How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Structural, ferroelectric and optical properties of Bi2VO5.5 thin films deposited on platinized silicon {(100) Pt/TiO2/SiO2/Si} substrates

Bismuth vanadate (Bi2VO5.5, BVO) thin films have been deposited by a pulsed laser ablation technique on platinized silicon substrates. The surface morphology of the BVO thin films has been studied by atomic force microscopy (AFM). The optical properties of the BVO thin films were investigated using spectroscopic ellipsometric measurements in the 300–820 nm wavelength range. The refractive index (n), extinction coefficient (k) and thickness of the BVO thin films have been obtained by fitting the ellipsometric experimental data in a four-phase model (air/BVOrough/BVO/Pt). The values of the optical constants n and k that were determined through multilayer analysis at 600 nm were 2.31 and 0.056, respectively. For fitting the ellipsometric data and to interpret the optical constants, the unknown dielectric function of the BVO films was constructed using a Lorentz model. The roughness of the films was modeled in the Brugmann effective medium approximation and the results were compared with the AFM observations.

Dielectric, Ferroelectric and Relaxor Behavior of BaLaxBi4-xTi4O15 Ceramics

Monophasic BaLaxBi4-xTi4O15 (x = 0, 0.2, 0.4, 0.6 and 0.8) ceramics, fabricated from the powders synthesized via the solid-state reaction route exhibited relaxor behavior. Dielectric properties of the well sintered ceramics were measured in a wide frequency range (1 kHz-1 MHz) at different temperatures (300-750 K). The temperature of dielectri maximum (T-m) was found to decrease significantly from 696 K for an undoped sample (x = 0) to 395 K for the sample corresponding to the composition x = 0.8 accompanied by a decrease in the magnitude ofdielectric maximum (epsilon(m)). The temperature variation of the dielectric constant on the high temperature slope of the peak (T > T-m) was analyzed by using the Lorentz-ype quadratic law and the diffuseness of the peak was found to increase with increasing x. Vogel-Fulcher modelling of dielectric relaxation showed a decrease in freezing temperature (T-VF) (from 678 to 340 K) and an increase in the activation energy (5 to 24 meV) for the frequency dispersion with increase in x (La-3 divided by content). Strength of frequency dispersion of the phase transition increased with lanthanum content. Polarization (P)-electric field (E) hysteresis loops recorded at 373 showed a transition from a nearly squarish to slim loop hysteresis behavior with increasing lanthanum content.

Dielectric, pyroelectric and ferroelectric properties of Bi4Ti2.98Nb0.01Ta0.01O12 ceramics

The electrical conductivity and electrical relaxation for ferroelectric Bi4Ti2.98Nb0.01Ta0.01O12 (BTNT) ceramics have been reported in the frequency range 0.1 Hz to 1 MHz and in the 300-550 degrees C temperature range. The electrical data was analyzed in the framework of the dielectric as well as the electric modulus formalisms. The bulk dc conductivity at various temperatures was extracted from the electrical relaxation data. The activation energy associated with the electrical relaxation determined from the electric modulus spectra was found to be 0.93 +/- 0.03 eV, close to that of the activation energy for dc conductivity (1.03 +/- 0.02 eV). It suggests that the movements of oxygen ions are responsible for both ionic conduction as well as the relaxation process. The pyroelectric coefficient was found to be 12 mu C m(-2) K-1 at room temperature which is higher than that of the reported value of pyroelectric coefficient for undoped Bi4Ti3O12 ceramics. (C) 2010 Elsevier B.V. All rights reserved.

Infrared spectrum of ferroelectric lithium hydrazinium sulphate [Li (N2H5) SO4]

Dielectric observations on lithium hydrazinium sulphate have shown earlier that it is ferroelectric over a range of temperatures from below −15° C. to above 80° C. and a new type of hydrogen bond rearrangement which would allow the protons to migrate along the chain has also been suggested by others. The infrared spectrum of LiH z S in the form of mull and as single crystal sections parallel and perpendicular to the ‘C’ axis exhibit about 21 well-defined absorption maxima. The position and the width of the maxima agree with the known structure of the crystal according to which the hydrazine group exists in the form of the hydrazinium ion, NH2·NH3+ and the observed N+-H frequencies agree better with the new correlation curve given by R. S. Krishnan and K. Krishnan (1964). However it has been pointed out that from a comparative study of the new infrared spectra of hydrazonium sulphate and lithium ammonium sulphate that the absorption band at 969 cm.−1 is due to N-N stretching vibration and that the fairly intense band between 2050–2170 cm.−1 is due to the bending vibrations of the NH3+ group.

