Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http://bioserver1.physics.iisc.ernet.in/hbcs/.

Properties of the correlated electronic states of pyrene and hydrogenated pyrene

Approximate calculations are reported on pyrene within the PPP model Hamiltonian using a novel restricted CI scheme which employs both molecular orbital and valence bond techniques. Also reported are detailed full CI results of the PPP model on 2,7-dihydropyrene obtained using the valence bond method. Spectral studies, charge and spin density calculations in ground and excited states, and ring current calculations in the ground state of the molecules are presented. In pyrene, the calculated excitation energies are in good agreement with experiment. The closed structure pi-conjugated molecule pyrene appears to show smaller distortions from the ground state geometry compared with the open structure pi-conjugated molecule 2,7-dihydropyrene. The ground state equilibrium structure of 2,7-dihydropyrene can be viewed as two hexatriene molecules connected by a vinyl crosslink, as is evident from bond order and ring current calculations. This is consistent with the only Kekule resonant structure possible for this molecule.

Studies on elastic coupling parameters of fracture modes in orthotropic materials

The characterisation of cracks is usually done using the well known three basic fracture modes, namely opening, shearing and tearing modes. In isotropic materials these modes are uncoupled and provide a convenient way to define the fracture parameters. It is well known that these fracture modes are coupled in anisotropic materials. In the case of orthotropic materials also, coupling exists between the fracture modes, unless the crack plane coincides with one of the axes of orthotropy. The strength of coupling depends upon the orientation of the axes of orthotropy with respect to the crack plane and so the energy release rate components associated with each of the modes vary with crack orientation. The variation, of these energy release rate components with the crack orientation with respect to orthotropic axes, is analyzed in this paper. Results indicate that in addition to the orthotropic planes there exists other planes with reference to which fracture modes are uncoupled.

Hydrogen bonding in peptide helices - Analysis of two independent helices in the crystal structure of a peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe

The crystal structure determination of the heptapeptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe reveals two peptide helices in the asymmetric unit, Crystal parameters are: space group P2(1), a = 10.356(2) Angstrom, b = 19.488(5) Angstrom, c = 23.756(6) Angstrom, beta = 102.25(2)degrees), V = 4685.4 Angstrom(3), Z = 4 and R = 5.7% for 7615 reflections [I>3 sigma(I)]. Both molecules adopt largely alpha-helical conformations with variations at the C-terminus, Helix type Is determined by analysing both 4-->1 and 5-->1 hydrogen-bond interactions and comparison with the results of analysis of protein structures. The presence of two 4-->1 hydrogen-bond interactions, besides four 5-->1 interact ions in both the conformations provides an opportunity to characterize bifurcated hydrogen bonds at high resolution, Comparison of the two helical conformations with related peptide structures suggests that distortions at the C-terminus are more facile than at the N-terminus.

Facile C-O bond scission in alcohols on Zn surfaces

Interaction of methanol, ethanol, and 2-propanol with polycrystalline as well as (0001) surfaces of Zn has been investigated by photoelectron spectroscopy and vibrational energy loss spectroscopy. All the alcohols show evidence for the condensed species along with the chemisorbed species at 80 K. With increase in temperature to similar to 120 K, the condensed species desorbs, leaving the chemisorbed species which decomposes to give the alkoxy species. The alkoxy species is produced increasingly at lower temperatures as we go from methanol to 2-propanol, the 2-propoxy species occurring even at 80 K. The alkoxy species undergo C-O bond scission giving rise to a hydrocarbon species and oxygen. The C-O bond cleavage occurs at a relatively low temperature of similar to 150 K. The effect of preadsorbed oxygen is to stabilize the methoxy species and prevent C-O bond scission. On the other hand, coadsorption of oxygen with methanol favors the formation of the methoxy species and gives rise to hydrocarbon species arising from the C-O bond scission even at 80 K.

Determination of diffusion parameters and activation energy of diffusion in V3Si phase with A15 crystal structure

Diffusion such is the integrated diffusion coefficient of the phase, the tracer diffusion coefficient of species at different temperatures and the activation energy for diffusion, are determined in V3Si phase with A15 crystal structure. The tracer diffusion coefficient of Si Was found to be negligible compared to the tracer diffusion coefficient of V. The calculated diffusion parameters will help to validate the theoretical analysis of defect structure of the phase, which plays an important role in the superconductivity.

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.

