Fragment Finder 2.0: a computing server to identify structurally similar fragments

Fragment Finder 2.0 is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone C alpha angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs, STAMP and PROFIT, provided in the server. The freely available Java plug-in Jmol has been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

Selective colorimetric detection of nanomolar Cr (VI) in aqueous solutions using unmodified silver nanoparticles

In this study we present a colorimetric detection method for Cr (VI) in aqueous solution based on as synthesized silver nanoparticles (Ag NPs) without surface functionalization. The method principle involves reduction of Cr (VI) to Cr (III) by excess reductant present in as synthesized Ag NP dispersion, and subsequent aggregation of Ag NPs by Cr (III) leading to red-shift of the surface plasmon resonance (SPR) peak. The UV-vis absorption spectra. Zeta potentials, dynamic light scattering measurements, and scanning electron microscopy (SEM) confirmed the aggregation of the Ag NPs. Under the optimized conditions, a good linear relationship (correlation coefficient r=0.981) was obtained between the ratio of the absorbance at 550 nm to that at 390 nm (A(550/390)) and the concentration of Cr (VI) over the range of 10(-3)-10(-9) M 50 mg/L to 50 ng/L]. The reported probe has a limit of detection down to 1 nM, which, to the best of our knowledge, is the lowest ever reported for the colorimetric detection of Cr (VI). Furthermore, a remarkable feature of this method is that it involves a simple technique exhibiting high selectivity to Cr (VI) over other tested heavy metal ions. (C) 2012 Elsevier BM. All rights reserved.

Structural, EPR, optical and Raman studies of Nd2O3:Cu2+ nanophosphors

Nanocrystalline Nd2O3:Cu2+ (2 mol %) phosphors have been prepared by a low temperature solution combustion technique. Powder X-ray diffraction (PXRD) results confirm that hexagonal A-type Nd2O3 (900 degrees C, 3 h) and the lattice parameters have been evaluated by Rietveld refinement. Surface morphology of as-formed and Cu2+ doped Nd2O3 phosphors show that the particles are irregular in shape and porous in nature. TEM results also confirm the nature and size of the particles. The EPR spectrum exhibits two resonance signals with effective g values at g(parallel to) approximate to 2.12 and g(perpendicular to) approximate to 2.04. The g values indicate that the site symmetry of Cu2+ ions is octahedral symmetry with elongated tetragonal distortion. Raman studies show major peaks, which are assigned, to F-g and combination of A(g) + E-g modes. It is observed that the Raman peaks and intensity have been reduced in Cu2+ doped samples. UV-Visible absorption spectra exhibit a strong and broad absorption band at similar to 240 nm. Further, the absorption peak shifts to similar to 14 nm in Cu2+ doped samples. The optical band gap is estimated to be 5.28 eV for Cu doped Nd2O3 nanoparticles which are higher than the bulk Nd2O3 (4.7 eV). This can be attributed to the quantum confinement effect of the nanoparticles. (C) 2012 Elsevier B.V. All rights reserved.

Is meridional circulation important in modelling irregularities of the solar cycle?

We explore the importance of meridional circulation variations in modelling the irregularities of the solar cycle by using the flux transport dynamo model. We show that a fluctuating meridional circulation can reproduce some features of the solar cycle like the Waldmeier effect and the grand minimum. However, we get all these results only if the value of the turbulent diffusivity in the convection zone is reasonably high.

Cadmium deoxycholate: a new and efficient precursor for highly luminescent CdSe nanocrystals

We have demonstrated that cadmium deoxycholate (1), a Cd-salt, provides a convenient and inexpensive route to high quality CdSe nanocrystals with photoluminescence (PL) in the blue to red region of the visible spectrum, with reproducible quantum yields as high as similar to 47%. Owing to the high thermal stability of the bile acid based cadmium precursor (decomposition point: 332 degrees C), it was possible to achieve high injection and growth temperatures (similar to 300 degrees C) for the nanocrystals, which was essential for obtaining larger CdSe nanocrystals emitting in the red region (625-650 nm) with a sharp full width at half maximum (FWHM) (23 nm) and multiple (6-7) excitonic absorption features. The as-prepared CdSe nanocrystals synthesized from cadmium deoxycholate represent a series of highly efficient emitters with pure colours and controllable sizes, shapes and structures.

