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.

Strip based coding for large images using wavelets

Thanks to advances in sensor technology, today we have many applications (space-borne imaging, medical imaging, etc.) where images of large sizes are generated. Straightforward application of wavelet techniques for above images involves certain difficulties. Embedded coders such as EZW and SPIHT require that the wavelet transform of the full image be buffered for coding. Since the transform coefficients also require storing in high precision, buffering requirements for large images become prohibitively high. In this paper, we first devise a technique for embedded coding of large images using zero trees with reduced memory requirements. A 'strip buffer' capable of holding few lines of wavelet coefficients from all the subbands belonging to the same spatial location is employed. A pipeline architecure for a line implementation of above technique is then proposed. Further, an efficient algorithm to extract an encoded bitstream corresponding to a region of interest in the image has also been developed. Finally, the paper describes a strip based non-embedded coding which uses a single pass algorithm. This is to handle high-input data rates. (C) 2002 Elsevier Science B.V. All rights reserved.

An extended Cahn-Hilliard model for interfaces with cubic anisotropy

For studying systems with a cubic anisotropy in interfacial energy sigma, we extend the Cahn-Hilliard model by including in it a fourth-rank term, namely, gamma (ijlm) [partial derivative (2) c/(partial derivativex(i) partial derivativex(j))] [partial derivative (2) c/(partial derivativex(l) partial derivativex(m))]. This term leads to an additional linear term in the evolution equation for the composition parameter field. It also leads to an orientation-dependent effective fourth-rank coefficient gamma ([hkl]) in the governing equation for the one-dimensional composition profile across a planar interface. The main effect of a non-negative gamma ([hkl]) is to increase both sigma and interfacial width w, each of which, upon suitable scaling, is related to gamma ([hkl]) through a universal scaling function. In this model, sigma is a differentiable function of interface orientation (n) over cap, and does not exhibit cusps; therefore, the equilibrium particle shapes (Wulff shapes) do not contain planar facets. However, the anisotropy in the interfacial energy can be large enough to give rise to corners in the Wulff shapes in two dimensions. In particles of finite sizes, the corners become rounded, and their shapes tend towards the Wulff shape with increasing particle size.

Solution combustion synthesis of gamma(L)-Bi(2)MoO(6) and photocatalytic activity under solar radiation

The facile method of solution combustion was used to synthesize gamma(L)-Bi(2)MoO(6). The material was crystallized in a purely crystalline orthorhombic phase with sizes varying from 300 to 500 nm. Because the band gap was 2.51 eV, the degradation of wide variety of cationic and anionic dyes was investigated under solar radiation. Despite the low surface area (< 1 m(2)/g) of the synthesized material, gamma(L)-Bi(2)MoO(6) showed high photocatalytic activity under solar radiation due to its electronic and morphological properties. (C) 2011 Elsevier Ltd. All rights reserved.

Role of spacer lengths of gemini surfactants in the synthesis of silver nanorods in micellar media

In this work, we have prepared Ag-nanorods using biscationic gemini surfactant micelles as the media by a seed-mediated wet synthesis method. Towards this end, we first synthesized Ag-nanoseeds of diameter similar to 7 nm stabilized by trisodium citrate (as the capping agent). Then these Ag-nanoseeds were used to synthesize Ag-nanorods of different aspect ratios. With decreasing Ag-nanoseed concentration, the aspect ratios of the Ag-nanorods stabilized by these gemini surfactants increased gradually. Various Ag-nanoseeds and Ag-nanospecies were characterized using UV-Vis spectroscopy (to know the surface plasmon bands), transmission electron microscopy (to find out their particle sizes and distribution), energy-dispersive X-ray spectroscopy and X-ray diffraction. When we used micelles derived from gemini surfactants of shorter spacer-(CH(2))(n)-(n = 2 or 4) to stabilize the Ag-nanorods, the lambda(max) of the longitudinal band shifted more towards the blue region compared to that of the gemini surfactant micelles with a longer spacer-(CH(2))(n)-(n = 5, 12) at a given amount of the Ag-nanoseed solution. So, the growth of Ag-nanorods in the gemini micellar solutions depends on the spacer-chain length of gemini surfactants employed.

