Thermal and photochemical cycloaddition reactions of thiocarbonyls: a qualitative molecular orbital analysis

A comprehensive analysis of thermal and photochemical reactions of thiocarbonyls has been undertaken within the PMO framework employing MINDO/3 orbital energies and wavefunctions. The model is generally successful in rationalizing the observed regiochemistry of such reactions. In particular, the indicated regiochemistry for [4 + 2] thermal cycloadditions of saturated thiones to 2-substituted dienes, for the dimerization of α,β-unsaturated thiones, and for the photochemical cycloadditions of thioketones and thioenones are all in agreement with experimental observations. Interesting predictions are also made concerning cycloadditions of saturated, conjugated, and arylalkyl thiones which have not yet been studied experimentally. The analysis reveals the decisive role played by secondary orbital interactions in determining the observed product selectivity in the photochemical reactions between thioenone and olefins.

Synthetic and conformational studies on dehydrophenylalanine containing model peptides

Four model dipeptides containing a Z-dehydrophenylalanine residue (ΔZPhe) at the C-terminal, Boc-X-ΔZ Phe-NHMe (X = Ala (1), Gly (2), Pro (3), and Val (4)), have been synthesised and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. N.m.r. studies on these peptides clearly show the presence of intramolecularly hydrogen bonded structures in CHCl3 solutions while such structures appear to be absent in the corresponding saturated peptides. This conclusion is also supported by i.r. studies. Studies of the nuclear Overhauser effect provided evidence for the occurrence of a significant population of β-turn structures in solvents like CDCl3 and (CD3)2SO. The observed NOES are consistent with a major contribution from Type II β-turn structure in CDCl3, while in (CD3)2SO solutions there is evidence of a partially extended structure also.

The Relay Selection and Transmission Trade-off in Cooperative Communication Systems

A common and practical paradigm in cooperative communication systems is the use of a dynamically selected `best' relay to decode and forward information from a source to a destination. Such systems use two phases - a relay selection phase, in which the system uses transmission time and energy to select the best relay, and a data transmission phase, in which it uses the spatial diversity benefits of selection to transmit data. In this paper, we derive closed-form expressions for the overall throughput and energy consumption, and study the time and energy trade-off between the selection and data transmission phases. To this end, we analyze a baseline non-adaptive system and several adaptive systems that adapt the selection phase, relay transmission power, or transmission time. Our results show that while selection yields significant benefits, the selection phase's time and energy overhead can be significant. In fact, at the optimal point, the selection can be far from perfect, and depends on the number of relays and the mode of adaptation. The results also provide guidelines about the optimal system operating point for different modes of adaptation. The analysis also sheds new insights on the fast splitting-based algorithm considered in this paper for relay selection.

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Background: Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues. Results: Here we describe an integrated approach called ``PeptideMine'' for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which can be used for the identification and analysis of peptides, peptide homologues or functional patterns from the interacting sequence space of a protein. To further facilitate experimental validation, the PeptideMine webserver also provides a list of physico-chemical parameters corresponding to the peptide to determine the feasibility of using the peptide for in vitro biochemical or biophysical studies. Conclusions: The strategy described here involves the integration of data and tools to identify potential interacting partners for a protein and design criteria for peptides based on desired biochemical properties. Alongside the search for interacting protein sequences using three different search programs, the server also provides the biochemical characteristics of candidate peptides to prune peptide sequences based on features that are most suited for a given experiment. The PeptideMine server is available at the URL: http://caps.ncbs.res.in/peptidemine

Bearing Capacity of Clays whose Cohesion Increases Linearly with Depth

Experimental studies (Bishop 1966) show that for saturated normally consolidated clay the cohesion varies linearly with depth. The ultimate bearing capacity in such soil is generally obtained by limit equilibrium and limit analysis methods. Sokolovski's (1960) approach to the method of characteristics is used to find the ultimate bearing capacity of saturated clay whose cohesion is homogeneous and isotropic. In this technical note, the method of characteristics is further developed to determine ultimate bearing capacity of clay whose cohesion varies linearly with depth.

