mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/.

Projection Error Propagation-based Regularization (PEPR) method for resistivity reconstruction in Electrical Impedance Tomography (EIT)

A novel Projection Error Propagation-based Regularization (PEPR) method is proposed to improve the image quality in Electrical Impedance Tomography (EIT). PEPR method defines the regularization parameter as a function of the projection error developed by difference between experimental measurements and calculated data. The regularization parameter in the reconstruction algorithm gets modified automatically according to the noise level in measured data and ill-posedness of the Hessian matrix. Resistivity imaging of practical phantoms in a Model Based Iterative Image Reconstruction (MoBIIR) algorithm as well as with Electrical Impedance Diffuse Optical Reconstruction Software (EIDORS) with PEPR. The effect of PEPR method is also studied with phantoms with different configurations and with different current injection methods. All the resistivity images reconstructed with PEPR method are compared with the single step regularization (STR) and Modified Levenberg Regularization (LMR) techniques. The results show that, the PEPR technique reduces the projection error and solution error in each iterations both for simulated and experimental data in both the algorithms and improves the reconstructed images with better contrast to noise ratio (CNR), percentage of contrast recovery (PCR), coefficient of contrast (COC) and diametric resistivity profile (DRP). (C) 2013 Elsevier Ltd. All rights reserved.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Structural Investigations on the Compositional Anomalies in Lanthanum Zirconate System Synthesized by Coprecipitation Method

The study set out to investigate the compositional inconsistency in lanthanum zirconate system revealed the presence of nonstoichiometry in lanthanum zirconate powders when synthesized by coprecipitation route. X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) investigations confirmed the depletion of La3+ ions in the system. Analysis using Vegard's law showed the La/Zr mole ratio in the sample to be around 0.45. An extra step of ultrasonication, introduced during the washing stage followed by the coprecipitation reaction, ensured the formation of stoichiometric La2Zr2O7. Noteworthy is also the difference between crystal sizes in the samples prepared by with and without ultrasonication step. This difference has been explained in light of the formation of individual nuclei and their scope of growth within the precipitate core. The differential scanning calorimetry (DSC) analyses revealed that optimum pH for the synthesis of La2Zr2O7 is about 11. The ultrasonication step was pivotal in assuring consistency in mixing and composition for the lanthanum zirconate powders.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

A Modified Fluorimetric Method for Determination of Hydrogen Peroxide Using Homovanillic Acid Oxidation Principle

Hydrogen peroxide (H2O2) level in biological samples is used as an important index in various studies. Quantification of H2O2 level in tissue fractions in presence of H2O2 metabolizing enzymes may always provide an incorrect result. A modification is proposed for the spectrofluorimetric determination of H2O2 in homovanillic acid (HVA) oxidation method. The modification was included to precipitate biological samples with cold trichloroacetic acid (TCA, 5% w/v) followed by its neutralization with K2HPO4 before the fluorimetric estimation of H2O2 is performed. TCA was used to precipitate the protein portions contained in the tissue fractions. After employing the above modification, it was observed that H2O2 content in tissue samples was >= 2 fold higher than the content observed in unmodified method. Minimum 2 h incubation of samples in reaction mixture was required for completion of the reaction. The stability of the HVA dimer as reaction product was found to be > 12 h. The method was validated by using known concentrations of H2O2 and catalase enzyme that quenches H2O2 as substrate. This method can be used efficiently to determine more accurate tissue H2O2 level without using internal standard and multiple samples can be processed at a time with additional low cost reagents such as TCA and K2HPO4.

