Effect of soil tillage on erosion and nutrient transport in plough layer runoff

Yhteenveto: Viljelymenetelmien vaikutus eroosioon ja ravinteiden huuhtoutumiseen

Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

Effect of natural ventilation on the boundary layer separation and near-wake vortex shedding characteristics of a sphere

Experiments were conducted in water and wind tunnels on spheres in the Reynolds number range 6 x 10(3) to 6.5 x 10(5) to study the effect of natural ventilation on the boundary layer separation and near-wake Vortex shedding characteristics. In the subcritical range of Re (<2 x 10(5)), ventilation caused a marginal downstream shift in the location of laminar boundary layer separation; there was only a small change in the vortex shedding frequency. In the supercritical range (Re > 4 x 10(5)), ventilation caused a downstream shift in the mean locations of boundary layer separation and reattachment; these lines showed significant axisymmetry in the presence of venting. No distinct vortex shedding frequency was found. Instead, a dramatic reduction occurred in the wake unsteadiness at all frequencies. The reduction of wake unsteadiness is consistent with the reduction in total drag already reported. Based on the present results and those reported earlier, the effects of natural ventilation on the flow past a sphere can be categorized in two broad regimes, viz., weak and strong interaction regimes. In the weak interaction regime (subcritical Re), the broad features of the basic sphere are largely unaltered despite the large addition of mass in the near wake. Strong interaction is promoted by the closer proximity of the inner and outer shear layers at supercritical Re. This results in a modified and steady near-wake flow, characterized by reduced unsteadiness and small drag.

Effect of surfactants on drop breakage in turbulent liquid dispersions

The existingm odels of drop breakage in stirred dispersions grossly overpredict the maximum drop size when surface active agents are present inspite of using the lowered value of interfacial tension. It is shown that the difference in the values of dynamic and static interfacial tension, aids the turbulent stresses in drop breakage. When the difference is zero, e.g. for pure liquids and for high concentration of surfactants, the influence of the addition of surfactant is merely to reduce the interfacial tension and can be accounted for by existingm odels. A modified model has been developed, where the drop breakage is assumed to be represented by a Voigt element. The deforming stresses are due to turbulence and the difference between dynamic and static interfacial tensions. The resisting stresses arise due to interfacial tension and the viscous flow inside the drop. The model yields the existing expressions for dmax as special cases. The model has been found to be satisfactory when tested against experimental results using the styrene-water-teepol system.

A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G(7)) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of similar to1.5 Angstrom from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400 K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

The effect of structure on the dilute solution properties of branched polysaccharides studied with SEC and AsFlFFF

Cereal arabinoxylans, guar galactomannans, and dextrans produced by lactic acid bacteria(LAB) are a structurally diverse group of branched polysaccharides with nutritional and industrial functions. In this thesis, the effect of the chemical structure on the dilute solution properties of these polysaccharides was investigated using size-exclusion chromatography(SEC) and asymmetric flow field-flow fractionation (AsFlFFF) with multiple-detection. The chemical structures of arabinoxylans were determined, whereas galactomannan and dextran structures were studied in previous investigations. Characterization of arabinoxylans revealed differences in the chemical structures of cereal arabinoxylans. Although arabinoxylans from wheat, rye, and barley fiber contained similar amounts of arabinose side units, the substitution pattern of arabinoxylans from different cereals varied. Arabinoxylans from barley husks and commercial low-viscosity wheat arabinoxylan contained a lower number of arabinose side units. Structurally different dextrans were obtained from different LAB. The structural effects on the solution properties could be studied in detail by modifying pure wheat and rye arabinoxylans and guar galactomannan with specific enzymes. The solution characterization of arabinoxylans, enzymatically modified galactomannans, and dextrans revealed the presence of aggregates in aqueous polysaccharide solutions. In the case of arabinoxylans and dextrans, the comparison of molar mass data from aqueous and organic SEC analyses was essential in confirming aggregation, which could not be observed only from the peak or molar mass distribution shapes obtained with aqueous SEC. The AsFlFFF analyses gave further evidence of aggregation. Comparison of molar mass and intrinsic viscosity data of unmodified and partially debranched guar galactomannan, on the other hand, revealed the aggregation of native galactomannan. The arabinoxylan and galactomannan samples with low or enzymatically extensively decreased side unit content behaved similarly in aqueous solution: lower molar mass samples stayed in solution but formed large aggregates, whereas the water solubility of the higher-molar-mass samples decreased significantly. Due to the restricted solubility of galactomannans in organic solvents, only aqueous galactomannan solutions were studied. The SEC and AsFlFFF results differed for the wheat arabinoxylan and dextran samples. Column matrix effects and possible differences in the separation parameters are discussed, and a problem related to the non-established relationship between the separation parameters of the two separation techniques is highlighted. This thesis shows that complementary approaches in the solution characterization of chemically heterogeneous polysaccharides are needed to comprehensively investigate macromolecular behavior in solution. These results may also be valuable when characterizing other branched polysaccharides.