A probabilistic constrained nonlinear optimization framework to optimize RED parameters

The random early detection (RED) technique has seen a lot of research over the years. However, the functional relationship between RED performance and its parameters viz,, queue weight (omega(q)), marking probability (max(p)), minimum threshold (min(th)) and maximum threshold (max(th)) is not analytically availa ble. In this paper, we formulate a probabilistic constrained optimization problem by assuming a nonlinear relationship between the RED average queue length and its parameters. This problem involves all the RED parameters as the variables of the optimization problem. We use the barrier and the penalty function approaches for its Solution. However (as above), the exact functional relationship between the barrier and penalty objective functions and the optimization variable is not known, but noisy samples of these are available for different parameter values. Thus, for obtaining the gradient and Hessian of the objective, we use certain recently developed simultaneous perturbation stochastic approximation (SPSA) based estimates of these. We propose two four-timescale stochastic approximation algorithms based oil certain modified second-order SPSA updates for finding the optimum RED parameters. We present the results of detailed simulation experiments conducted over different network topologies and network/traffic conditions/settings, comparing the performance of Our algorithms with variants of RED and a few other well known adaptive queue management (AQM) techniques discussed in the literature.

The Influence of Processing Parameters on Characteristics of an Aluminum Alloy Spray Deposition

In the present investigation, two nozzle configurations are used for spray deposition, convergent nozzle (nozzle-A), and convergent nozzle with 2 mm parallel portion attached at its end (nozzle-C) without changing the exit area. First, the conditions for subambient aspiration pressure, i.e., pressure at the tip of the melt delivery tube, are established by varying the protrusion length of the melt delivery tube at different applied gas pressures for both of the nozzles. Using these conditions, spray deposits in a reproducible manner are successfully obtained for 7075 Al alloy. The effect of applied gas pressure, flight distance, and nozzle configuration on various characteristics of spray deposition, viz., yield, melt flow rate, and gas-to-metal ratio, is examined. The over-spray powder is also characterized with respect to powder size distribution, shape, and microstructure. Some of the results are explained with the help of numerical analysis presented in an earlier article.

Dependence of metal Auger intensity ratios on the effective charge on metal atoms

Metal Auger line intensity ratios were shown by Rao and others to be directly related to the occupancy of valence states. It is now shown that these intensity ratios are more generally related to the effective charge on the metal atom. The Auger intensity ratios are also directly proportional to valence band intensities of metals. Correlations of the intensity ratios with Auger parameters have also been examined.

He II spectra of La, Ce and Yb: Novel features in the valence band region

He II photoelectron spectra of La, Ce and Yb show features which cannot be explained in terms of single electron excitations. It is proposed that these are due to formation of electron-hole paris.

An E-Convergence Method For The Evaluation Of Critical Parameters

A simple cconversence technique is applied to obtain accurate estimates of critical temperatures and critical it\ponmts of a few two- and threpdiniensional king models. When applied to the virial series for hard spheres and hard discs, this method predicts a divergence of the equation-of-state at the density of closest packing.

Zeeman effect of chlorine nuclear quadrupole resonance and hydrogen bonding in 2,6-, 2,5- and 3,5-dichlorophenols

The Zeeman effect of chlorine nuclear quadrupole resonance in polycrystalline samples of 2,6-, 2,5 and 3,5-dichlorophenol has been investigated at room temperature in order to study the effect of hydrogen bonding on the electric field gradient asymmetry parameter n. While the two n.q.r. lines in 3,5-dichlorophenol gave an asymmetry parameter of 10%, those in 2,6- and 2,5-dichlorophenol gave different values of n for the two chlorines. The chlorine atom which is ortho to the OH group and involved in hydrogen bonding (i.e., corresponding to the low frequency line) gave an asymmetry parameter of 0.21 in 2,6-dichlorophenol and 0.17 in 2,5-dichlorophenol while the other chlorine (i.e., corresponding to the high frequency line) gave a lower value of 0.12 in 2,6-dichlorophenol and 0.11 in 2,5-dichlorophenol. These values of n are discussed in terms of hydrogen bonding and bond parameters.

Modeling of a pressure modulated desalination system using bond graph methodology

A desalination system is a complex multi energy domain system comprising power/energy flow across several domains such as electrical, thermal, and hydraulic. The dynamic modeling of a desalination system that comprehensively addresses all these multi energy domains is not adequately addressed in the literature. This paper proposes to address the issue of modeling the various energy domains for the case of a single stage flash evaporation desalination system. This paper presents a detailed bond graph modeling of a desalination unit with seamless integration of the power flow across electrical, thermal, and hydraulic domains. The paper further proposes a performance index function that leads to the tracking of the optimal chamber pressure giving the optimal flow rate for a given unit of energy expended. The model has been validated in steady state conditions by simulation and experimentation.