Brown adipose tissue mitochondria are cytochrome c — subsaturated

The oxidative activity of mitochondria freshly isolated from brown adipose tissue of rats was stimulated two-fold on the addition of small concentrations of exogenous cytochrome c to the reaction medium. Loss of membrane-bound cytochrome c did not occur during isolation of mitochondria. Estimation of the high-affinity binding sites on the organelle membrane indicated that less than a third of these sites remained saturated with cytochrome c. The pigment is thus shown to be a functionally limiting electron transport component in brown adipose tissue.

Estimation of soil hydraulic properties and their uncertainty: comparison between laboratory and field experiment

Often the soil hydraulic parameters are obtained by the inversion of measured data (e.g. soil moisture, pressure head, and cumulative infiltration, etc.). However, the inverse problem in unsaturated zone is ill-posed due to various reasons, and hence the parameters become non-unique. The presence of multiple soil layers brings the additional complexities in the inverse modelling. The generalized likelihood uncertainty estimate (GLUE) is a useful approach to estimate the parameters and their uncertainty when dealing with soil moisture dynamics which is a highly non-linear problem. Because the estimated parameters depend on the modelling scale, inverse modelling carried out on laboratory data and field data may provide independent estimates. The objective of this paper is to compare the parameters and their uncertainty estimated through experiments in the laboratory and in the field and to assess which of the soil hydraulic parameters are independent of the experiment. The first two layers in the field site are characterized by Loamy sand and Loamy. The mean soil moisture and pressure head at three depths are measured with an interval of half hour for a period of 1 week using the evaporation method for the laboratory experiment, whereas soil moisture at three different depths (60, 110, and 200 cm) is measured with an interval of 1 h for 2 years for the field experiment. A one-dimensional soil moisture model on the basis of the finite difference method was used. The calibration and validation are approximately for 1 year each. The model performance was found to be good with root mean square error (RMSE) varying from 2 to 4 cm(3) cm(-3). It is found from the two experiments that mean and uncertainty in the saturated soil moisture (theta(s)) and shape parameter (n) of van Genuchten equations are similar for both the soil types. Copyright (C) 2010 John Wiley & Sons, Ltd.

Sensitive high-resolution ion microprobe U-Pb dating of prograde and retrograde ultrahigh-temperature metamorphism as exemplified by Sri Lankan granulites

Ultrahigh-temperature (UHT) granulites of the central Highland Complex, Sri Lanka, underwent some of the highest known peak temperatures of crustal metamorphism. Zircon and monazite U-Pb systems in granulites near Kandy, the highest grade region (similar to 1050 degrees C; 0.9 GPa), preserve both a record of the timing of prograde and retrograde phases of UHT metamorphism and evidence for the ages of older protolith components. Zircon grains from a quartz-saturated granulite containing relics of the peak UHT assemblage have remnant detrital cores with dates of ca. 2.5-0.83 Ga. Date clusters of ca. 1.7 and 1.04-0.83 Ga record episodes of zircon growth in the source region of the protolith sediment. Two generations of overgrowths with contrasting Th/U record metamorphic zircon growth at 569 +/- 5 and 551 +/- 7 Ma, probably in the absence and presence of monazite, respectively. The age of coexisting metamorphic monazite (547 +/- 7 Ma) is indistinguishable from that of the younger, low-Th/U zircon overgrowths. Zircon from a quartz-undersaturated monazite-absent UHT granulite with a mainly retrograde assemblage is mostly metamorphic (551 +/- 5 Ma). The ca. 570 Ma zircon overgrowths in the quartz-saturated granulite probably record partial melting just before or at the metamorphic peak. The ca. 550 Ma zircon in both rocks, and the ca. 550 Ma monazite in the quartz-saturated sample, record post-peak isothermal decompression. A possible model for this pressure-temperature-time evolution is ultrahot collisional orogeny during the assembly of Gondwana, locally superheated by basaltic underplating, followed by fast extensional exhumation.