The influence of Fe3+ ions at tetrahedral sites on the magnetic properties of nanocrystalline ZnFe2O4

A systematic study on the variation of Mössbauer hyperfine parameters with grain size in nanocrystalline zinc ferrite is lacking. In the present study, nanocrystalline ZnFe2O4 ferrites with different grain sizes were prepared by ball-milling technique and characterised by X-ray, EDAX, magnetisation and Mössbauer studies. The grain size decreases with increasing milling time and lattice parameter is found to be slightly higher than the bulk value. Magnetisation at room temperature (RT) and at 77 K could not be saturated with a magnetic field of 7 kOe and the observed magnetisation at these temperatures can be explained on the basis of deviation of cation distribution from normal spinel structure. The Mössbauer spectra were recorded at different temperatures between RT and 16 K. The values of quadrupole splitting at RT are higher for the milled samples indicating the disordering of ZnFe2O4 on milling. The strength of the magnetic hyperfine interactions increases with grain size reduction and this can be explained on the basis of the distribution of Fe3+ ions at both tetrahedral and octahedral sites.

Effect of Reagent Addition Rate and Temperature on Synthesis of Gold Nanoparticles in Microemulsion Route

Nanoparticle synthesis in a microemulsion route is typically controlled by changing the water to surfactant ratio, concentration of precursors, and/or concentration of micelles. The experiments carried out in this work with chloroauric acid and hydrazine hydrate as precursors in water/AOT-Brij30/isooctane microemulsions show that the reagent addition rate can also be used to tune the size of stable spherical gold nanoparticles to some extent. The particle size goes through a minimum with variation in feed addition rate. The increase in particle size with an increase in reaction temperature is in agreement with an earlier report. A population balance model is used to interpret the experimental findings. The reduced extent of nucleation at low feed addition rates and suppression of nucleation due to the finite rate of mixing at higher addition rates produce a minimum in particle size. The increase in particle size at higher reaction temperatures is explained through an increase in fusion efficiency of micelles which dissipates supersaturation; increase in solubility is shown to play an insignificant role. The moderate polydispersity of the synthesized particles is due to the continued nucleation and growth of particles. The polydispersity of micelle sizes by itself plays a minor role.

A note on the damping and oscillations of a fluid drop moving in another fluid

The oscillations of a drop moving in another fluid medium have been studied at low values of Reynolds number and Weber number by taking into consideration the shape of the drop and the viscosities of the two phases in addition to the interfacial tension. The deformation of the drop modifies the Lamb's expression for frequency by including a correction term while the viscous effects split the frequency into a pair of frequencies—one lower and the other higher than Lamb's. The lower frequency mode has ample experimental support while the higher frequency mode has also been observed. The two modes almost merge with Lamb's frequency for the asymptotic cases of a drop in free space or a bubble in a dense viscous fluid but the splitting becomes large when the two fluids have similar properties. Instead of oscillations, aperiodic damping modes are found to occur in drops with sizes smaller than a critical size ($\sim\hat{\rho}\hat{\nu}^2/T $). With the help of these calculations, many of the available experimental results are analyzed and discussed.

Superconductivity of embedded lead nano particles in metallic and amorphous matrices

Nanodispersed lead in metallic and amorphous matrices was synthesized by rapid solidification processing. The optimum microstructure was tailored to avoid percolation of the particles. With these embedded particles it is possible to study quantitatively the effect of size on the superconducting transition temperature by carrying out quantitative microstructural characterization and magnetic measurements. Our results suggest the role of the matrices in enhancement or depression of superconducting transition temperature of lead. The origin of this difference in behavior with respect to different matrices and sizes is discussed.

A Study of Nanostructures of Thin Films in B–C–N System Produced by Pulsed Laser Deposition and Nitrogen Ion-Beam-Assisted Pulsed Laser Deposition

We report the synthesis of thin films of B–C–N and C–N deposited by N+ ion-beam-assisted pulsed laser deposition (IBPLD) technique on glass substrates at different temperatures. We compare these films with the thin films of boron carbide synthesized by pulsed laser deposition without the assistance of ion-beam. Electron diffraction experiments in the transmission electron microscope shows that the vapor quenched regions of all films deposited at room temperature are amorphous. In addition, shown for the first time is the evidence of laser melting and subsequent rapid solidification of B4C melt in the form of micrometer- and submicrometer-size round particulates on the respective films. It is possible to amorphize B4C melt droplets of submicrometer sizes. Solidification morphologies of micrometer-size droplets show dispersion of nanocrystallites of B4C in amorphous matrix within the droplets. We were unable to synthesize cubic carbon nitride using the current technique. However, the formation of nanocrystalline turbostratic carbo- and boron carbo-nitrides were possible by IBPLD on substrate at elevated temperature and not at room temperature. Turbostraticity relaxes the lattice spacings locally in the nanometric hexagonal graphite in C–N film deposited at 600 °C leading to large broadening of diffraction rings.

