Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Spatial variation of seismicity parameters across India and adjoining areas

An attempt has been made to quantify the variability in the seismic activity rate across the whole of India and adjoining areas (0–45°N and 60–105°E) using earthquake database compiled from various sources. Both historical and instrumental data were compiled and the complete catalog of Indian earthquakes till 2010 has been prepared. Region-specific earthquake magnitude scaling relations correlating different magnitude scales were achieved to develop a homogenous earthquake catalog for the region in unified moment magnitude scale. The dependent events (75.3%) in the raw catalog have been removed and the effect of aftershocks on the variation of b value has been quantified. The study area was divided into 2,025 grid points (1°91°) and the spatial variation of the seismicity across the region have been analyzed considering all the events within 300 km radius from each grid point. A significant decrease in seismic b value was seen when declustered catalog was used which illustrates that a larger proportion of dependent events in the earthquake catalog are related to lower magnitude events. A list of 203,448 earth- quakes (including aftershocks and foreshocks) occurred in the region covering the period from 250 B.C. to 2010 A.D. with all available details is uploaded in the website http://www.civil.iisc.ernet.in/*sreevals/resource.htm.

Impact dynamics of high Weber number drops on chemically modified metallic surfaces

Hydrophobic/superhydrophobic metallic surfaces prepared via chemical treatment are encountered in many industrial scenarios involving the impingement of spray droplets. The effectiveness of such surfaces is understood through the analysis of droplet impact experiments. In the present study, three target surfaces with aluminum (Al-6061) as base material-acid-etched, Octadecyl Trichloro Silane (OTS) coated, and acid-etched plus OTS-coated-were prepared. Experiments on the impact of inertia dominated water drops on these chemically modified aluminum surfaces were carried out with the objective to highlight the effect of chemical treatment on the target surfaces on key sub-processes occurring in drop impact phenomenon. High speed videos of the entire drop impact dynamics were captured at three Weber number (We) conditions representative of high We (We > 200) regime. During the early stages of drop spreading, the drop impact resulted in ejection of secondary droplets from spreading drop front on the etched surfaces resembling prompt splash on rough surfaces whereas no such splashing was observable on untreated aluminum surface. Prominent development of undulations (fingers) were observed at the rim of drop spreading on the etched surfaces; between the etched surfaces the OTS-coated surface showed a subdued development of fingers than the uncoated surface. The impacted drops showed intense receding on OTS-coated surfaces whereas on the etched surface a highly irregular receding, with drop liquid sticking to the surface, was observed. Quantitative analyses were performed to reveal the effect of target surface characteristics on drop impact parameters such as temporal variation of spread factor of drop lamella, temporal variation of average finger length during spreading phase, maximum drop spreading, time taken to attain maximum spreading, sensitivity of maximum spreading to We, number of fingers at maximum spreading, and average receding velocity of drop lamella. Existing models for maximum drop spreading showed reasonably good agreement with the experimental measurements on the target surfaces except the acid-etched surface. (C) 2014 Elsevier B.V. All rights reserved.

Comparative Studies on the Bioremediation of Hexavalent and Trivalent Chromium using Citrobacter freundii: Part I-Effect of parameters controlling Biosorption

The potential of Citrobacter freundii, a Gram negative bacteria for the remediation of hexavalent chromium (Cr(VI)) and trivalent chromium (Cr(III))) from aqueous solutions was investigated. Bioremediation of Cr(VI) involved both biosorption and bioreduction processes, as compared to only biosorption process observed with respect to Cr(III) bioremediation. In the case of Cr(VI) bioremediation studies, about 59 % biosorption was achieved at an equilibrium time of 2 h, initial Cr(VI) concentration of 4 mg/L, pH 1 and a biomass loading of 5x10(11) cells/mL. The remainder, 41 %, was found to be in the form of Cr(111) ions owing to bioreduction of Cr(VI) by the bacteria resulting in the absence of Cr(VI) ions in the residue, there by meeting the USEPA specifications. Similar studies were carried out using Cr(III) solution for an equilibrium time of 2 h, Cr(III) concentration of 4 mg/L, pH 3 and a biomass loading of 6.3x10(11) cells/mL., wherein a maximum biosorption of about 30 % was achieved.

A bottom-up approach for optimization of friction stir processing parameters; a study on aluminium 2024-T3 alloy

