rules, and show that the optimal rule can significantly reduce the SEP.

A Comparison of mechanical and tribological behavior of nanostructured and conventional WC-12Co detonation-sprayed coatings

In the present study, WC-12Co coatings were deposited by detonation-spraying technique using conventional and nanostructured WC-12Co feedstock at four different oxy/fuel ratios (OF ratio). The coatings exhibited the presence of phases like W2C and W due to the decarburization of the WC phase, and the proportions of these phases were higher in the nano WC-12Co coatings compared with conventional WC-12Co coatings. Coating hardness and fracture toughness were measured. The tribological performance of coatings was examined under dry sand rubber wheel abrasion wear, and solid particle erosion wear conditions. The mechanical and wear properties of coatings were influenced by degree of decarburization and more so in the case of nanostructured WC-Co coatings. The results indicate that the extent of decarburization has a substantial influence on the elastic modulus of the coating which in turn is related to the extent of intersplat cracking of the coating.

Rapid determination of main constituents of packed juices by reverse phase-high performance liquid chromatography: an insight in to commercial fruit drinks

The present work reports the compositional analysis of thirteen different packed fruit juices using high performance liquid chromatography (HPLC). Vitamin C, organic acids (citric and malic) and sugars (fructose, glucose and sucrose) were separated, analyzed and quantified using different reverse phase methods. A new rapid reverse phase HPLC method was developed for routine analysis of vitamin C in fruit juices. The precision results of the methods showed that the relative standard deviations of the repeatability and reproducibility were < 0.05 and < 0.1 respectively. Correlation coefficient of the calibration models developed was found to be higher than 0.99 in each case. It has been found that the content of Vitamin C was less variable amongst different varieties involved in the study. It is also observed that in comparison to fresh juices, the packed juices contain lesser amounts of vitamin C. Citric acid was found as the major organic acids present in packed juices while maximum portion of sugars was of sucrose. Comparison of the amount of vitamin C, organic acids and sugars in same fruit juice of different commercial brands is also reported.

Performance evaluation of typical approximation algorithms for nonconvex l(p)-minimization in diffuse optical tomography

The sparse estimation methods that utilize the l(p)-norm, with p being between 0 and 1, have shown better utility in providing optimal solutions to the inverse problem in diffuse optical tomography. These l(p)-norm-based regularizations make the optimization function nonconvex, and algorithms that implement l(p)-norm minimization utilize approximations to the original l(p)-norm function. In this work, three such typical methods for implementing the l(p)-norm were considered, namely, iteratively reweighted l(1)-minimization (IRL1), iteratively reweighted least squares (IRLS), and the iteratively thresholding method (ITM). These methods were deployed for performing diffuse optical tomographic image reconstruction, and a systematic comparison with the help of three numerical and gelatin phantom cases was executed. The results indicate that these three methods in the implementation of l(p)-minimization yields similar results, with IRL1 fairing marginally in cases considered here in terms of shape recovery and quantitative accuracy of the reconstructed diffuse optical tomographic images. (C) 2014 Optical Society of America

A performance-based framework for assessing liquefaction potential based on CPT data

This article describes a new performance-based approach for evaluating the return period of seismic soil liquefaction based on standard penetration test (SPT) and cone penetration test (CPT) data. The conventional liquefaction evaluation methods consider a single acceleration level and magnitude and these approaches fail to take into account the uncertainty in earthquake loading. The seismic hazard analysis based on the probabilistic method clearly shows that a particular acceleration value is being contributed by different magnitudes with varying probability. In the new method presented in this article, the entire range of ground shaking and the entire range of earthquake magnitude are considered and the liquefaction return period is evaluated based on the SPT and CPT data. This article explains the performance-based methodology for the liquefaction analysis – starting from probabilistic seismic hazard analysis (PSHA) for the evaluation of seismic hazard and the performance-based method to evaluate the liquefaction return period. A case study has been done for Bangalore, India, based on SPT data and converted CPT values. The comparison of results obtained from both the methods have been presented. In an area of 220 km2 in Bangalore city, the site class was assessed based on large number of borehole data and 58 Multi-channel analysis of surface wave survey. Using the site class and peak acceleration at rock depth from PSHA, the peak ground acceleration at the ground surface was estimated using probabilistic approach. The liquefaction analysis was done based on 450 borehole data obtained in the study area. The results of CPT match well with the results obtained from similar analysis with SPT data.

Sodium-ion battery cathodes Na2FeP2O7 and Na2MnP2O7: diffusion behaviour for high rate performance

Na-ion batteries are currently the focus of significant research activity due to the relative abundance of sodium and its consequent cost advantages. Recently, the pyrophosphate family of cathodes has attracted considerable attention, particularly Li2FeP2O7 related to its high operating voltage and enhanced safety properties; in addition the sodium-based pyrophosphates Na2FeP2O7 and Na2MnP2O7 are also generating interest. Herein, we present defect chemistry and ion migration results, determined via atomistic simulation techniques, for Na2MP2O7 (where M = Fe, Mn) as well as findings for Li2FeP2O7 for direct comparison. Within the pyrophosphate framework the most favourable intrinsic defect type is found to be the antisite defect, in which alkali-cations (Na/Li) and M ions exchange positions. Low activation energies are found for long-range diffusion in all crystallographic directions in Na2MP2O7 suggesting three-dimensional (3D) Na-ion diffusion. In contrast Li2FeP2O7 supports 2D Li-ion diffusion. The 2D or 3D nature of the alkali-ion migration pathways within these pyrophosphate materials means that antisite defects are much less likely to impede their transport properties, and hence important for high rate performance.

High specific surface area alpha-Fe2O3 nanostructures as high performance electrode material for supercapacitors

Porous alpha-Fe2O3 nanostructures have been synthesized by a simple sol-gel route. The alpha-Fe2O3 nanostructures are poorly crystalline and porous with BET surface area of 386 m(2) g(-1). The high discharge capacitance of alpha-Fe2O3 electrodes is 300 F g(-1) when the electrodes are cycled in 0.5 M Na2SO3 at a current density of 1 A g(-1). The capacitance retention after 1000 cycles is about 73% of the initial capacitance at a current density of 2 A g(-1). The high discharge capacitance of alpha-Fe2O3 in comparison with the literature reports are attributed to high surface area and porosity of the iron oxide prepared in the present study. As the iron oxides are inexpensive, the capacity of alpha-Fe2O3 is expected to be of potential use for supercapacitor application. (C) 2014 Elsevier B.V. All rights reserved.