Optimization of degree of sphericity of primary phase during cooling slope casting of A356 Al alloy: Taguchi method and regression analysis

The present work presents the results of experimental investigation of semi-solid rheocasting of A356 Al alloy using a cooling slope. The experiments have been carried out following Taguchi method of parameter design (orthogonal array of L-9 experiments). Four key process variables (slope angle, pouring temperature, wall temperature, and length of travel of the melt) at three different levels have been considered for the present experimentation. Regression analysis and analysis of variance (ANOVA) has also been performed to develop a mathematical model for degree of sphericity evolution of primary alpha-Al phase and to find the significance and percentage contribution of each process variable towards the final outcome of degree of sphericity, respectively. The best processing condition has been identified for optimum degree of sphericity (0.83) as A(3), B-3, C-2, D-1 i.e., slope angle of 60 degrees, pouring temperature of 650 degrees C, wall temperature 60 degrees C, and 500 mm length of travel of the melt, based on mean response and signal to noise ratio (SNR). ANOVA results shows that the length of travel has maximum impact on degree of sphericity evolution. The predicted sphericity obtained from the developed regression model and the values obtained experimentally are found to be in good agreement with each other. The sphericity values obtained from confirmation experiment, performed at 95% confidence level, ensures that the optimum result is correct and also the confirmation experiment values are within permissible limits. (c) 2014 Elsevier Ltd. All rights reserved.

Dynamic Site Characterization and Correlation of Shear Wave Velocity with Standard Penetration Test `N' Values for the City of Agartala, Tripura State, India

Seismic site characterization is the basic requirement for seismic microzonation and site response studies of an area. Site characterization helps to gauge the average dynamic properties of soil deposits and thus helps to evaluate the surface level response. This paper presents a seismic site characterization of Agartala city, the capital of Tripura state, in the northeast of India. Seismically, Agartala city is situated in the Bengal Basin zone which is classified as a highly active seismic zone, assigned by Indian seismic code BIS-1893, Indian Standard Criteria for Earthquake Resistant Design of Structures, Part-1 General Provisions and Buildings. According to the Bureau of Indian Standards, New Delhi (2002), it is the highest seismic level (zone-V) in the country. The city is very close to the Sylhet fault (Bangladesh) where two major earthquakes (M (w) > 7) have occurred in the past and affected severely this city and the whole of northeast India. In order to perform site response evaluation, a series of geophysical tests at 27 locations were conducted using the multichannel analysis of surface waves (MASW) technique, which is an advanced method for obtaining shear wave velocity (V (s)) profiles from in situ measurements. Similarly, standard penetration test (SPT-N) bore log data sets have been obtained from the Urban Development Department, Govt. of Tripura. In the collected data sets, out of 50 bore logs, 27 were selected which are close to the MASW test locations and used for further study. Both the data sets (V (s) profiles with depth and SPT-N bore log profiles) have been used to calculate the average shear wave velocity (V (s)30) and average SPT-N values for the upper 30 m depth of the subsurface soil profiles. These were used for site classification of the study area recommended by the National Earthquake Hazard Reduction Program (NEHRP) manual. The average V (s)30 and SPT-N classified the study area as seismic site class D and E categories, indicating that the city is susceptible to site effects and liquefaction. Further, the different data set combinations between V (s) and SPT-N (corrected and uncorrected) values have been used to develop site-specific correlation equations by statistical regression, as `V (s)' is a function of SPT-N value (corrected and uncorrected), considered with or without depth. However, after considering the data set pairs, a probabilistic approach has also been presented to develop a correlation using a quantile-quantile (Q-Q) plot. A comparison has also been made with the well known published correlations (for all soils) available in the literature. The present correlations closely agree with the other equations, but, comparatively, the correlation of shear wave velocity with the variation of depth and uncorrected SPT-N values provides a more suitable predicting model. Also the Q-Q plot agrees with all the other equations. In the absence of in situ measurements, the present correlations could be used to measure V (s) profiles of the study area for site response studies.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

And yet it shrinks: A novel method for correcting bias in forest tree growth estimates caused by water-induced fluctuations

