Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Moment-Matched Lognormal Modeling of Uplink Interference with Power Control and Cell Selection

We develop an alternate characterization of the statistical distribution of the inter-cell interference power observed in the uplink of CDMA systems. We show that the lognormal distribution better matches the cumulative distribution and complementary cumulative distribution functions of the uplink interference than the conventionally assumed Gaussian distribution and variants based on it. This is in spite of the fact that many users together contribute to uplink interference, with the number of users and their locations both being random. Our observations hold even in the presence of power control and cell selection, which have hitherto been used to justify the Gaussian distribution approximation. The parameters of the lognormal are obtained by matching moments, for which detailed analytical expressions that incorporate wireless propagation, cellular layout, power control, and cell selection parameters are developed. The moment-matched lognormal model, while not perfect, is an order of magnitude better in modeling the interference power distribution.

Synthesis of biodiesel in supercritical alcohols and supercritical carbon dioxide

Biodiesel was synthesized in supercritical fluids by two routes: non-catalytically in supercritical alcohols and by enzyme catalysis in supercritical carbon dioxide. Two oils, sesame oil and mustard oil, and two alcohols, methanol and ethanol, were used for the synthesis. Complete conversion was observed for synthesis in supercritical alcohols whereas only a maximum of 70% conversion was observed for the enzymatic synthesis in supercritical carbon dioxide. For the synthesis in supercritical alcohols, the activation energies and pseudo-first order rate constants were determined. For the reactions in supercritical carbon dioxide, a mechanism based on ping pong bi-bi was proposed and the kinetic parameters were determined. (C) 2009 Elsevier Ltd. All rights reserved.

Charge-order driven multiferroic and magneto-dielectric properties of rare earth manganates

Charge-order driven magnetic ferroelectricity is shown to occur in several rare earth manganates of the general formula, Ln(1-x)A(x)MnO(3) (In = rare earth, A = alkaline earth). Charge-ordered manganates exhibit dielectric constant anomalies around the charge-ordering or the antiferromagnetic transition temperature. Magnetic fields have a marked effect on the dielectric properties of these compounds, indicating the presence of coupling between the magnetic and electrical order parameters. Magneto-dielectric properties are retained in small particles of the manganates. The observation of magneto-ferroelectricity in these manganates is in accordance with theoretical predictions.

Charge-order driven multiferroic and magneto-dielectric properties of rare earth manganates

Charge-order driven magnetic ferroelectricity is shown to occur in several rare earth manganates of the general formula, Ln(1-x)A(x)MnO(3) (In = rare earth, A = alkaline earth). Charge-ordered manganates exhibit dielectric constant anomalies around the charge-ordering or the antiferromagnetic transition temperature. Magnetic fields have a marked effect on the dielectric properties of these compounds, indicating the presence of coupling between the magnetic and electrical order parameters. Magneto-dielectric properties are retained in small particles of the manganates. The observation of magneto-ferroelectricity in these manganates is in accordance with theoretical predictions.

Effect of mode of rolling on development of texture and microstructure in two-phase (alpha plus beta) brass

The evolution of microstructure and texture during deformation of two-phase (alpha + beta) brass was studied for different initial microstructure and texture. The deformation processing involved unidirectional and multi-step cross-rolling. The bulk textures were determined by measuring the pole figures and calculating the orientation distribution function ODF for both alpha (fcc) and beta (bcc) phases, while the microstructure and other microstructural parameters were measured through optical microscopy and scanning electron microscopy with electron back scatter diffraction (SEM-EBSD). Results indicate that textures developed after unidirectional rolling and multi-step cross-rolling are significantly different. The variation in initial texture had a pronounced effect on the development of texture in the alpha phase during subsequent deformation. (C) 2010 Elsevier B.V. All rights reserved.

