Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Impact of water drops onto the junction of a hydrophobic texture and a hydrophilic smooth surface

Wettability gradient surfaces play a significant role in control and manipulation of liquid drops. The present work deals with the analysis of water drops impacting onto the junction line between hydrophobic texture and hydrophilic smooth portions of a dual-textured substrate made using stainless steel material. The hydrophobic textured portion of the substrate comprised of unidirectional parallel groove-like and pillar-like structures of uniform dimensions. A high-speed video camera recorded the spreading and receding dynamics of impacting drops. The drop impact dynamics during the early inertia driven impact regime remains unaffected by the dual-texture feature of the substrate. A larger retraction speed of drop liquid observed on the hydrophobic portion of the substrate during the impact of low velocity drops makes the drop liquid on the higher wettability portion to advance further (secondary drop spreading). The net horizontal drop velocity towards the hydrophilic portion of the dual-textured substrate decreases with increasing drop impact velocity. The available experimental results suggest that the movement of bulk drop liquid away from the impact point during drop impact on the dual-textured substrate is larger for the impact of low inertia drops. (C) 2010 Elsevier B.V. All rights reserved.

Geometries of the antiproton-nucleus optical potentials at 180 MeV

The moments of the real and the absorptive parts of the antiproton optical potentials are evaluated for the first time to study the geometries of the potentials at 180 MeV. Interesting features are revealed which are found to be comparable to the proton case in general despite the presence of strong annihilation. A few interesting deviations, however, are also found compared to the proton case.

Studies in biogas technology. Part IV. A novel biogas plant incorporating a solar water-heater and solar still

A reduction in the heat losses from the top of the gas holder of a biogas plant has been achieved by the simple device of a transparent cover. The heat losses thus prevented have been deployed to heat a water pond formed on the roof of the gas holder. This solar-heated water is mixed with the organic input for ‘ hot-charging ’ of the biogas plant. A thermal analysis of such a solar water-heater ‘ piggy-backing ’ on the gas holder of a biogas plant has been carried out.To test whether the advantages indicated by the thermal analysis can be realised in practice, a biogas plant of the ASTRA design was modified to incorporate a roof-top solar water-heater. The operation of such a modified plant, even under ‘ worst case ’ onditions, shows a significant improvement in the gas yield compared to the unmodified plant. Hence, the innovation reported here may lead to drastic reductions in the sizes and therefore costs of biogas plants. By making the transparent cover assume a tent-shape, the roof-top solar heater can serve the additional function of a solar still to yield distilled water. The biogas plant-cum-solar water-heater-cum-solar still described here is an example of a spatially integrated hybrid device which is extremely cost-effective.

Potentiodynamic behaviour of β-lead dioxide in neutral media at positive potentials

The behaviour of the PbO2 electrode in NaNO3, Na2SO4 NaClO4 and NaCl in the pH range 3.0–10.5 has been studied by cyclic voltammetry. When the electrode is cycled between 0.30 and 1.90 V, a large cathodic current peak appears in the negative scan; in the subsequent cycle, two anodic peaks appear. The addition of H2O2 at low concentrations to the electrolyte also results in two anodic peaks at the same potentials. A number of possible explanations for the appearance of the cathodic peak, and a mechanism for the oxidation of PbO to PbO2 through Pb3O4 corresponding to the two anodic peaks, are proposed.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

A simple n-state model for water

A simple n-state configurational excitation model which takes into account the presence of weakly connected pentamer units in liquid water is proposed. The model has features of both the “continuum” and “mixture” models. Calculations based on this model satisfactorily account for the important, diagnostic thermodynamic properties of water such as the density maximum, fraction of monomers and so on.

Signal subspace approach in localization of sound source in shallow water

A new algorithm based on signal subspace approach is proposed for localizing a sound source in shallow water. In the first instance we assumed an ideal channel with plane parallel boundaries and known reflection properties. The sound source is assumed to emit a broadband stationary stochastic signal. The algorithm takes into account the spatial distribution of all images and reflection characteristics of the sea bottom. It is shown that both range and depth of a source can be measured accurately with the help of a vertical array of sensors. For good results the number of sensors should be greater than the number of significant images; however, localization is possible even with a smaller array but at the cost of higher side lobes. Next, we allowed the channel to be stochastically perturbed; this resulted in random phase errors in the reflection coefficients. The most singular effect of the phase errors is to introduce into the spectral matrix an extra term which may be looked upon as a signal generated coloured noise. It is shown through computer simulations that the signal peak height is reduced considerably as a consequence of random phase errors.

Solution of a Boundary-Value Problem associated with Diffraction of Water Waves by a Nearly Vertical Barrier

An exact solution is derived for a boundary-value problem for Laplace's equation which is a generalization of the one occurring in the course of solution of the problem of diffraction of surface water waves by a nearly vertical submerged barrier. The method of solution involves the use of complex function theory, the Schwarz reflection principle, and reduction to a system of two uncoupled Riemann-Hilbert problems. Known results, representing the reflection and transmission coefficients of the water wave problem involving a nearly vertical barrier, are derived in terms of the shape function.

Entropy and dynamics of water in hydration layers of a bilayer

We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (T Delta S) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules. (C) 2010 American Institute of Physics. doi:10.1063/1.3494115]

Empirical torsional potential functions from protiesn structure DATA Phi- and Psi-Potentials for Non-glycyl Amino Acid Residues

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα-C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)-plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l-configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°). The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Influence of Osmotic Suction on the Soil-Water Characteristic Curves of Compacted Expansive Clay

Unsaturated clays are subject to osmotic suction gradients in geoenvironmental engineering applications and it therefore becomes important to understand the effect of these chemical concentration gradients on soil-water characteristic curves (SWCCs). This paper brings out the influence of induced osmotic suction gradient on the wetting SWCCs of compacted clay specimens inundated with sodium chloride solutions/distilled water at vertical stress of 6.25 kPa in oedometer cells. The experimental results illustrate that variations in initial osmotic suction difference induce different magnitudes of osmotic induced consolidation and osmotic consolidation strains thereby impacting the wetting SWCCs and equilibrium water contents of identically compacted clay specimens. Osmotic suction induced by chemical concentration gradients between reservoir salt solution and soil-water can be treated as an equivalent net stress component, (p(pi)) that decreases the swelling strains of unsaturated specimens from reduction in microstructural and macrostructural swelling components. The direction of osmotic flow affects the matric SWCCs. Unsaturated specimens experiencing osmotic induced consolidation and osmotic consolidation develop lower equilibrium water content than specimens experiencing osmotic swelling during the wetting path. The findings of the study illustrate the need to incorporate the influence of osmotic suction in determination of the matric SWCCs.

Structure of a cyclic water tetramer in a nucleotide crystal host and a hypothetical model for water cluster growth

Structure of a cyclic water tetramer in channels (pores) formed by self-assembly of N6-methyl-5'-AMP center dot Na-2 molecules is described and a hypothetical model is proposed for growth of water clusters. (C) 2010 Elsevier B.V. All rights reserved.