Friction stir processing (FSP) is emerging as one of the most competent severe plastic deformation (SPD) method for producing bulk ultra-fine grained materials with improved properties. Optimizing the process parameters for a defect free process is one of the challenging aspects of FSP to mark its commercial use. For the commercial aluminium alloy 2024-T3 plate of 6 mm thickness, a bottom-up approach has been attempted to optimize major independent parameters of the process such as plunge depth, tool rotation speed and traverse speed. Tensile properties of the optimum friction stir processed sample were correlated with the microstructural characterization done using Scanning Electron Microscope (SEM) and Electron Back-Scattered Diffraction (EBSD). Optimum parameters from the bottom-up approach have led to a defect free FSP having a maximum strength of 93% the base material strength. Micro tensile testing of the samples taken from the center of processed zone has shown an increased strength of 1.3 times the base material. Measured maximum longitudinal residual stress on the processed surface was only 30 MPa which was attributed to the solid state nature of FSP. Microstructural observation reveals significant grain refinement with less variation in the grain size across the thickness and a large amount of grain boundary precipitation compared to the base metal. The proposed experimental bottom-up approach can be applied as an effective method for optimizing parameters during FSP of aluminium alloys, which is otherwise difficult through analytical methods due to the complex interactions between work-piece, tool and process parameters. Precipitation mechanisms during FSP were responsible for the fine grained microstructure in the nugget zone that provided better mechanical properties than the base metal. (C) 2014 Elsevier Ltd. All rights reserved.

MULTI-PITCH TRACKING USING GAUSSIAN MIXTURE MODEL WITH TIME VARYING PARAMETERS AND GRATING COMPRESSION TRANSFORM

Grating Compression Transform (GCT) is a two-dimensional analysis of speech signal which has been shown to be effective in multi-pitch tracking in speech mixtures. Multi-pitch tracking methods using GCT apply Kalman filter framework to obtain pitch tracks which requires training of the filter parameters using true pitch tracks. We propose an unsupervised method for obtaining multiple pitch tracks. In the proposed method, multiple pitch tracks are modeled using time-varying means of a Gaussian mixture model (GMM), referred to as TVGMM. The TVGMM parameters are estimated using multiple pitch values at each frame in a given utterance obtained from different patches of the spectrogram using GCT. We evaluate the performance of the proposed method on all voiced speech mixtures as well as random speech mixtures having well separated and close pitch tracks. TVGMM achieves multi-pitch tracking with 51% and 53% multi-pitch estimates having error <= 20% for random mixtures and all-voiced mixtures respectively. TVGMM also results in lower root mean squared error in pitch track estimation compared to that by Kalman filtering.

Phase evolutions, growth kinetics and diffusion parameters in the Co-Ni-Ta system

Diffusion couple experiments are conducted to study phase evolutions in the Co-rich part of the Co-Ni-Ta phase diagram. This helps to examine the available phase diagram and propose a correction on the stability of the Co2Ta phase based on the compositional measurements and X-ray analysis. The growth rate of this phase decreases with an increase in Ni content. The same is reflected on the estimated integrated interdiffusion coefficients of the components in this phase. The possible reasons for this change are discussed based on the discussions of defects, crystal structure and the driving forces for diffusion. Diffusion rate of Co in the Co2Ta phase at the Co-rich composition is higher because of more number of Co-Co bonds present compared to that of Ta-Ta bonds and the presence of Co antisites for the deviation from the stoichiometry. The decrease in the diffusion coefficients because of Ni addition indicates that Ni preferably replaces Co antisites to decrease the diffusion rate. (C) 2014 Elsevier B.V. All rights reserved.

Assignment of the C-13 NMR spectrum by correlation to dipolar coupled proton-pairs and estimation of order parameters of a thiophene based liquid crystal

Materials with widely varying molecular topologies and exhibiting liquid crystalline properties have attracted considerable attention in recent years. C-13 NMR spectroscopy is a convenient method for studying such novel systems. In this approach the assignment of the spectrum is the first step which is a non-trivial problem. Towards this end, we propose here a method that enables the carbon skeleton of the different sub-units of the molecule to be traced unambiguously. The proposed method uses a heteronuclear correlation experiment to detect pairs of nearby carbons with attached protons in the liquid crystalline core through correlation of the carbon chemical shifts to the double-quantum coherences of protons generated through the dipolar coupling between them. Supplemented by experiments that identify non-protonated carbons, the method leads to a complete assignment of the spectrum. We initially apply this method for assigning the C-13 spectrum of the liquid crystal 4-n-pentyl-4'-cyanobiphenyl oriented in the magnetic field. We then utilize the method to assign the aromatic carbon signals of a thiophene based liquid crystal thereby enabling the local order-parameters of the molecule to be estimated and the mutual orientation of the different sub-units to be obtained.

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

Effect of sputtering parameters on the structure, microstructure and magnetic properties of Tb-Fe films

The effect of sputtering parameters such as gas pressure and power on the structure, microstructure and magnetic properties of sputtered Tb-Fe thin films was investigated. X-ray diffraction and transmission electron microscopy studies showed that all the films were amorphous in nature irrespective of the sputtering parameters. A fine island kind of morphology was observed at low sputtering power whereas large clusters were seen at higher sputtering power. While the composition of Tb-Fe films remained constant with increasing sputtering power, the magnetic behaviour was found to change from superparamagnetic to ferromagnetic. On the other hand, the increase in argon gas pressure was found to deplete the iron concentration in Tb-Fe thin films, which in turn reduced the anisotropy and Curie temperature. Annealing of the films at 773 K did not result in any crystallization and the magnetic properties were also found to remain unchanged. (C) 2015 Elsevier B.V. All rights reserved.

