On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (DeltaCp), enthalpy (DeltaH) and entropy (DeltaS) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (DeltaCp) and enthalpy (DeltaH) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

Microstructural evolution of tungsten oxide thin films

Tungsten oxide thin films are of great interest due to their promising applications in various optoelectronic thin film devices. We have investigated the microstructural evolution of tungsten oxide thin films grown by DC magnetron sputtering on silicon substrate. The structural characterization and surface morphology were carried out using X-ray diffraction and Scanning Electron Microscopy (SEM). The as deposited films were amorphous, where as, thin films annealed above 400 degrees C were crystalline. In order to explain the microstructural changes due to annealing, we have proposed a ``instability wheel'' model for the evolution of the microstructure. This model explains the transformation of mater into various geometries within them selves, followed by external perturbation.

Topological close packed mu phase formation and the determination of diffusion parameters in the Co-Mo system

The study on the formation and growth of topological close packed (TCP) compounds is important to understand the performance of turbine blades in jet engine applications. These deleterious phases grow mainly by diffusion process in the superalloy substrate. Significant volume change was found because of growth of the p phase in Co-Mo system. Growth kinetics of this phase and different diffusion parameters, like interdiffusion, intrinsic and tracer diffusion coefficients are calculated. Further the activation energy, which provides an idea about the mechanism, is determined. Moreover, the interdiffusion coefficient in Co(Mo) solid solution and impurity diffusion coefficient of Mo in Co are determined.

Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H-nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin

Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.

Characterization of anomalous relaxation using the time-fractional Bloch equation and multiple echo T2 *-weighted magnetic resonance imaging at 7T

PURPOSE To study the utility of fractional calculus in modeling gradient-recalled echo MRI signal decay in the normal human brain. METHODS We solved analytically the extended time-fractional Bloch equations resulting in five model parameters, namely, the amplitude, relaxation rate, order of the time-fractional derivative, frequency shift, and constant offset. Voxel-level temporal fitting of the MRI signal was performed using the classical monoexponential model, a previously developed anomalous relaxation model, and using our extended time-fractional relaxation model. Nine brain regions segmented from multiple echo gradient-recalled echo 7 Tesla MRI data acquired from five participants were then used to investigate the characteristics of the extended time-fractional model parameters. RESULTS We found that the extended time-fractional model is able to fit the experimental data with smaller mean squared error than the classical monoexponential relaxation model and the anomalous relaxation model, which do not account for frequency shift. CONCLUSIONS We were able to fit multiple echo time MRI data with high accuracy using the developed model. Parameters of the model likely capture information on microstructural and susceptibility-induced changes in the human brain.

Influence of roughness parameters and surface texture on friction during sliding of pure lead over 080 M40 steel

In the present investigation, tests were conducted on a tribological couple made of cylindrical lead pin with spherical tip against 080 M40 steel plates of different textures with varying roughness under both dry and lubricated conditions using an inclined pin-on-plate sliding tester. Surface roughness parameters of the steel plates were measured using optical profilometer. The morphologies of the worn surfaces of the pins and the formation of transfer layer on the counter surfaces were observed using a scanning electron microscope. It was observed that the coefficient of friction and the formation of transfer layer depend primarily on the surface texture of hard surfaces. A newly formulated non-dimensional hybrid roughness parameter called 'xi' (a product of number of peaks and maximum profile peak height) of the tool surface plays an important role in determining the frictional behaviour of the surfaces studied. The effect of surfaces texture on coefficient of friction was attributed to the variation of plowing component of friction, which in turn depends on the roughness parameter 'xi'.

Comparison of performance parameters of poly(3,4 ethylenedioxythiophene) (PEDOT) based electrochromic device on glass with and without counter electrode

Conjugated polymers are promising materials for electrochromic device technology. Aqueous dispersions of poly(3,4-ethylenedioxythiophene)-(PEDOT) were spin coated onto transparent conducting oxide (TCO) coated glass substrates. A seven-layer electrochromic device was fabricated with the following configuration: glass/transparent conducting oxide (TCO)/PEDOT (main electrochromic layer)/gel electrolyte/prussian blue (counter electrode)/TCO/glass. The device fabricated with counter electrode (Prussian blue) showed a contrast of 18% and without counter electrode showed visible contrast of 5% at 632 nm at a voltage of 1.9 V. The comparison of the device is done in terms of the colouration efficiency of the devices with and without counter electrode.