Accuracy in tree woody growth estimates is important to global carbon budget estimation and climate-change science. Tree growth in permanent sampling plots (PSPs) is commonly estimated by measuring stem diameter changes, but this method is susceptible to bias resulting from water-induced reversible stem shrinkage. In the absence of bias correction, temporal variability in growth is likely to be overestimated and incorrectly attributed to fluctuations in resource availability, especially in forests with high seasonal and inter-annual variability in water. We propose and test a novel approach for estimating and correcting this bias at the community level. In a 50-ha PSP from a seasonally dry tropical forest in southern India, where tape measurements have been taken every four years from 1988 to 2012, for nine trees we estimated bias due to reversible stem shrinkage as the difference between woody growth measured using tree rings and that estimated from tape. We tested if the bias estimated from these trees could be used as a proxy to correct bias in tape-based growth estimates at the PSP scale. We observed significant shrinkage-related bias in the growth estimates of the nine trees in some censuses. This bias was strongly linearly related to tape-based growth estimates at the level of the PSP, and could be used as a proxy. After bias was corrected, the temporal variance in growth rates of the PSP decreased, while the effect of exceptionally dry or wet periods was retained, indicating that at least a part of the temporal variability arose from reversible shrinkage-related bias. We also suggest that the efficacy of the bias correction could be improved by measuring the proxy on trees that belong to different size classes and census timing, but not necessarily to different species. Our approach allows for reanalysis - and possible reinterpretation of temporal trends in tree growth, above ground biomass change, or carbon fluxes in forests, and their relationships with resource availability in the context of climate change. (C) 2014 Elsevier B.V. All rights reserved.

Filter Configuration and PWM Method For Single Phase Inverters with Reduced Conducted EMI Noise

Electromagnetic Interference (EMI) noise is one of the major issues during the design of the grid-tied power converters. Presence of high dv/dt in Common Mode (CM) voltage, excites the parasitic capacitances and causes injection of narrow peaky current to ground. This results in high EMI noise level. A topology consisting of a single phase PWM-rectifier with LCL filter, utilising bipolar PWM method is proposed which reduces the EMI noise level by more than 30dB. This filter topology is shown to be insensitive to the switching delays between the legs of the inverter. The proposed topology eliminates high dv/dt from the dc-bus CM voltage by making it sinusoidal. Hence, the high frequency CM current injection to ground is minimized.

ADAPTATION OF MW LEVEL NATURAL GAS LEAN BURN ENGINE FOR PRODUCER GAS OPERATION A GRID CONNECTED POWER PLANT

Availability of producer gas engines at MW being limited necessitates to adapt engine from natural gas operation. The present work focus on the development of necessary kit for adapting a 12 cylinder lean burn turbo-charged natural gas engine rated at 900 kWe (Waukesha make VHP5904LTD) to operate on producer and set up an appropriate capacity biomass gasification system for grid linked power generation in Thailand. The overall plant configuration had fuel processing, drying, reactor, cooling and cleaning system, water treatment, engine generator and power evacuation. The overall project is designed for evacuation of 1.5 MWe power to the state grid and had 2 gasification system with the above configuration and 3 engines. Two gasification system each designed for about 1100 kg/hr of woody biomass was connected to the engine using a producer gas carburetor for the necessary Air to fuel ratio control. In the use of PG to fuel IC engines, it has been recognized that the engine response will differ as compared to the response with conventional fueled operation due to the differences in the thermo-physical properties of PG. On fuelling a conventional engine with PG, power de-rating can be expected due to the lower calorific value (LCV), lower adiabatic flame temperature (AFT) and the lower than unity product to reactant more ratio. Further the A/F ratio for producer gas is about 1/10th that of natural gas and requires a different carburetor for engine operation. The research involved in developing a carburetor for varying load conditions. The patented carburetor is based on area ratio control, consisting of a zero pressure regulator and a separate gas and air line along with a mixing zone. The 95 litre engine at 1000 rpm has an electrical efficiency of 33.5 % with a heat input of 2.62 MW. Each engine had two carburetors designed for producer gas flow each capable of handling about 1200 m3/hr in order to provide similar engine heat input at a lower conversion efficiency. Cold flow studies simulating the engine carburetion system results showed that the A/F was maintained in the range of 1.3 +/- 0.1 over the entire flow range. Initially, the gasification system was tested using woody biomass and the gas composition was found to be CO 15 +/- 1.5 % H-2 22 +/- 2% CH4 2.2 +/- 0.5 CO2 11.25 +/- 1.4 % and rest N-2, with the calorific value in the range of 5.0 MJ/kg. After initial trials on the engine to fine tune the control system and adjust various engine operating parameter a peak load of 800 kWe was achieved, while a stable operating conditions was found to be at 750 kWe which is nearly 85 % of the natural gas rating. The specific fuel consumption was found to be 0.9 kg of biomass per kWh.

