An infinite family of tight triangulations of manifolds

We give explicit construction of vertex-transitive tight triangulations of d-manifolds for d >= 2. More explicitly, for each d >= 2, we construct two (d(2) + 5d + 5)-vertex neighborly triangulated d-manifolds whose vertex-links are stacked spheres. The only other non-trivial series of such tight triangulated manifolds currently known is the series of non-simply connected triangulated d-manifolds with 2d + 3 vertices constructed by Kuhnel. The manifolds we construct are strongly minimal. For d >= 3, they are also tight neighborly as defined by Lutz, Sulanke and Swartz. Like Kuhnel complexes, our manifolds are orientable in even dimensions and non-orientable in odd dimensions. (c) 2013 Elsevier Inc. All rights reserved.

Dissecting pi-helices: sequence, structure and function

A new procedure for the identification of regular secondary structures using a C-alpha trace has identified 659 pi-helices in 3582 protein chains, solved at high resolution. Taking advantage of this significantly expanded database of pi-helices, we have analysed the functional and structural roles of helices and determined the position-wise amino acid propensity within and around them. These helices range from 5 to 18 residues in length with the average twist and rise being 85.2 +/- 7.2 and 1.28 +/- 0.31 angstrom, respectively. A total of 546 (similar to 83%) out of 659 pi-helices occur in conjunction with alpha-helices, with 101 pi-helices being interspersed between two alpha-helices. The majority of interspersed pi-helices were found to be conserved across a large number of structures within a protein family and produce a significant bend in the overall helical segment as well as local distortions in the neighbouring a-helices. The presence of a pi-helical fragment leads to appropriate orientation of the constituent residues, so as to facilitate favourable interactions and also help in proper folding of the protein chain. In addition to intra helical 6 -> 1 N H center dot center dot center dot O hydrogen bonds, pi-helices are also stabilized by several other non-bonded interactions. pi-Helices show distinct positional residue preferences, which are different from those of a-helices.

New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study

Human Guanine Monophosphate Synthetase (hGMPS) converts XMP to GMP, and acts as a bifunctional enzyme with N-terminal ``glutaminase'' (GAT) and C-terminal ``synthetase'' domain. The enzyme is identified as a potential target for anticancer and immunosuppressive therapies. GAT domain of enzyme plays central role in metabolism, and contains conserved catalytic residues Cys104, His190, and Glu192. MD simulation studies on GAT domain suggest that position of oxyanion in unliganded conformation is occupied by one conserved water molecule (W1), which also stabilizes that pocket. This position is occupied by a negatively charged atom of the substrate or ligand in ligand bound crystal structures. In fact, MD simulation study of Ser75 to Val indicates that W1 conserved water molecule is stabilized by Ser75, while Thr152, and His190 also act as anchor residues to maintain appropriate architecture of oxyanion pocket through water mediated H-bond interactions. Possibly, four conserved water molecules stabilize oxyanion hole in unliganded state, but they vacate these positions when the enzyme (hGMPS)-substrate complex is formed. Thus this study not only reveals functionally important role of conserved water molecules in GAT domain, but also highlights essential role of other non-catalytic residues such as Ser75 and Thr152 in this enzymatic domain. The results from this computational study could be of interest to experimental community and provide a testable hypothesis for experimental validation. Conserved sites of water molecules near and at oxyanion hole highlight structural importance of water molecules and suggest a rethink of the conventional definition of chemical geometry of inhibitor binding site.

Deciphering the Distinct Role for the Metal Coordination Motif in the Catalytic Activity of Mycobacterium smegmatis Topoisomerase I

Mycobacterium smegmatis topoisomerase I (Mstopol) is distinct from typical type IA topoisomerases. The enzyme binds to both single- and double-stranded DNA with high affinity, making specific contacts. The enzyme comprises conserved regions similar to type IA topoisomerases from Escherichia coli and other eubacteria but lacks the typically found zinc fingers in the carboxy-terminal domain. The enzyme can perform DNA cleavage m the absence of Mg2+ but religation needs exogenously added Mg2+. One molecule of Mg2+ tightly bound to the enzyme has no role in DNA cleavage but is needed only for the religation reaction. The toprim. (topoisomerase-primase) domain in MstopoI comprising the Mg2+ binding pocket, conserved in both type IA and type II topoisomerases, was subjected to mutagenesis to understand the role of Mg2+, in different steps of the reaction. The residues D108, D110, and E112 of the enzyme, which form the acidic triad in the DXDXE motif, were changed to alanines. D108A mutation resulted in an enzyme that is Mg2+ dependent for DNA cleavage unlike Mstopol and exhibited enhanced DNA cleavage property and reduced religation activity. The mutant was toxic for cell growth, most likely due to the imbalance in cleavage-religation equilibrium. In contrast, the E112A mutant behaved like wild-type enzyme, cleaving DNA in a Mg2+-independent fashion, albeit to a reduced extent. Intra- and intermolecular religation assays indicated specific roles for D108 and E112 residues during the reaction. Together, these results indicate that the D108 residue has a major role during cleavage and religation, while E112 is important for enhancing the efficiency of cleavage. Thus, although architecturally and mechanistically similar to topoisomerase I from E. coli, the metal coordination pattern of the mycobacterial enzyme is distinct, opening up avenues to exploit the enzyme to develop inhibitors.