Structured Dispersion Matrices From Division Algebra Codes for Space-Time Shift Keying

We propose a novel method of constructing Dispersion Matrices (DM) for Coherent Space-Time Shift Keying (CSTSK) relying on arbitrary PSK signal sets by exploiting codes from division algebras. We show that classic codes from Cyclic Division Algebras (CDA) may be interpreted as DMs conceived for PSK signal sets. Hence various benefits of CDA codes such as their ability to achieve full diversity are inherited by CSTSK. We demonstrate that the proposed CDA based DMs are capable of achieving a lower symbol error ratio than the existing DMs generated using the capacity as their optimization objective function for both perfect and imperfect channel estimation.

An estimate of equilibrium sensitivity of global terrestrial carbon cycle using NCAR CCSM4

Increasing concentrations of atmospheric CO2 influence climate, terrestrial biosphere productivity and ecosystem carbon storage through its radiative, physiological and fertilization effects. In this paper, we quantify these effects for a doubling of CO2 using a low resolution configuration of the coupled model NCAR CCSM4. In contrast to previous coupled climate-carbon modeling studies, we focus on the near-equilibrium response of the terrestrial carbon cycle. For a doubling of CO2, the radiative effect on the physical climate system causes global mean surface air temperature to increase by 2.14 K, whereas the physiological and fertilization on the land biosphere effects cause a warming of 0.22 K, suggesting that these later effects increase global warming by about 10 % as found in many recent studies. The CO2-fertilization leads to total ecosystem carbon gain of 371 Gt-C (28 %) while the radiative effect causes a loss of 131 Gt-C (10 %) indicating that climate warming damps the fertilization-induced carbon uptake over land. Our model-based estimate for the maximum potential terrestrial carbon uptake resulting from a doubling of atmospheric CO2 concentration (285-570 ppm) is only 242 Gt-C. This highlights the limited storage capacity of the terrestrial carbon reservoir. We also find that the terrestrial carbon storage sensitivity to changes in CO2 and temperature have been estimated to be lower in previous transient simulations because of lags in the climate-carbon system. Our model simulations indicate that the time scale of terrestrial carbon cycle response is greater than 500 years for CO2-fertilization and about 200 years for temperature perturbations. We also find that dynamic changes in vegetation amplify the terrestrial carbon storage sensitivity relative to a static vegetation case: because of changes in tree cover, changes in total ecosystem carbon for CO2-direct and climate effects are amplified by 88 and 72 %, respectively, in simulations with dynamic vegetation when compared to static vegetation simulations.

Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis

The synthesis of the dipeptide antibiotic bacilysin involves the sequential action of multiple enzymes in the bac operon. YwfH (also referred to as BacG) catalyzes the stereoselective reduction of dihydro-hydroxyphenylpyruvate (H2HPP) to tetrahydro-hydroxyphenylpyruvate (H4HPP) in this biosynthetic pathway. YwfH is an NADPH-dependent reductase that facilitates the conjugate addition of a hydride at the C4 olefin terminus of H2HPP. Here, the structure of YwfH is described at three conformational steps: the apo form, an apo-like conformation and the NADPH complex. YwfH is structurally similar to other characterized short-chain dehydrogenase/reductases despite having marginal sequence similarity. The structures of YwfH in different conformational states provide a rationale for the ping-pong reaction mechanism. The identification and role of the residues in the catalytic tetrad (Lys113Tyr117Ser155Asn158) in proton transfer were examined by mutational analysis. Together, the structures and biochemical features revealed synchronized conformational changes that facilitate cofactor specificity and catalysis of H4HPP formation en route to tetrahydrotyrosine synthesis.

