Protein structure prediction aided by geometrical and probabilistic constraints

Database-assisted ab initio protein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community-wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints.     

A bounded convection scheme for the overlapping control volume approach

This paper introduces a flux-limited scheme FLOCV for the overlapping control volume (OCV) approach to 2D steady and unsteady convection–diffusion problems on structured non-orthogonal grids. FLOCV switches from second- to first-order interpolation in the presence of extrema. Smooth switching between the two is ensured by weighted average second- and first-order upwind differencing, with the weights being dynamically determined. Five convective test problems are solved using this scheme and results are compared with known analytical solutions. It is found that FLOCV approximately retains second-order accuracy of the base discretization scheme on uniform grids and smooth non-uniform orthogonal grids. It is also found effective in removing oscillations for problems with discontinuities on both orthogonal and non-orthogonal grids, with little degradation of accuracy. © 1997 John Wiley & Sons, Ltd.     

Preparation and characterization of chemically deposited (Cd0.7‐Zn0.3)S:CdCl2,Gd nanocrystalline films

Nanocrystalline films of (Cd_0.7‐Zn_0.3)S:CdCl₂,Gd are prepared by chemical deposition technique on microscopic glass substrates with varied concentrations of capping agents thiophenol and methanol. The deposition is based on the principle of precipitation followed by condensation. Results of XRD, SEM, optical absorption spectra and photoluminescence emission spectra are presented. The crystalline nature of (Cd_0.7‐Zn_0.3)S:CdCl₂,Gd was found by XRD studies in which different diffraction peaks of CdS and ZnS are observed. The SEM micrographs show long tubes and irregular distributions of particles in presence of capping agents. The blue shift observed from optical absorption spectra in the present case indicates a quantization effect. Band gaps are also found to increase due to particle size reduction. The photoluminescence emission spectra show shift of peaks in the lower wavelength side due to reduction in particle size. The particle sizes are determined from optical absorption and XRD studies. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric

The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an α-helical lid (residues 82–96) away from the active site on moving from water (high dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic interactions play an important role in this process. We have used linearized Poisson–Boltzmann calculations to examine the key electrostatic interactions which contribute to lid stability in the closed and open states. It is the two charged residues of the lid, Arg86 and Asp91, that form the strongest electrostatic interactions with the rest of the protein. We identify key residues whose interactions with the lid are significantly perturbed by the change in the dielectric of the medium: Asp61, Arg80, Lys109, Glu117 and the active-site residues Asp203 and Asp256, all of which lie within approximately 20 ? of the lid. We suggest that these residues are good candidates for site-specific mutation studies, which could help elucidate their role in the lipase activation mechanism. Received: 27 May 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

Influence of simultaneous doping of Tl and Bi on microstructure and critical current density of HgBa2Ca2Cu3O8+δ

It has been found that simultaneous doping of Tl and Bi at Hg site of HgBa₂Ca₂Cu₃O_8+δ HTSC phase induces interesting microstructural variants in the form of long period polytypoid (LPP) like structure embodying native defect substructures. It has been observed that the as synthesized (HgTl_0.2−xBi_x)Ba₂Ca₂Cu₃O_8+δ (with x = 0.05, 0.10, 0.15) phases have superconducting onset transition temperature (T_c) of about ∼133 K. However, the intragrain critical current density (J_c) for the various materials with different compositions varies significantly. It varies from 6.2 × 10⁶ A/cm² to 2.9 × 10⁶ A/cm² at 5 K and 1 T for (HgTl_0.10Bi₁₀)Ba₂Ca₂Cu₃O_8+δ and (HgTl_0.15Bi_0.05)Ba₂Ca₂Cu₃O_8+δ HTSC phase respectively. A correlation between the intragrain J_c and the defect substructures has been found to be present. This correlation has been described and disscussed. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

On the Role of Interacting Particles and Limited Resources in the Regulation of Lattice Length Dynamics

Journal of Statistical Physics - Motivated by the significant effect of particle–particle interactions on the driven stochastic transport system, we examine how interacting particles control...     

Shock unsteadiness in a thrust optimized parabolic nozzle

This paper discusses the nature of shock unsteadiness, in an overexpanded thrust optimized parabolic nozzle, prevalent in various flow separation modes experienced during start up and shut down sequences. The results are based on simultaneously acquired data from real-time wall pressure measurements using Kulite pressure transducers, high-speed schlieren (2 kHz) of the exhaust flow-field and from strain-gauges installed on the nozzle bending tube. Shock unsteadiness in the separation region is seen to increase significantly just before the onset of each flow transition, even during steady nozzle operation. The intensity of this measure (rms level) is seen to be strongly influenced by relative locations of normal and overexpansion shock, the decrease in radial size of re-circulation zone in the back-flow region, and finally, the local nozzle wall contour. During restricted shock separation, the pressure fluctuations in separation region exhibit periodic characteristics rather than the usually observed characteristics of intermittent separation. The possible physical mechanisms responsible for the generation of flow unsteadiness in various separation modes are discussed. The results are from an experimental study conducted in P6.2 cold-gas subscale test facility using a thrust optimized parabolic nozzle of area-ratio 30.

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Surface flow studies of restricted shock separation in a thrust optimized parabolic nozzle

In this paper, surface flow features such as length of separation region and separation bubble are studied during restricted shock separation condition in a thrust optimized parabolic nozzle. It is found that peaks in the variation of these surface flow features are directly related to beginning of conditions for flow transition suggesting changes in exhaust flow features which are responsible for initiating flow transitions in a nozzle. Results are obtained from surface oil tests performed during the shut down phase for a range of nozzle pressure ratio during which restricted shock separation condition is prevalent.     

时间分辨与偏振红外光谱研究电场诱导下手性反铁电液晶的翻转过程

手性反铁电液晶分子中的各个不同片段、不同基团在电场诱导下展现不同的取向与取向分布.在交变电场的作用下,分子中各个部分的翻转动力学行为也表现的不同.