Microbial aspects of acid generation and bioremediation with relevance to indian mining

The role of Acidithiobacillus group of bacteria in acid generation and heavy metal dissolution was studied with relevance to some Indian mines. Microorganisms implicated in acid generation such as Acidithiobacillus Acidithicibacillus thiooxidans and Leptospirillum ferrooxidans were isolated from abandoned mines, waste rocks and tailing dumps. Arsenite oxidizing Thiomonas and Bacillus group of bacteria were isolated and their ability to oxidize As (111) to As (V) established. Mine isolated Sulfate reducing bacteria were used to remove dissolved copper, zinc, iron and arsenic from solutions.

Ultrasonic spray pyrolysis of CZTS solar cell absorber layers and characterization studies

CZTS (Copper Zinc Tin Sulphide) is a wide band gap quartnery chalcopyrite which has a band gap of about 1.45 eV and an absorption coefficient of 10(4) cm(-1); thus making it an ideal material to be used as an absorber layer in solar cells. Ultrasonic Spray Pyrolysis is a deposition technique, where the solution is atomized ultrasonically, thereby giving a fine mist having a narrow size distribution which can be used for uniform coatings on substrates. An Ultrasonic Spray Pyrolysis equipment was developed and CZTS absorber layers were successfully grown with this technique on soda lime glass substrates using aqueous solutions. Substrate temperatures ranging from 523 K to 723 K were used to deposit the CZTS layers and these films were characterized using SEM, EDAX and XRD. It was observed that the film crystallized in the kesterite structure and the best crystallites were obtained at 613 K. It was observed that the grain size progressively increased with temperature. The optical band gap of the material was obtained as 1.54 eV.

Cerebroprotective activity of Wedelia calendulacea on global cerebral ischemia in rats

The present study was to investigate the effect of W. calendulacea on ischemia and reperfusion-induced cerebral injury. Cerebral ischemia was induced by occluding right and left common carotid arteries (global cerebral ischemia) for 30 min followed by reperfusion for 1 h and 4 h individually. Various biochemical alterations, produced subsequent to the application of bilateral carotid artery occlusion (BCAO) followed by reperfusion viz. increase in lipid peroxidation (LPO), hydrogen peroxide (H(2)O(2)), and decrease in reduced glutathione (GSH), catalase (CAT) and superoxide dismutase (SOD), level in the brain tissue, Western blot analysis (Cu-Zn-SOD and CAT) and assessment of cerebral infarct size were measured. All those enzymes are markedly reversed and restored to near normal level in the groups pre-treated with W. calendulacea (250 and 500 mg/kg given orally in single and double dose/day for 10 days) in dose-dependent way. The effect of W. calendulacea had increased significantly the protein expression of copper/zinc superoxide dismutase (Cu-Zn-SOD) and CAT in cerebral ischemia. W. claendulacea was markedly decrease cerebral infarct damages but results are not statistically significant. It can be concluded that W. calendulacea possesses a neuroprotective activity against cerebral ischemia in rat.

Nucleosynthesis in the outflows associated with accretion disks of type II collapsars

We investigate nucleosynthesis inside the outflows from gamma-ray burst (GRB) accretion disks formed by the Type II collapsars. In these collapsars, massive stars undergo core collapse to form a proto-neutron star initially, and a mild supernova (SN) explosion is driven. The SN ejecta lack momentum, and subsequently this newly formed neutron star gets transformed to a stellar mass black hole via massive fallback. The hydrodynamics and the nucleosynthesis in these accretion disks have been studied extensively in the past. Several heavy elements are synthesized in the disk, and much of these heavy elements are ejected from the disk via winds and outflows. We study nucleosynthesis in the outflows launched from these disks by using an adiabatic, spherically expanding outflow model, to understand which of these elements thus synthesized in the disk survive in the outflow. While studying this, we find that many new elements like isotopes of titanium, copper, zinc, etc., are present in the outflows. Ni-56 is abundantly synthesized in most of the cases in the outflow, which implies that the outflows from these disks in a majority of cases will lead to an observable SN explosion. It is mainly present when outflow is considered from the He-rich, Ni-56/Fe-54-rich zones of the disks. However, outflow from the Si-rich zone of the disk remains rich in silicon. Although emission lines of many of these heavy elements have been observed in the X-ray afterglows of several GRBs by Chandra, BeppoSAX, XMM-Newton, etc., Swift seems to have not yet detected these lines.