Thermal vibration analysis of monolayer graphene embedded in elastic medium based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of single-layer graphene sheet embedded in polymer elastic medium, using the plate theory and nonlocal continuum mechanics for small scale effects. The graphene is modeled based on continuum plate theory and axial stress caused by the thermal effects is also considered. Nonlocal governing equation of motion for this graphene sheet system is derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using the Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temperature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. The thermal vibration analysis of single- and double-layer graphene sheets are considered for the analysis. The mode shapes of the respective graphene system are also captured in this work. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the graphene.

Probing hemoglobin confinement inside submicron silica tubes using synchrotron SAXS and electrochemical response

The configuration of hemoglobin in solution and confined inside silica nanotubes has been studied using synchrotron small angle X-ray scattering and electrochemical activity. Confinement inside submicron tubes of silica aid in preventing protein aggregation, which is vividly observed for unconfined protein in solution. The radius of gyration (R-g) and size polydispersity (p) of confined hemoglobin was found to be lower than that in solution. This was also recently demonstrated in case of confined hemoglobin inside layered polymer capsules. The confined hemoglobin displayed a higher thermal stability with Rg and p showing negligible changes in the temperature range 25-75 degrees C. The differences in configuration between the confined and unconfined protein were reflected in their electrochemical activity. Reversible electrochemical response (from cyclic voltammograms) obtained in case of the confined hemoglobin, in contrary to the observance of only a cathodic response for the unconfined protein, gave direct indication of the differences between the residences of the electroactive heme center in a different orientation compared to that in solution state. The confined Hb showed loss of reversibility only at higher temperatures. The electron transfer coefficient (alpha) and electron transfer rate constant (k(s)) were also different, providing additional evidence regarding structural differences between the unconfined and confined states of hemoglobin. Thus, absence of any adverse effects due to confinement of proteins inside the inorganic matrices such as silica nanotubes opens up new prospects for utilizing inorganic matrices as protein ``encapsulators'', as well as sensors at varying temperatures.

Biotin-conjugated tumour-targeting photocytotoxic iron(III) complexes

Iron(III) complexes FeL(B)] (1-4) of a tetradentate phenolate-based ligand (H3L) and biotin-conjugated dipyridophenazine bases (B), viz. 7-aminodipyrido 3,2-a: 2',3'-c]-phenazine (dppza in 1), (N-dipyrido3,2-a: 2',3'-c]-phenazino) amidobiotin (dppzNB in 2), dipyrido 3,2-a: 2',3'-c]-phenazine-11-carboxylic acid (dppzc in 3) and 2-((2-biotinamido) ethyl) amidodipyrido 3,2-a: 2',3'-c]-phenazine (dppzCB in 4) are prepared, characterized and their interaction with streptavidin and DNA and their photocytotoxicity and cellular uptake in various cells studied. The high-spin iron(III) complexes display Fe(III)/Fe(II) redox couple near -0.7V versus saturated calomel electrode in dimethyl sulfoxide-0.1M tetrabutylammonium perchlorate. The complexes show non-specific interaction with DNA as determined from the binding studies. Complexes with appended biotin moiety show similar binding to streptavidin as that of free biotin, suggesting biotin conjugation to dppz does not cause any loss in its binding affinity to streptavidin. The photocytotoxicity of the complexes is tested in HepG2, HeLa and HEK293 cell lines. Complex 2 shows higher photocytotoxicity in HepG2 cells than in HeLa or HEK293, forming reactive oxygen species. This effect is attributed to the presence of overexpressed sodium-dependent multi-vitamin transporters in HepG2 cells. Microscopic studies in HepG2 cells show internalization of the biotin complexes 2 and 4 essentially occurring by receptor-mediated endocytosis, which is similar to that of native biotin and biotin fluorescein isothiocyanate conjugate.