Effect of HCl on the adsorption of oxygen on Cu(110) surface: An eels study

Oxygen is shown to adsorb molecularly on a clean Cu(110) surface at 80 K and dissociate around 150 K forming atomic oxygen. Adsorption of oxygen on an HCl covered surface at low temperatures results in the formation of adsorbed hydroxyl groups and water in addition to adsorbed molecular oxygen. The molecular oxygen species is stable up to 190 K on the HCl covered surface.

A Study on Effect of Wetting on Mechanism of Coalescence in a Model Coalescer

In order to depict the mechanism of coalescence in fibrous bed coalescers, a model coalescer was fabricated. Both water/oil and oil/water dispersions were run through this model coalescer to check for coalescence on PTFE and glass surfaces. The equilibrium contact angle and the dynamic contact angle of the dispersed drops were measured on these surfaces in the presence of the continuous phase. Coalescence was monitored using a microscope. Based on these observations a mechanism of coalescence in the model coalescer is proposed. Different modes of coalescence are correlated to the equilibrium contact angle and the dynamic contact angle. Deposition of dirt on the coalescing surface is observed to result in change of wettability, leading to redispersion of the already coalesced dispersed phase into larger droplets.

Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Effect of heat-treatment on strength of clays

The main objective of this investigation was to understand the strength development of clays below fusion or vitrification temperatures of 900°C. The other objective was to establish threshold temperatures to produce a satisfactory construction material from clayey sediments from the Western Beaufort Sea for shore protection of artificial islands with minimum expense of thermal energy. Studies were, therefore, conducted using kaolinite, bentonite, and a clayey sediment from the Beaufort Sea. Unconfined-compressive-strength tests were conducted on clay samples heat treated from 110 to 700°C. Furthermore, to understand the factors responsible for strength-development-thermogravimetric studies and pore-size analysis, using mercury porosimetry, were also conducted. A gradual increase in strength was obtained with an increase in firing temperature. However, substantial and permanent increase in strength occurred only after dehydroxylation of all the clays studied; Clay samples heated to temperatures above dehydroxylation became resistant to disintegration upon immersion in water. Results indicate that the clayey sediments from Western Beaufort Sea have to be heat treated to about 600°C to produce granular material for use as a fill or shore-protection material for artificial islands.

A note on the effect of wall compliance on lowest?order mode propagation in fluid?filled/submerged impedance tubes

Wave propagation in fluid?filled/submerged tubes is of interest in large HVAC ducts, and also in understanding and interpreting the experimental results obtained from fluid?filled impedance tubes. Based on the closed form analytical solution of the coupled wave equations, an eigenequation, which is the determinant of an 8×8 matrix, is derived and solved to obtain the axial wave number of the lowest?order longitudinal modes for cylindrical ducts of various diameter and wall thickness. The dispersion behavior of the wave motion is analyzed. It is observed that the larger the diameter of the duct and/or the smaller its wall thickness, the more flexible the impedance tube leading to more coupling between the waves in the elastic media. Also, it is shown that the wave motion in water?filled ducts submerged in water exhibits anomalous dispersion behavior. The axial attenuation characteristics of plane waves along water?filled tubes submerged in water or air are also investigated. Finally, investigations on the sound intensity level difference characteristics of the wall of the air?filled tubes are reported.

The effect of constituent metal ions on the electrokinetics of chalcopyrite

Chalcopyrite in contact with water is thermodynamically unstable in the presence of oxygen. Oxidation of chalcopyrite may take place due to various factors, e.g., geological environment, mining/comminution, and storage. In this work oxidation of chalcopyrite has been investigated through interfacial electrokinetics. The characteristics of samples obtained from different geological locations as well as the effects of ageing and laboratory oxidation have been delineated. Variation of the solid-liquid ratio was found to have a significant effect on the zeta-potential characteristics of chalcopyrite. The role of constituent metal ions, namely copper and iron, has been studied in the absence and presence of externally added metal ions. The results indicated that the ratio of Cu/Fe on the surface of oxidized chalcopyrite determines the Stern layer potential and under appropriate solution chemistry conditions influences charge reversals. The mineral surfaces, thus, could be either copper-rich or iron-rich as reflected by a shift in pH(iep),,(s). The observed charge reversals have been explained on the basis of a model proposed by James and Healy. (C) 1997 Academic Press.

Effect of absorption in aqueous and hygrothermal media on the compressive properties of glass fiber reinforced syntactic foam

Absorption due to immersion in aqueous media consisting of either saline or seawater or due to exposure to water vapor conditions and the attendant effect on the compressive properties of syntactic foam reinforced with E-glass fibers in the form of chopped strands were studied. Whereas the compressive strength decreased in samples exposed to water vapor, the saline or seawater immersed samples showed increase when compared to the dry sample. The decrease in strength in the vapor-exposed case is ascribed to higher absorption of water and to debonding and damaged features for interfaces. The enhancement of strength values for the samples immersed in saltish media is traced to the larger size of the chloride ion and resultant changes in the stress state around the fiber-bearing regions. Recourse to an analysis of scanning electron microscopic pictures of the compression-failed samples is taken to explain the observed trends.