Effect of electrical parameters on morphology and in-vitro corrosion resistance of plasma electrolytic oxidized films formed on zirconium

The objective of the present work is to study the effect of electrical process Parameters (duty cycle and frequency) on morphological, structural, and in-vitro corrosion characteristics of oxide films formed on zirconium by plasma electrolytic oxidation in an electrolyte system consisting of 5 g/L of trisodium orthophosphate. The oxide films fabricated on zirconium by systematically varying the duty cycle and frequency are characterized for its phase composition, surface morphology, chemical composition, roughness, wettability, surface energy, scratch resistance, corrosion resistance, apatite forming ability and osteoblast cell adhesion. X-ray diffraction pattern of all the oxide films showed the predominance of m-ZrO2 phase. Dense and uniform films with thickness varying from 9 to 15 mu m and roughness in the range of 0.62 to 1.03 mu m are formed. Porosity of oxide films is found to be increased with an increase infrequency. The water contact angle results demonstrated that the oxide films exhibited similar hydrophilicity to zirconium substrate. All oxide films showed improved corrosion resistance, as indicated by far lower corrosion current density and passive corrosion potential compared to the zirconium substrate in simulated body fluid environment, and among the four different combinations of duty cycle and frequency employed in the present study, the oxide film formed at 95% duty cycle and 50 Hz frequency (HDLF film) showed superior pitting corrosion resistance, which can be attributed to its pore free morpholOgy. Scratch test results showed that the HDLF oxide film adhered firmly to the substrate by developing a notable scratch resistance at 19.5 +/- 1.2.N. Besides the best corrosion resistance and scratch retistance, the HDLF film also showed good apatite forming ability and osteo sarcoma cell adhesion on its surface. The HDLF oxide film on zirconium with superior surface characteristics is believed to be useful for various types of implants in the dental and orthopedic fields. (C) 2015 Elsevier B.V. All rights reserved.

Comparative evaluation of inversion approaches of the radiative transfer model for estimation of crop biophysical parameters

The inversion of canopy reflectance models is widely used for the retrieval of vegetation properties from remote sensing. This study evaluates the retrieval of soybean biophysical variables of leaf area index, leaf chlorophyll content, canopy chlorophyll content, and equivalent leaf water thickness from proximal reflectance data integrated broadbands corresponding to moderate resolution imaging spectroradiometer, thematic mapper, and linear imaging self scanning sensors through inversion of the canopy radiative transfer model, PROSAIL. Three different inversion approaches namely the look-up table, genetic algorithm, and artificial neural network were used and performances were evaluated. Application of the genetic algorithm for crop parameter retrieval is a new attempt among the variety of optimization problems in remote sensing which have been successfully demonstrated in the present study. Its performance was as good as that of the look-up table approach and the artificial neural network was a poor performer. The general order of estimation accuracy for para-meters irrespective of inversion approaches was leaf area index > canopy chlorophyll content > leaf chlorophyll content > equivalent leaf water thickness. Performance of inversion was comparable for broadband reflectances of all three sensors in the optical region with insignificant differences in estimation accuracy among them.

Simulation studies on Performance parameters of a TPC Polarimeter

X-ray polarimeters based on Time Projection Chamber (TPC) geometry are currently being studied and developed to make sensitive measurement of polarization in 2-10keV energy range. TPC soft X-ray polarimeters exploit the fact that emission direction of the photoelectron ejected via photoelectric effect in a gas proportional counter carries the information of the polarization of the incident X-ray photon. Operating parameters such as pressure, drift field and drift-gap affect the performance of a TPC polarimeter. Simulations presented here showcase the effect of these operating parameters on the modulation factor of the TPC polarimeter. Models of Garfield are used to study photoelectron interaction in gas and drift of electron cloud towards Gas Electron Multiplier (GEM). The emission direction is reconstructed from the image and modulation factor is computed. Our study has shown that Ne/DME (50/50) at lower pressure and drift field can be used for a TPC polarimeter with modulation factor of 50-65%.

Drift parameters optimization of a TPC polarimeter: a simulation study

Time Projection Chamber (TPC) based X-ray polarimeters using Gas Electron Multiplier (GEM) are currently being developed to make sensitive measurement of polarization in 2-10 keV energy range. The emission direction of the photoelectron ejected via photoelectric effect carries the information of the polarization of the incident X-ray photon. Performance of a gas based polarimeter is affected by the operating drift parameters such as gas pressure, drift field and drift-gap. We present simulation studies carried out in order to understand the effect of these operating parameters on the modulation factor of a TPC polarimeter. Models of Garfield are used to study photoelectron interaction in gas and drift of electron cloud towards GEM. Our study is aimed at achieving higher modulation factors by optimizing drift parameters. Study has shown that Ne/DME (50/50) at lower pressure and drift field can lead to desired performance of a TPC polarimeter.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.