Dipole patterns in the structures of some ferroelectrics and antiferroelectrics

The dipole patterns in the ferroelectric and antiferroelectric structures are drawn according to experimentally determined symmetry changes in the ferroelectrics and antiferroelectrics. For the ferroelectrics the dipoles of the unit cells for one domain are oriented in parallel and the directions of the polarisation in the adjacent domains are at definite angles to each other. It is assumed for the antiferroelectrics, that the superstructural unit cell is formed by the adjacent cells of the paraelectrical modification; the subcells having the antiparallel directions of the polarisation. It is these superstructural cells of the antiferroelectrics that are determined during the experimental investigations of the antiferroelectrics. The superstructural cells of the adjacent domains are different. In one case, the difference is that in the adjacent domains, the directions of the polarisation in the subcells form an angle (e.g., in PbZrO3). In other cases the superstructural cells have not only different directions of the polarisation in the subcells but different signs of the enantiomorphism (e.g., NH4H2PO4). In the third case, the only difference is that the superstructural unit cells in the adjacent domains are turned by an angle to each other round the direction of the subcell polarisation [e.g., (NH4)2H3IO6], etc.

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently the employment of Cascade PSI-BLAST where we perform PSI-BLAST for many 'generations', initiating searches from new homologues as well. Such a rigorous propagation through generations of PSI-BLAST employs effectively the role of intermediates in detecting distant similarities between proteins. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is similar to 35% better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/similar to CASCADE/CascadeBlast.html.

Theoretical foundations for multiple rendezvous of glowworm-inspired mobile agents with variable local-decision domains

We present the theoretical foundations for the multiple rendezvous problem involving design of local control strategies that enable groups of visibility-limited mobile agents to split into subgroups, exhibit simultaneous taxis behavior towards, and eventually rendezvous at, multiple unknown locations of interest. The theoretical results are proved under certain restricted set of assumptions. The algorithm used to solve the above problem is based on a glowworm swarm optimization (GSO) technique, developed earlier, that finds multiple optima of multimodal objective functions. The significant difference between our work and most earlier approaches to agreement problems is the use of a virtual local-decision domain by the agents in order to compute their movements. The range of the virtual domain is adaptive in nature and is bounded above by the maximum sensor/visibility range of the agent. We introduce a new decision domain update rule that enhances the rate of convergence by a factor of approximately two. We use some illustrative simulations to support the algorithmic correctness and theoretical findings of the paper.

Effect of √-irradiation on the structure and dynamics of domains in triglycine selenate

A comparative study of the switching properties of pure and √-irradiated TGSe crystals has been carried out to see the effect of irradiation on the structure and dynamics of domains. The switching behaviour of √-irradiated TGSe has been found to be qualitatively similar to that of unirradiated crystal and this has been interpreted in terms of structural inhibition caused by the formation of radiolysis products as well as the difference between the domain structures of the unirradiated and irradiated samples. Confirmation of this has been obtained by studying the domain patterns using the etch method.

Polarization reversal studies in ferroelectric taap

Telluric Acid Ammonium Phosphate (Te(OH)62(NH4)H2PO4(NH4)2HPO4) reffered to as TAAP is a recently discovered class m ferroelectric.1 It undergoes FE-PE transition at 48°C. Switching studies in this crystal has been carried out in the temperature range -14°C to 39°C by applying fields up to 4 kV/cm. Measurements were carried out on (101) plates cut from the crystals grown from solution. X-ray irradiation was carried out at room temperature by means of an x-ray tube operating at 25 kV and 15 mA with copper target. Air drying silver paste was used as electrodes. Samples were checked for hysteresis loop using a modified Sawyer-Tower circuit. The Ps value obtained from the loop is 2.1 μC/cm2 which is comparable to the earlier reported value. It was however noticed that the loop was slightly shifted to right with respect to the origin indicating the presence of a small internal bias which was 100 V/cm in the virgin crystal. This bias could not be removed even after repeated crystallization. On irradiation the internal biasing field increased which was indicated by a further shift of the hysteresis loop. The bias seems to saturate at about 750 V/cm for which the crystal had to be irradiated for about 3 hours.

Evidence of ferromagnetic domains in the La0.67Ca0.33Mn0.9Fe0.1O3 perovskite

The nature of the low-temperature magnetic state of polycrystalline La0.67Ca0.33Mn0.9Fe0.1O3 has been studied by magnetization, neutron diffraction, and neutron depolarization measurements. Neutron depolarization measurements indicate the existence of ferromagnetic domains with low net magnetic moments below 108 K. The substitution of Mn3+ by Fe3+ reduces the number of available hopping sites for the Mn e(g) (up) electron and suppresses the double exchange, resulting in the reduction of ferromagnetic exchange. The competition between the ferromagnetic double-exchange interactions and the coexisting antiferromagnetic superexchange interactions and its randomness due to random substitutions of Mn3+ with Fe3+ drive the system into a randomly canted ferromagnetic state at low temperatures.