Ion channel formation by zervamicin-IIB. A molecular modelling study.

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomeric Zrv-IIB is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K+, Cl- and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are "optimized" in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.

Methyl ethyl ketone plus water plus secondary butyl alcohol: A potential system for the exploration of a quadruple critical point

We report preliminary experiments on the ternary-liquid mixture, methyl ethyl ketone (MEK)+water (W)+secondary butyl alcohol (sBA)-a promising system for the realization of the quadruple critical point (QCP). The unusual tunnel-shaped phase diagram shown by this system is characterized and visualized by us in the form of a prismatic phase diagram. Light-scattering experiments reveal that (MEK+W+sBA) shows near three-dimensional-Ising type of critical behavior near the lower critical solution temperatures, with the susceptibility exponent (gamma) in the range of 1.217 <=gamma <= 1.246. The correlation length amplitudes (xi(o)) and the critical exponent (nu) of the correlation length (xi) are in the ranges of 3.536 <=xi(o)<= 4.611 A and 0.619 <=nu <= 0.633, respectively. An analysis in terms of the effective susceptibility exponent (gamma(eff)) shows that the critical behavior is of the Ising type for MEK concentrations in the ranges of 0.1000 <= X <= 0.1250 and X >= 0.3000. But, for the intermediate range of 0.1750 <= X < 0.3000, the system shows a tendency towards mean-field type of critical behavior. The advantages of the system (MEK+W+sBA) over the system (3-methylpyridine+water+heavy water+potassium Iodide) for the realization of a QCP are outlined.

Flow structure and heat transfer characteristics behind a diaphragm in the presence of a diffusion flame

The characteristics of the separated flow behind a diaphragm over a burning surface are investigated experimentally. This complex problem of practical significance involving recirculation, blowing and combustion reactions is studied in a two-dimensional combustion tunnel. The flame structure, recirculation patterns and heat transfer to the surface are presented for a range of values of free stream and fuel injection velocities as well as for different heights of the diaphragm. The trends of heat transfer vs axial distance are shown to be similar to those resulting from a non-reactive heated stream with a diaphragm. Treating the case of a boundary layer diffusion flame as that corresponding to the zero height of the diaphragm, the heat transfer augmentation due to recirculation is estimated. It is found that at considerable downstream distances (xfh > 3), the heat transfer rates with diaphragm overtake the rates from a developing boundary layer case. Flow visualization studies with particle track photography show that there are many similarities between the reactive and the non-reactive cases.

Accelerometer-Based Force Balance for High Enthalpy Facilities

A single component accelerometer-based force balance is developed, calibrated, and used for high enthalpy applications. Functionality of this force balance, for such applications, is demonstrated for the first time during high enthalpy tests in a newly established free piston-driven shock tunnel, HST3, using a 60 degrees apex angle blunt cone model at 0 degrees angle of incidence. Usefulness of this force balance is also confirmed, for much complicated high enthalpy flow situations, during the drag reduction studies with counterflow supersonic jet from the stagnation point.

The contribution of polarons, bipolarons and intersite tunneling to low temperature conductivity in doped polypyrrole

The conductivity of highly doped polypyrrole is less than that of intermediately doped samples, by two orders of magnitude, at 4.2 K. This may be due to more number of bipolarons in highly doped samples. Bipolarons require four times more activation energy than single polarons to hop by thermally induced virtual transitions to intermediate dissociated polaron states than by the nondissociated process. The conduction process in these polyconjugated systems involve ionization from deep trapped states, having a View the MathML source dependence, hopping from localised states, having View the MathML source dependence, and intersite tunnel percolation, having T−1 dependence. The interplay of these factors leads to a better fit by View the MathML source. The mechanism for this exponential behaviour need not be same as that of Motts variable range hopping. Conduction by percolation is possible, if an infinite cluster of chains can be connected by impurity centers created by dopant ions. The tendency for the saturation of conductivity at very low temperatures is due to the possibility of intersite tunnel percolation is disordered polaronic systems.

