Disallowed Ramachandran conformations of amino acid residues in protein structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (phi, psi). Residues falling outside the defined "broad allowed limits" on the Ramachandran map were chosen and the reported B-factor value of the alpha-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific phi, psi angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal "Ala-dipeptide" constructed using disallowed dihedral angle (phi, psi) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.     

Proteome of human endometrium: Identification of differentially expressed proteins in proliferative and secretory phase endometrium

Purpose: To exploit the potential of proteomics to identify and study additional yet‐unidentified important proteins present in human endometrium. Experimental design: The proteome of human endometrium would be established using 2‐DE and MALDI and the data analyzed to identify differential protein expression in the proliferative and secretory phase of the menstrual cycle using PDQuest software and MALDI. Results: In the present work, 2‐DE of human endometrium protein led to the resolution of over 200 spots. Subsequent MALDI analysis of 215 spots allowed the identification of 194 proteins. A total of 57 out of the 215 spots were found to be differentially expressed, out of which 49 could be identified using MALDI. These differentially expressed proteins included structural proteins, molecular chaperones, signaling proteins, metabolic proteins, proteins related to immunity, RNA biogenesis, protein biosynthesis and others. The differential expressions of seven representative proteins in secretory and proliferative phase endometrium tissue were confirmed by immunoblot analysis. Conclusion and clinical relevance: This study establishes the 2‐D proteome of human endometrium represented by 194 identified protein spots. The present data provides an important clue towards determining the function of these proteins with respect to endometrium related diseases.     

An investigation of the electrical transport properties of graphene-oxide thin films

The electrical transport properties of graphene-oxide (GO) thin films were investigated. The GO was synthesized by a modified Hummers method and was characterized by X-ray diffraction and UV-visible spectroscopy. The thin film of GO was made on a Si/SiO₂ substrate by drop-casting. The surface morphology of the GO film was analyzed by using scanning electron microscopy and atomic force microscopy techniques. Temperature dependent resistance and current-voltage measurements were studied using four-terminal method at various temperatures (120, 150, 175, 200, 250 and 300 K) and their charge transport followed the 3D variable range hopping mechanism which was well supported by Raman spectra analysis. The presence of various functional groups in GO were identified by using high resolution X-ray photo electron (XPS) and Fourier transform infra red (FT-IR) spectroscopic techniques. Graphene-oxide thin film field effect transistor devices show p-type semiconducting behavior with a hole mobility of 0.25 cm² V⁻¹ s⁻¹ and 0.59 cm² V⁻¹ s⁻¹ when measured in air and vacuum respectively.     

Effects of entrainment and agglomeration of particles on combustion of nano-aluminum and water mixtures

The combustion of nano-aluminum and water mixtures is studied theoretically for a particle size of 80 nm and over a pressure range of 1–10 MPa. Emphasis is placed on the effects of entrainment and agglomeration of particles on the burning rate and its dependence on pressure. The flame thickness increases by a factor of ∼10, when particle entrainment is considered. This lowers the conductive heat flux at the ignition front, thereby reducing the burning rate. The pressure dependence of the burning rate is attributed to the changes in the burning time and velocity of particles with pressure. In the diffusion limit, the pressure exponent increases from 0 to 0.5, when the entrainment index increases from 0 to 1.0. A similar trend is observed in the kinetics-controlled regime, although the corresponding value exceeds the diffusion counterpart by 0.5. The kinetics-controlled model significantly over-predicts the burning rate and its pressure exponent, depending on the entrainment index. The present analysis suggests that nano-particles formed closely-packed agglomerates of diameter 3–5 μm, which may burn under diffusion-controlled conditions at high pressures.     

Study of friction welding characteristics of Al/SiC composite and application of grey-based TOPSIS

The present work investigates the possibility of producing friction welded joints with an advanced material like Al/SiC (aluminum–silicon carbide) composite. The study also discloses the multi response optimization in the process of continuous drive friction welding using a hybrid algorithm of grey-based TOPSIS (technique for order of performance by similarity to ideal solution). The friction welding parameters (frictional pressure, upset pressure, burn off length and rotational speed) were optimized considering the multiple performance characteristics such as proof stress, tensile strength, and microhardness. Taguchi’s L₂₇ orthogonal array was used for conducting the welding trials. The confirmation test was conducted at the optimal setting, to sort out the effectiveness of the proposed hybrid algorithm. The macro photographs of the joints and optical micrographs of the weld zone were studied. The scanning electron microscope images of the fractured surface were also examined to identify the failure mode of joints. The significant improvements in the performance characteristics prove the effectiveness of the grey-based TOPSIS method in experimental welding optimization.     

Effect of packing density on flame propagation of nickel-coated aluminum particles

The combustion-wave propagation of nickel-coated aluminum particles is studied theoretically for packing densities in the range of 10–100% of the theoretical maximum density. Emphasis is placed on the effect of packing density on the burning properties. The energy conservation equation is solved numerically and the burning rate is determined by tracking the position of the flame front. Atomic diffusion coefficients and reaction rate of isolated nickel-coated aluminum particles are input parameters to the model. The burning behaviors and combustion wave structures are dictated by the heat transfer from the flame zone to the unburned region. Five different models for the effective thermal conductivity of the mixture are employed. The impact of radiation heat transfer is also assessed. As a specific example, the case with a particle size of 79 μm is considered in detail. The burning rate remains nearly constant (<1 cm/s) up to a packing density of 60%, and then increases sharply toward the maximum value of 11.55 cm/s at a density of 100%. The Maxwell–Eucken–Bruggeman model of thermal conductivity offers the most accurate predictions of the burning rate for all loading densities.     

Performance of gas chlorination in decolourization of textile dyeing wastewater: a pilot study

This study presents performance of gas chlorination in decolourization/degradation of textile dyeing wastewater, optimisation of operating parameters and process kinetics of gas chlorination since it eliminates the generation of hazardous sludge and economical treatment method. The pH, contact time and chlorine dosage were found optimised at 9, 30 min and 300 ppm, respectively. Colour (m^?1) of raw effluent was found in the range of 17–85, 14–52 and 15–24 and after the treatment, it was 3–7, 2–4 and 1–3 complying with the International colour standards at 436, 525 and 620 nm wavelengths, respectively. The percentage of colour removal and COD degradation were in the range of 89–95 and 28–45, respectively. Rate of reaction on colour removal and COD degradation were behaved in first order with kinetic rate constant ranged from 0.274 to 0.373 (min^?1) and 0.046 to 0.103 (min^?1), respectively. Performance of colour removal was achieved better than COD degradation.     

Restoration of saline greenhouse soil and its effect on crop’s growth through in situ field-scale electrokinetic technology

An in situ electrokinetic (EK) system was designed and applied to highly saline greenhouse soil with a view to investigating the effects of the EK process on growing crops. In situ EK tests in field scale were conducted on the salt accumulated lands in the greenhouse where cabbages and lettuces were being cultivated. A voltage gradient of 0.25–0.6 V cm^?1 was applied for 50 days in the cultivated lands. The changes in the process, viz. current, voltage, and soil temperatures, were monitored. After the EK process, the initial electrical conductivity (EC, 6.0 dS m^?1) of the soil was reduced to about 1.7 dS m^?1 homogeneously below the recommended value (2.5 dS m^?1). The growth rate of cabbages and lettuces under EK treatment was about twice higher than those in the untreated area. The present study revealed that the EK process encourages the growth of the crops considerably and also removes the salts in the soil efficiently during the growth of the crops.