Thermal decomposition studies on copolyurethanes based on hydroxyl terminated polybutadiene and poly(12-hydroxy stearic acid-co-TMP) ester polyol

Thermal degradation of copolyurethanes based on hydroxyl terminated polybutadiene (HTPB) and poly(12-hydroxy stearic acid-co-TMP) ester polyol (PEP) with varying compositions has been studied by thermo-gravimetric and pyrolysis-GC techniques. The copolyurethanes were found to decompose in multiple stages and the kinetic parameters were found to be dependent on the method of their evaluation. The activation energy for the initial stage of decomposition was found to increase, and for the main stage decreases with the increase in PEP content. The pyrolysis-GC studies on the ammonium perchlorate filled copolyurethanes (solid propellants) showed that the major products during the pyrolysis were C-2, C-3 hydrocarbons and butadiene. The amount of C-2 fraction in the pyrolyslate increased with solid loading, as well as with the HTPB content in the copolyurethanes. A linear relationship apparently exists between the amount of C-2 fraction and the burn rates of the solid propellants. (C) 2000 Elsevier Science Ltd. All rights reserved.

A self-consistent formulation for analysis and generation of non-uniform DNA structure

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

Crosstalk between the sympathetic nervous system, inflammation and coagulation in gestational diabetes; a therapeutic approach in postmenopausal hypertension

The occurrence of gestational diabetes (GDM) during pregnancy is a powerful sign of a risk of later type 2 diabetes (T2D) and cardiovascular diseases (CVDs). The physiological basis for this disease progression is not yet fully understood, but increasing evidence exists on interplay of insulin resistance, subclinical inflammation, and more recently, on unbalance of the autonomic nervous system. Since the delay in development of T2D and CVD after GDM ranges from years to decades, better understanding of the pathophysiology of GDM could give us new tools for primary prevention. The present study was aimed at investigating the role of the sympathetic nervous system (SNS) in GDM and its associations with insulin and a variety of inflammatory cytokines and coagulation and fibrinolysis markers. This thesis covers two separate study lines. Firstly, we investigated 41 women with GDM and 22 healthy pregnant and 14 non-pregnant controls during the night in hospital. Blood samples were drawn at 24:00, 4:00 and 7:00 h to determine the concentrations of plasma glucose, insulin, noradrenaline (NA) and adrenomedullin, markers of subclinical inflammation, coagulation and fibrinolysis variables and platelet function. Overnight holter ECG recording was performed for analysis of heart rate variability (HRV). Secondly, we studied 87 overweight hypertensive women with natural menopause. They were randomised to use a central sympatholytic agent, moxonidine (0.3mg twice daily), the β-blocking agent atenolol (50 mg once daily+blacebo once daily) for 8 weeks. Inflammatory markers and adiponectin were analysed at the beginning and after 8 weeks. Activation of the SNS (increase in NA, decreased HRV) was seen in pregnant vs. non-pregnant women, but no difference existed between GDM and normal pregnancy. However, modulation (internal rhythm) of HRV was attenuated in GDM. Insulin and inflammatory cytokine levels were comparable in all pregnant women but nocturnal variation of concentrations of C-reactive protein, serum amyloid A and insulin were reduced in GDM. Levels of coagulation factor VIII were lower in GDM compared with normal pregnancy, whereas no other differences were seen in coagulation and fibrinolysis markers. No significant associations were seen between NA and the studied parameters. In the study of postmenopausal women, moxonidine treatment was associated with favourable changes in the inflammatory profile, seen as a decrease in TNFα concentrations (increase in atenolol group) and preservation of adiponectin levels (decrease in atenolol group). In conclusion, our results did not support our hypotheses of increased SNS activity in GDM or a marked association between NA and inflammatory and coagulation markers. Reduced biological variation of HRV, insulin and inflammatory cytokines suggests disturbance of autonomic and hormonal regulatory mechanisms in GDM. This is a novel finding. Further understanding of the regulatory mechanisms could allow earlier detection of risk women and the possibility of prevention. In addition, our results support consideration of the SNS as one of the therapeutic targets in the battle against metabolic diseases, including T2D and CVD.

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.

Synthesis and characterization of spherical and rod like nanocrystalline Nd2O3 phosphors

Spherical and rod like nanocrystalline Nd2O3 phosphors have been prepared by solution combustion and hydrothermal methods respectively The Powder X-ray diffraction (PXRD) results confirm that hexagonal A-type Nd2O3 has been obtained with calcination at 900 C for 3 h and the lattice parameters have been evaluated by Rietveld refinement Surface morphology of Nd2O3 phosphors show the formation of nanorods in hydrothermal synthesis whereas spherical particles in combustion method TEM results also confirm the same Raman studies show major peaks which are assigned to F-g and combination of A(g) + E-g modes The PL spectrum shows a series of emission bands at similar to 326-373 nm (UV) 421-485 nm (blue) 529-542 nm (green) and 622 nm (red) The UV blue green and red emission in the PL spectrum indicates that Nd2O3 nanocrystals are promising for high performance materials and white light emitting diodes (LEDs) (C) 2010 Elsevier B V All rights reserved