Soft chemical synthesis of new layered and three-dimensional oxide hydrates, hxVxW1-xO3×yH2O, related to WO3×2 H2O and WO3. times.1/3 H2O

Two new vanadium-tungsten oxide hydrates of the formulas, H0.125V0.125W0.875O3.1.5H2O (I) and Ho.33V0.33W0.67O3.1/3H2O (II), have been synthesized by acid-leaching of LiVWO6 with aqueous HNO3/HCl. While phase I obtained by treatment of LiVWO6 with dilute HNO3/HCl possesses an orthorhombic structure (a = 7.77(3), b = 13.87(6), c = 7.44(3) angstrom) related to WO3.2H2O, phase II, prepared by refluxing LiVWO6 with concentrated HNO3, is isostructural with WO3.1/3H2O. Dehydration of II around 330-degrees-C yields a hexagonal phase (III, a = 7.25(4), c = 7.74(3) angstrom) isotypic with hexagonal WO3. Both land III exhibit redox and acid-base intercalation reactivity characteristic of layered and tunnel structures.

Wind loading over the top portions of tall stacks with and without external landing platforms

The variation of the drag force near the top portions of tall stacks with and without external landing platforms, and with the exit open and closed, has been examined by model studies in a wind tunnel at Reynolds numbers of about 10(5). Pressure measurements on three models of different height to diameter ratios have been supplemented by flow visualisation studies. Observations confirm that when there is no platform, significant load enhancement over the top three to four diameters occurs, due to the high suction caused by the sharp separation of the flow over the top from the rim, in the aft regions of the stack. The enhanced loading is found to be greater if the exit is closed. A platform at the top, of less than twice the exit diameter, further increases the drag force near the top, but a still larger platform at the top, of about three times the exit diameter, decreases the drag force to values less than those much further below, effectively nullifying the enhanced drag force. It was found that such a reduction of the enhanced drag force in the top regions can also be achieved by a smaller platform of 1.1 to 1.3 times the local diameter, located at about three to five diameters below the top.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Studies on the effects of test gas on the flow field around large angle blunt cone flying at hypersonic Mach number

The effect of the test gas on the flow field around a 120degrees apex angle blunt cone has been investigated in a shock tunnel at a nominal Mach number of 5.75. The shock standoff distance around the blunt cone was measured by an electrical discharge technique using both carbon dioxide and air as test gases. The forebody laminar convective heat transfer to the blunt cone was measured with platinum thin-film sensors in both air and carbon dioxide environments. An increase of 10 to 15% in the measured heat transfer values was observed with carbon dioxide as the test gas in comparison to air. The measured thickness of the shock layer along the stagnation streamline was 3.57 +/- 0.17 mm in air and 3.29 +/- 0.26 mm in carbon dioxide. The computed thickness of the shock layer for air and carbon dioxide were 3.98 mm and 3.02 mm, respectively. The observed increase in the measured heat transfer rates in carbon dioxide compared to air was due to the higher density ratio across the bow shock wave and the reduced shock layer thickness.

Two-channel Kondo physics in odd impurity chains

We study odd-membered chains of spin-1/2 impurities, with each end connected to its own metallic lead. For antiferromagnetic exchange coupling, universal two-channel Kondo (2CK) physics is shown to arise at low energies. Two overscreening mechanisms are found to occur depending on coupling strength, with distinct signatures in physical properties. For strong interimpurity coupling, a residual chain spin-1/2 moment experiences a renormalized effective coupling to the leads, while in the weak-coupling regime, Kondo coupling is mediated via incipient single-channel Kondo singlet formation. We also investigate models in which the leads are tunnel-coupled to the impurity chain, permitting variable dot filling under applied gate voltages. Effective low-energy models for each regime of filling are derived, and for even fillings where the chain ground state is a spin singlet, an orbital 2CK effect is found to be operative. Provided mirror symmetry is preserved, 2CK physics is shown to be wholly robust to variable dot filling; in particular, the single-particle spectrum at the Fermi level, and hence the low-temperature zero-bias conductance, is always pinned to half-unitarity. We derive a Friedel-Luttinger sum rule and from it show that, in contrast to a Fermi liquid, the Luttinger integral is nonzero and determined solely by the ``excess'' dot charge as controlled by gate voltage. The relevance of the work to real quantum dot devices, where interlead charge-transfer processes fatal to 2CK physics are present, is also discussed. Physical arguments and numerical renormalization-group techniques are used to obtain a detailed understanding of these problems.