Gaussian mixture model based switched split vector quantization of LSF parameters

We address the issue of rate-distortion (R/D) performance optimality of the recently proposed switched split vector quantization (SSVQ) method. The distribution of the source is modeled using Gaussian mixture density and thus, the non-parametric SSVQ is analyzed in a parametric model based framework for achieving optimum R/D performance. Using high rate quantization theory, we derive the optimum bit allocation formulae for the intra-cluster split vector quantizer (SVQ) and the inter-cluster switching. For the wide-band speech line spectrum frequency (LSF) parameter quantization, it is shown that the Gaussian mixture model (GMM) based parametric SSVQ method provides 1 bit/vector advantage over the non-parametric SSVQ method.

Computationally efficient optimum weighting function for vector quantization of LSF parameters

We propose a new weighting function which is computationally simple and an approximation to the theoretically derived optimum weighting function shown in the literature. The proposed weighting function is perceptually motivated and provides improved vector quantization performance compared to several weighting functions proposed so far, for line spectrum frequency (LSF) parameter quantization of both clean and noisy speech data.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

Microstructural stability and creep in nanocrystals

Microstructural stability is an important consideration during high temperature deformation and processing of nanomaterials. We will address issues relating to triple junctions in limiting grain growth during creep as well as densification. Although early studies on deformation have considered diffusion creep as a possible rate controlling deformation mechanism in nanocrystals, a critical inspection of available data indicates that there is no strong evidence for conventional diffusion creep in such materials. The possibility of diffusion creep by rapid diffusion along triple junctions will be analyzed, and interface controlled diffusion creep will also be discussed critically. It is shown that the critical grain size for dislocation activity is similar to that for occurrence of conventional diffusion creep.

Influence of surface texture and roughness parameters on friction and transfer layer formation during sliding of aluminium pin on steel plate

Surface texture of harder mating surfaces plays an important role during sliding against softer materials and hence the importance of characterizing the surfaces in terms of roughness parameters. In the present investigation, basic studies were conducted using inclined pin-on-plate sliding tester to understand the surface texture effect of hard surfaces on coefficient of friction and transfer layer formation. A tribological couple made of a super purity aluminium pin against steel plate was used in the tests. Two surface parameters of steel plates, namely roughness and texture, were varied in the tests. It was observed that the transfer layer formation and the coefficient of friction along with its two components, namely, the adhesion and plowing, are controlled by the surface texture and are independent of surface roughness (R-a). Among the various surface roughness parameters, the average or the mean slope of the profile was found to explain the variations best. Under lubricated conditions, stick-slip phenomena was observed, the amplitude of which depends on the plowing component of friction. The presence of stick-slip motion under lubricated conditions could be attributed to the molecular deformation of the lubricant component confined between asperities. (C) 2009 Elsevier B. V. All rights reserved.

Numerical studies on channel formation and growth during solidification: Effect of process parameters

In the present work, solidification of a hyper-eutectic ammonium chloride solution in a bottom-cooled cavity (i.e. with stable thermal gradient) is numerically studied. A Rayleigh number based criterion is developed, which determines the conditions favorable for freckles formation. This criterion, when expressed in terms of physical properties and process parameters, yields the condition for plume formation as a function of concentration, liquid fraction, permeability, growth rate of a mushy layer and thermophysical properties. Subsequently, numerical simulations are performed for cases with initial and boundary conditions favoring freckle formation. The effects of parameters, such as cooling rate and initial concentration, on the formation and growth of freckles are investigated. It was found that a high cooling rate produced larger and more defined channels which are retained for a longer durations. Similarly, a lower initial concentration of solute resulted in fewer but more pronounced channels. The number and size of channels are also found to be related to the mushy zone thickness. The trends predicted with regard to the variation of number of channels with time under different process conditions are in accordance with the experimental observations reported in the literature.

ZnO nanocrystalline thin films: a correlation of microstructural, optoelectronic properties

The compositional, structural, microstructural, dc electrical conductivity and optical properties of undoped zinc oxide films prepared by the sol-gel process using a spin-coating technique were investigated. The ZnO films were obtained by 5 cycle spin-coated and dried zinc oxide films followed by annealing in air at 600 A degrees C. The films deposited on the platinum coated silicon substrate were crystallized in a hexagonal wurtzite form. The energy-dispersive X-ray (EDX) spectrometry shows Zn and O elements in the products with an approximate molar ratio. TEM image of ZnO thin film shows that a grain of about 60-80 nm in size is really an aggregate of many small crystallites of around 10-20 nm. Electron diffraction pattern shows that the ZnO films exhibited hexagonal structure. The SEM micrograph showed that the films consist in nanocrystalline grains randomly distributed with voids in different regions. The dc conductivity found in the range of 10(-5)-10(-6) (Omega cm)(-1). The optical study showed that the spectra for all samples give the transparency in the visible range.