Oxidative copolymerization: microstructure analysis of the terpolymer of styrene, methyl methacrylate, and oxygen

This paper reports the first study of the microstructure of a copolyperoxide by nuclear magnetic resonance spectroscopy. The copolyperoxides of styrene and methyl methacrylate (MMA) of various compositions have been synthesized. An analysis of the resonance signal of the backbone methylene protons gave the diad sequence probabilities which led to the calculation of the oxidative copolymerization reactivity ratios for styrene and MMA and the microstructural parameters like average chain length of the repeat unit sequences, run number, etc. The results point to the tendency of the SO1 and MO:! units to alternate in the chain. Compared to poly(styrene peroxide), the aromatic C1 seems to be stereosensitive in the terpolymers.

Fatigue crack propagation model and size effect in concrete using dimensional analysis

It is well known that fatigue in concrete causes excessive deformations and cracking leading to structural failures. Due to quasi-brittle nature of concrete and formation of a fracture process zone, the rate of fatigue crack growth depends on a number of parameters, such as, the tensile strength, fracture toughness, loading ratio and most importantly the structural size. In this work, an analytical model is proposed for estimating the fatigue crack growth in concrete by using the concepts of dimensional analysis and including the above parameters. Knowing the governed and the governing parameters of the physical problem and by using the concepts of self-similarity, a relationship is obtained between different parameters involved. It is shown that the proposed fatigue law is able to capture the size effect in plain concrete and agrees well with different experimental results. Through a sensitivity analysis, it is shown that the structural size plays a dominant role followed by loading ratio and the initial crack length in fatigue crack propagation. (C) 2010 Elsevier Ltd. All rights reserved.

Abrasive Jet Machining - Process variables and current applications

brusive Jet Machining (AJM) or Micro Blast Machining is a non-traditional machining process, wherein material removal is effected by the erosive action of a high velocity jet of a gas, carrying fine-grained abrasive particles, impacting the work surface. The AJM process differs from conventional sand blasting in that the abrasive is much finer and the process parameters and cutting action are carefully controlled. The process is particularly suitable to cut intricate shapes in hard and brittle materials which are sensitive to heat and have a tendency to chip easily. In other words, AJM can handle virtually any hard or brittle material. Already the process has found its ways Into dozens of applications; sometimes replacing conventional alternatives often doing jobs that could not be done in any other way. This paper reviews the current status of this non-conventional machining process and discusses the unique advantages and possible applications.

Oxidation of aqueous sulphur dioxide catalysed by poly-4-vinylpyridine-Cu(II) complex .2. Combined homogeneous and heterogeneous phase oxidation

Aqueous phase oxidation of sulphur dioxide at low concentrations catalysed by a PVP-Cu complex in the solid phase and dissolved Cu(II) in the liquid phase is studied in a rotating catalyst basket reactor (RCBR). The equilibrium adsorption of Cu(II) and S(VI) on PVP particles is found to be of the Langmuir-type. The diffusional effects of S(IV) species in PVP-Cu resin are found to be insignificant whereas that of product S(VI) are found to be significant. The intraparticle diffusivity of S(VI) is obtained from independent tracer experiments. In the oxidation reaction HSO3- is the reactive species. Both the S(IV) species in the solution, namely SO2(aq) and HSO3- get adsorbed onto the active PVP-Cu sites of the catalyst, but only HSO3- undergoes oxidation. A kinetic mechanism is proposed based on this feature which shows that SO2(aq) has a deactivating effect on the catalyst. A rate model is developed for the three-phase reaction system incorporating these factors along with the effect of concentration of H2SO4 on the solubility of SO2 in the dilute aqueous solutions of Cu(II). Transient oxidation experiments are conducted at different conditions of concentration of SO2 and O-2 in the gas phase and catalyst concentration, and the rate parameters are estimated from the data. The observed and calculated profiles are in very good agreement. This confirms the deactivating effect of nonreactive SO2(aq) on the heterogeneous catalysis.