Structure, dielectric, and magnetic properties of Sr2TiMnO6 ceramics

Sr2TiMnO6, a double perovskite associated with high degree of B-site cation disorder was investigated in detail for its structural, magnetic, and dielectric properties. Though x-ray powder diffraction analysis confirms its cubic structure, first order Raman scattering and infrared reflectivity spectra indicate a breaking of the local cubic symmetry. The magnetization study reveals an anomaly at 14 K owing to a ferrimagnetic/canted antiferromagneticlike ordering arising from local Mn-O-Mn clusters. Saturated M-H hysteresis loops obtained at 5 K also reflect the weak ferromagnetic exchange interactions present in the system and an approximate estimation of Mn3+/Mn4+ was done using the magnetization data for the samples sintered at different temperatures. The conductivity and dielectric behavior of this system has been investigated in a broad temperature range of 10 to 300 K. Intrinsic permittivity was obtained only below 100 K whereas giant permittivity due to conductivity and Maxwell-Wagner polarization was observed at higher temperatures. X-ray photoemission studies further confirmed the presence of mixed oxidation states of Mn and the valence band spectra analysis was carried out in detail. (C) 2010 American Institute of Physics. doi: 10.1063/1.3500369]

Bioleaching of sulphides under applied potentials

The influence of applied DC potentials on the activity and growth of Thiobacillus ferrooxidans, as well as on the dissolution behaviour of some base metal sulphides is discussed with reference to bioleaching. Selective bioleaching of zinc from sphalerite could be achieved under an applied potential of −500 mV (saturated calomel electrode) from binary mineral mixtures containing the zinc mineral and chalcopyrite or pyrite. On the other hand, bioleaching of pyrite and chalcopyrite was found to be enhanced under positive potentials of +400 mV and +600 mV, respectively. Probable mechanisms in the electrobioleaching of sulphides are examined with respect to galvanic, microbiological and applied potential effects.

A Parallel Progressive Refinement Image Rendering Algorithm on a Scalable Multithreaded VLSI Processor Array

In this paper we develop a multithreaded VLSI processor linear array architecture to render complex environments based on the radiosity approach. The processing elements are identical and multithreaded. They work in Single Program Multiple Data (SPMD) mode. A new algorithm to do the radiosity computations based on the progressive refinement approach[2] is proposed. Simulation results indicate that the architecture is latency tolerant and scalable. It is shown that a linear array of 128 uni-threaded processing elements sustains a throughput close to 0.4 million patches/sec.

Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Algorithms for Routing and Centralized Scheduling in IEEE 802.16 Mesh Networks

IEEE 802.16 standards for Wireless Metropolitan Area Networks (WMANs) include a mesh mode of operation for improving the coverage and throughput of the network. In this paper, we consider the problem of routing and centralized scheduling for such networks. We first fix the routing, which reduces the network to a tree. We then present a finite horizon dynamic programming framework. Using it we obtain various scheduling algorithms depending upon the cost function. Next we consider simpler suboptimal algorithms and compare their performances.

Free convection about cylinders of elliptic cross section embedded in a porous medium

Numerical solutions are presented for the free convection boundary layers over cylinders of elliptic cross section embedded in a fluid-saturated porous medium. The transformed conservation equations of the nonsimilar boundary layers are solved numerically by an efficient finite-difference method. The theory was applied to a number of cylinders and the results compared very well with published analytical solutions. The results are of use in the design of underground electrical cables, power plant steam, and water distribution lines, among others.

Functions Of Cytochrome-C In Regulation Of Electron-Transfer And Protein Folding

Cytochrome c, a "mobile electron carrier" of the mitochondrial respiratory chain, also occurs in detectable amounts in the cytosol, and can receive electrons from cytochromes present in endoplasmic reticulum and plasma membranes as well as from superoxide and ascorbate. The pigment was found to dissociate from mitochondrial membranes in liver and kidney when rats were subjected to heat exposure and starvation, respectively. Treating cytochrome c with hydroxylamine gives a partially deaminated product with altered redox properties; decreased stimulation of respiration by deficient mitochondria, increased reduction by superoxide, and complete loss of reducibility by plasma membranes. Mitochondria isolated from brown adipose tissue of cold-exposed rats are found to be sub-saturated with cytochrome c. The ability of cytochrome c to reactivate reduced ribonuclease is now reinterpreted as a molecular chaperone role for the hemoprotein.