Fastest Rapid Loading Methods of Vertical and Radial Consolidations

Fastest curve-fitting procedures are proposed for vertical and radial consolidations for rapid loading methods. In vertical consolidation, the next load increment can be applied at 50-60% consolidation (or even earlier if the compression index is known). In radial consolidation, the next load increment can be applied at just 10-15% consolidation. The effects of secondary consolidation on the coefficient of consolidation and ultimate settlement are minimized in both cases. A quick procedure is proposed in vertical consolidation that determines how far is calculated from the true , where is coefficient of consolidation. In radial consolidation no such procedure is required because at 10-15% the consolidation effects of secondary consolidation are already less in most inorganic soils. The proposed rapid loading methods can be used when the settlement or time of load increment is not known. The characteristic features of vertical, radial, three-dimensional, and secondary consolidations are given in terms of the rate of settlement. A relationship is proposed between the coefficient of the vertical consolidation, load increment ratio, and compression index. (C) 2013 American Society of Civil Engineers.

Asymptotic expansions for the structural wavenumbers of isotropic and orthotropic fluid-filled circular cylindrical shells in the intermediate frequency range

We consider wavenumbers in in vacuo and fluid-filled isotropic and orthotropic shells. Using the Donnell-Mushtari (DM) theory we find compact and elegant asymptotic expansions for the wavenumbers in the intermediate frequency range, i.e., around the ring frequency. This frequency range corresponds to the frequencies where there is a rapid change in the values of bending wavenumbers and is found to exist in isotropic and orthotropic shells (in vacua and fluid-filled) for low circumferential orders n only. The same is first identified using the n=0 mode of an orthotropic shell. Following this, using the expression for the intermediate frequency, asymptotic expansions are found for other cases. Here, in order to get compact expansions we consider slight orthotropy (epsilon << 1) and light fluid loading (mu << 1). Thus, the orthotropy parameter epsilon and the fluid loading parameter mu are used as asymptotic parameters along with the non-dimensional thickness parameter beta. The methodology can be extended to any order of epsilon, only the expansions become unwieldy. The expansions are matched with the numerical solutions of the corresponding dispersion relation. The match is found to be good.

Satellite Evaluation of Current status of Irrigation management in Rajolibanda diversion scheme command, Mahaboobnagar District, AP

This article presents the results of a study using satellite remote sensing techniques to evaluate the current status of canal system performance in terms of the spatial and temporal mismatch between water requirements and water releases within the command area The Rajolibanda Diversion Scheme(RDS)is the only operational major irrigation project in the drought prone district of Mahaboobnagar in Andra Pradesh. It is an inter-state project between Karnataka and Andra Pradesh which comprises of an anicut constructed in Karnataka in 1995 across river Thungabhdra and a 143 km long left bank main canel. The initial 42.6 km of the canel lies in Karnataka consisting of 12 distributaries and servers and serves an localised ayacut of 2739ha. In Andra Pradesh, the latter stretch of the main canal consists of distributaries 12A to 40, is localised to serve an ayacut of 35,410 ha.of which 14,215 ha during kharif season,19,332 ha, during rabi season and 1,863 ha.of perennial crops

Closed-form solutions for non-uniform Euler-Bernoulli free-free beams

In this paper, the free vibration of a non-uniform free-free Euler-Bernoulli beam is studied using an inverse problem approach. It is found that the fourth-order governing differential equation for such beams possess a fundamental closed-form solution for certain polynomial variations of the mass and stiffness. An infinite number of non-uniform free-free beams exist, with different mass and stiffness variations, but sharing the same fundamental frequency. A detailed study is conducted for linear, quadratic and cubic variations of mass, and on how to pre-select the internal nodes such that the closed-form solutions exist for the three cases. A special case is also considered where, at the internal nodes, external elastic constraints are present. The derived results are provided as benchmark solutions for the validation of non-uniform free-free beam numerical codes. (C) 2013 Elsevier Ltd. All rights reserved.