The effect of multisubstitution on the thermoelectric properties of chalcogenide-based Cu2.1Zn0.9Sn1-xInxSe4 (0 <= x <= 0.1)

Quinary chalcogenide compounds Cu2.1Zn0.9Sn1-xInxSe4 (0 <= x <= 0.1) were prepared by melting (1170K) followed by annealing (773 K) for 172 h. Powder X-ray diffraction (XRD) data accompanied by electron probe microanalysis (EPMA) and Raman spectra of all the samples confirmed the formation of a tetragonal kesterite structure with Cu2FeSnS4-type. The thermoelectric properties of all the samples were measured as a function of temperature in the range of 300-780K. The electrical resistivity of all the samples exhibits metallic-like behavior. The positive values of the Seebeck coefficient and the Hall coefficient reveal that holes are the majority charge carriers. The codoping of copper and indium leads to a significant increase of the electrical resistivity and the Seebeck coefficient as a function of temperature above 650 K. The thermal conductivity of all the samples decreases with increasing temperature. Lattice thermal conductivity is not significantly modified as the doping content may infer negligible mass fluctuation scattering for copper/zinc and indium/tin substitution. Even though, the power factors (S-2/rho) of indium-doped samples Cu2.1Zn0.9Sn1-xInxSe4 (x = 0.05, 0.075) are almost the same, the maximum zT = 0.45 at 773K was obtained for Cu2.1Zn0.9Sn0.925In0.075Se4 due to its smaller value of thermal conductivity. (C) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Non-linear couette flow with heat transfer using the B-G-K model

In recent years a large number of investigators have devoted their efforts to the study of flow and heat transfer in rarefied gases, using the BGK [1] model or the Boltzmann kinetic equation. The velocity moment method which is based on an expansion of the distribution function as a series of orthogonal polynomials in velocity space, has been applied to the linearized problem of shear flow and heat transfer by Mott-Smith [2] and Wang Chang and Uhlenbeck [3]. Gross, Jackson and Ziering [4] have improved greatly upon this technique by expressing the distribution function in terms of half-range functions and it is this feature which leads to the rapid convergence of the method. The full-range moments method [4] has been modified by Bhatnagar [5] and then applied to plane Couette flow using the B-G-K model. Bhatnagar and Srivastava [6] have also studied the heat transfer in plane Couette flow using the linearized B-G-K equation. On the other hand, the half-range moments method has been applied by Gross and Ziering [7] to heat transfer between parallel plates using Boltzmann equation for hard sphere molecules and by Ziering [83 to shear and heat flow using Maxwell molecular model. Along different lines, a moment method has been applied by Lees and Liu [9] to heat transfer in Couette flow using Maxwell's transfer equation rather than the Boltzmann equation for distribution function. An iteration method has been developed by Willis [10] to apply it to non-linear heat transfer problems using the B-G-K model, with the zeroth iteration being taken as the solution of the collisionless kinetic equation. Krook [11] has also used the moment method to formulate the equivalent continuum equations and has pointed out that if the effects of molecular collisions are described by the B-G-K model, exact numerical solutions of many rarefied gas-dynamic problems can be obtained. Recently, these numerical solutions have been obtained by Anderson [12] for the non-linear heat transfer in Couette flow,

Chelating and bridging bis(diphenylphosphino)aniline complexes of copper(I)

The ligand bis(diphenylphosphino)aniline (dppan) has been shown to be a versatile ligand sporting different coordination modes and geometries as dictated by copper(I) and the counter ion. The molecular structures of its Cu(I) complexes were characterized by X-ray crystallography. The ligand was found in a chelating mode and monomeric complexes were formed when the ligand to copper ratio was 2: 1 and the anion was non-coordinating. However, with thiocyanate as the counter anion, the ligand was found to adopt two different modes, with one ligand chelating and the other acting as a monodentate ligand. With CuX (X = Cl, Br), dppan formed a tetrameric complex when the ligand and metal were reacted in the ratio of 1:1. But reactions containing ligand and metal in the ratios of 1: 2 or 2: 1, resulted in the formation of a mixture of species in solution. Crystallization however, led to the isolation of the tetrameric complex. Variable temperature P-31{H-1} NMR spectra of the isolated tetramers did not show the presence of chelated structures in solution. Tetra-alkylammonium salts were added to solutions of various complexes of dppan and studied by P-31{H-1} NMR to probe the effect of anions on the stability of complexes in solution. The Cu-dppan complexes were robust and did not interconvert with other structures in solution unlike the bis(diphenylphosphino) isopropylamine complexes. (C) 2011 Elsevier B.V. All rights reserved.

The nature of non-equilibrium solidification of undercooled Agsingle bondCu alloys in contact with primary copper dendrites

Liquids of silver-copper alloys with near eutectic compositions embedded in a copper matrix were undercooled. The structural and microstructural investigations of these alloys solidified from undercooled temperature indicated the absence of both the eutectic reaction and diffusionless transformation below the equal free energy curve (T0). Instead the liquid maintained local equilibrium with the copper dendrites continuously until it intersected the extended solidus of the silver rich solid solution.