Novel Algorithm for estimation of Swell Pressure of Fine Grained Soils Based on Diffuse Double Layer (DDL) Theory

Use of engineered landfills for the disposal of industrial wastes is currently a common practice. Bentonite is attracting a greater attention not only as capping and lining materials in landfills but also as buffer and backfill materials for repositories of high-level nuclear waste around the world. In the design of buffer and backfill materials, it is important to know the swelling pressures of compacted bentonite with different electrolyte solutions. The theoretical studies on swell pressure behaviour are all based on Diffuse Double Layer (DDL) theory. To establish a relation between the swell pressure and void ratio of the soil, it is necessary to calculate the mid-plane potential in the diffuse part of the interacting ionic double layers. The difficulty in these calculations is the elliptic integral involved in the relation between half space distance and mid plane potential. Several investigators circumvented this problem using indirect methods or by using cumbersome numerical techniques. In this work, a novel approach is proposed for theoretical estimations of swell pressures of fine-grained soil from the DDL theory. The proposed approach circumvents the complex computations in establishing the relationship between mid-plane potential and diffused plates’ distances in other words, between swell pressure and void ratio.

Design enhancement of the underwater noise control linings through a parsimonious parametric study

Control of sound transmission through the structure and reflection from the structure immersed in fluid media impose highly conflicting requirements on the design of the carpeted noise control linings. These requirements become even more stringent if the structure is expected to be moving with considerable speed particularly under intense hydrostatic pressure. Numerous configurations are possible for designing these linings. Therefore, in this paper, a few lining configurations are identified from the literature for parametric study so that the designer is provided with an environment to analyze and design the lining. A scheme of finite element analysis is used to analyze these linings for their acoustic performance. Commercial finite element software, NISA®, is used as a platform to develop a customized environment wherein design parameters of different configurations can be varied with consistency checks and generate the finite element meshes using the 8-noded hexahedral element. Four types of designs proposed and analysed here address the parameters of interest such as the echo reduction and the transmission loss. Study of the effect of different surface distributions of the cavities is carried out. Effect of static pressure on different designs is reported.

Universality of scaling laws in correlation between velocity and shear stress in turbulent boundary layers

In this study, we analyse simultaneous measurements (at 50 Hz) of velocity at several heights and shear stress at the surface made during the Utah field campaign for the presence of ranges of scales, where distinct scale-to-scale interactions between velocity and shear stress can be identified. We find that our results are similar to those obtained in a previous study [Venugopal et al., 2003] (contrary to the claim in V2003, that the scaling relations might be dependent on Reynolds number) where wind tunnel measurements of velocity and shear stress were analysed. We use a wavelet-based scale-to-scale cross-correlation to detect three ranges of scales of interaction between velocity and shear stress, namely, (a) inertial subrange, where the correlation is negligible; (b) energy production range, where the correlation follows a logarithmic law; and (c) for scales larger than the boundary layer height, the correlation reaches a plateau.

Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum

The beta-hydroxyacyl-acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ is available in hexameric (active) and dimeric (inactive) forms. However, PfFabZ has not been crystallized with any bound inhibitors until now. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of four of these complexes. This is the first report on any FabZ enzyme with active site inhibitors that interact directly with the catalytic residues. Inhibitor binding not only stabilized the substrate binding loop but also revealed that the substrate binding tunnel has an overall shape of ``U''. In the crystal structures, residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed. Thus, Phe169, merely by changing its side chain conformation, appears to be controlling the length of the tunnel to make it suitable for accommodating longer substrates. The volume of the substrate binding tunnel is determined by the sequence as well as by the conformation of the substrate binding loop region and varies between organisms for accommodating fatty acids of different chain lengths. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. (C) 2011 Elsevier Inc. All rights reserved.

Aerodynamic Load Measurements at Hypersonic Speeds Using Internally Mounted Fiber-Optic Balance System

This paper describes the measurement of aerodynamic loads using fiber-optic strain gauge sensors and associated signal processors at hypersonic speeds in the 300mm hypersonic wind tunnel. at the Department of Aerospace Engineering, Indian Institute of Science. Fiber-optic sensors have been developed in USA since 1990, for variety of applications in experimental stress analysis, skin friction measurement in fluid flows, smart structures, smart materials, sensing of acoustic emission and more recently in the development of compact devices for measurement of displacement, stress/strain, pressure, temperature, acceleration etc. Our group at llSc has been playing a lead role in the use of these fiber - optic sensors for successful measurement of aerodynamic loads in wind tunnels and the first ever six-component wind tunnel strain gauge balance in the world based on fiber optic sensors was built at the Indian Institute of Science in the year 1999. We report here the results of our efforts in the development of an internal strain gauge balance for high-speed wind tunnel applications.