CROSS-SECTIONAL ANALYSIS OF PRE-TWISTED THICK BEAMS USING VARIATIONAL ASYMPTOTIC METHOD

An asymptotically-exact methodology is presented for obtaining the cross-sectional stiffness matrix of a pre-twisted moderately-thick beam having rectangular cross sections and made of transversely isotropic materials. The anisotropic beam is modeled from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy of the beam is computed making use of the constitutive law and the kinematical relations derived with the inclusion of geometrical nonlinearities and initial twist. Large displacements and rotations are allowed, but small strain is assumed. The Variational Asymptotic Method is used to minimize the energy functional, thereby reducing the cross section to a point on the reference line with appropriate properties, yielding a 1-D constitutive law. In this method as applied herein, the 2-D cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged as orders of the small parameters. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that renders the 1-D strain measures well-defined. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

Analysis of Transverse Shear Strains in Pre-Twisted Thick Beams using Variational Asymptotic Method

The cross-sectional stiffness matrix is derived for a pre-twisted, moderately thick beam made of transversely isotropic materials and having rectangular cross sections. An asymptotically-exact methodology is used to model the anisotropic beam from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy is computed making use of the beam constitutive law and kinematical relations derived with the inclusion of geometrical nonlinearities and an initial twist. The energy functional is minimized making use of the Variational Asymptotic Method (VAM), thereby reducing the cross section to a point on the beam reference line with appropriate properties, forming a 1-D constitutive law. VAM is a mathematical technique employed in the current problem to rigorously split the 3-D analysis of beams into two: a 2-D analysis over the beam cross-sectional domain, which provides a compact semi-analytical form of the properties of the cross sections, and a nonlinear 1-D analysis of the beam reference curve. In this method, as applied herein, the cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged in orders of the small parameters. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that render the 1-D strain measures well-defined. The zeroth-order 3-D warping field thus yielded is then used to integrate the 3-D strain energy density over the cross section, resulting in the 1-D strain energy density, which in turn helps identify the corresponding cross-sectional stiffness matrix. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

Filter Configuration and PWM Method For Single-Phase Inverters With Reduced Conducted EMI Noise

Electromagnetic interference (EMI) noise is one of the major issues during design of grid-tied power converters. A novel LCL filter topology for a single-phase pulsewidth modulation (PWM) rectifier that makes use of bipolar PWM method is proposed for a single-phase to three-phase motor drive power converter. The proposed topology eliminates high dv/dt from the dc-bus common-mode (CM) voltage by making it sinusoidal. Hence, the high-frequency CM current injection to the ground and the motor-side CM current are minimized. The proposed filter configuration makes the system insensitive to circuit non-idealities such as mismatch in inductors values, unequal turn-on and turn-off delays, and dead-time mismatch between the inverter legs. Different variants of the filter topology are compared to establish the effectiveness of the proposed circuit. Experimental results based on the EMI measurement on the grid side and the CM current measurement on the motor side are presented for a 5-kW motor drive. It is shown that the proposed filter topology reduces the EMI noise level by about 35 dB.