Efficient statistical modeling for the compression of tree structured intermediate code

We propose a scheme for the compression of tree structured intermediate code consisting of a sequence of trees specified by a regular tree grammar. The scheme is based on arithmetic coding, and the model that works in conjunction with the coder is automatically generated from the syntactical specification of the tree language. Experiments on data sets consisting of intermediate code trees yield compression ratios ranging from 2.5 to 8, for file sizes ranging from 167 bytes to 1 megabyte.

Tree structure for efficient data mining using rough sets

In data mining, an important goal is to generate an abstraction of the data. Such an abstraction helps in reducing the space and search time requirements of the overall decision making process. Further, it is important that the abstraction is generated from the data with a small number of disk scans. We propose a novel data structure, pattern count tree (PC-tree), that can be built by scanning the database only once. PC-tree is a minimal size complete representation of the data and it can be used to represent dynamic databases with the help of knowledge that is either static or changing. We show that further compactness can be achieved by constructing the PC-tree on segmented patterns. We exploit the flexibility offered by rough sets to realize a rough PC-tree and use it for efficient and effective rough classification. To be consistent with the sizes of the branches of the PC-tree, we use upper and lower approximations of feature sets in a manner different from the conventional rough set theory. We conducted experiments using the proposed classification scheme on a large-scale hand-written digit data set. We use the experimental results to establish the efficacy of the proposed approach. (C) 2002 Elsevier Science B.V. All rights reserved.

Continued self-similar breakup of drops in viscous continuous phase in agitated vessels

Drop breakup inviscous liquids in agitated vessels occurs in elongational flow around impeller blade edges. The drop size distributions measured over extended periods for impellers of different sizes show that breakup process continues up to 15-20 h, before a steady state is reached. The size distributions evolve in a self-similar way till the steady state is reached. The scaled size distributions vary with impeller size and impeller speed, in contrast with the near universal scaling known for drop breakup in turbulent flows. The steady state size of the largest drop follows inverse scaling with impeller tip velocity. The breadth of the scaled size distributions also shows a monotonic relationship with impeller tip velocity only. (C) 2011 Elsevier Ltd. All rights reserved.

The diatom genus Gomphonema Ehrenberg in India: Checklist and description of three new species

We have compiled a checklist of Gomphonema Ehrenberg taxa reported previously from India. From forty-nine references, over 100 Gomphonema taxa have been reported, including 39 new taxon descriptions. In addition to these previous reports of Gomphonema taxa, we describe three new species. G. gandhii Karthick & Kociolek, sp. nov., G. difformum Karthick & Kociolek, sp. nov. and G. diminutum Karthick & Kociolek, sp. nov., all from hill streams of Western Ghats, India. Frustule morphology, as studied in light and scanning electron microscopy, is compared with that of other recently described Gomphonema species from Africa and Asia. All three Indian species have distinctly dilated proximal raphe ends, in addition to differentiated apical pore fields, septa, pseudosepta and a round external stigma! opening. Gomphonema gandhii is linear-lanceolate-clavate, has a wide axial area, and is 19-51 mu m long, 3-7 mu m broad. Gomphonema difformum is smaller than G. gandhii, and has a hyaline area around the headpole. Gomphonema diminuta is much smaller and narrower than the other two species. These species are distinct from their closest congeners by their sizes, shape and structure of the head pole, and striae densities. All these species were described from low nutrient, neutral, low ionic content streams of Western Ghats. As most other species described from tropical region these three species appear to be endemic to India. Moreover, within India they have hitherto only been found in Western Ghats, one of the twelve biodiversity hotspots of the World.

Realizing a flexible constraint length Viterbi decoder for software radio on a de Bruijn interconnection network

Building flexible constraint length Viterbi decoders requires us to be able to realize de Bruijn networks of various sizes on the physically provided interconnection network. This paper considers the case when the physical network is itself a de Bruijn network and presents a scalable technique for realizing any n-node de Bruijn network on an N-node de Bruijn network, where n < N. The technique ensures that the length of the longest path realized on the network is minimized and that each physical connection is utilized to send only one data item, both of which are desirable in order to reduce the hardware complexity of the network and to obtain the best possible performance.