Measurement of energy and directional distribution of neutron ambient dose equivalent for the 7Li(p,n)7Be reaction.

Double differential neutron fluence distributions were measured in the 7Li(p,n)7Be reaction for proton beam energies 7, 9 and 12 MeV. Seven liquid scintillator based detectors were employed to measure neutron fluence distributions using the Time of Flight technique. Neutron ambient dose equivalents were determined from the measured fluence distribution using ICRP (International Commission on Radiological Protection) recommended fluence to dose equivalent conversion coefficients. Neutron dose equivalents were also measured using a conventional BF3 detector based REM counter. Ambient dose equivalent measured by the REM counter is found to be in agreement with that determined from the neutron fluence spectra within their uncertainties. Angular distributions of the ambient dose equivalents were also determined from the measured fluence distributions at different angles.

Granular cell tumor of the brain: case report and review of literature.

Granular cell tumors are rare tumors that develop from Schwann cells, which are glial cells surrounding neurons of the peripheral nervous system, which serve in the process of myelination. Granular cell tumors are rarely associated with the central nervous system in humans. In this report, we analyze a patient with granular cell tumor and review the current literature.

Optimization of beam dump shielding for K-130 cyclotron at VECC.

A compact and efficient beam dump shield has been designed using Monte Carlo simulation code FLUKA to facilitate low background measurement of neutron and gamma rays using K130 cyclotron at Variable Energy Cyclotron Centre, Kolkata (VECC). Iron, lead and high density Polyethylene (HDPE) were considered in the design of the beam dump shield. Representative FLUKA simulation results have been validated using in-beam experiment performed on the same beam dump constituents. Experimental neutron and gamma-rays energy spectra have been found to be in fair agreement with the simulation results. Activation of various beam dump shield components were also carried out.

Experimental Determination of η/s for Finite Nuclear Matter.

We present, for the first time, simultaneous determination of shear viscosity (η) and entropy density (s) and thus, η/s for equilibrated nuclear systems from A∼30 to A∼208 at different temperatures. At finite temperature, η is estimated by utilizing the γ decay of the isovector giant dipole resonance populated via fusion evaporation reaction, while s is evaluated from the nuclear level density parameter (a) and nuclear temperature (T), determined precisely by the simultaneous measurements of the evaporated neutron energy spectra and the compound nuclear angular momenta. The transport parameter η and the thermodynamic parameter s both increase with temperature, resulting in a mild decrease of η/s with temperature. The extracted η/s is also found to be independent of the neutron-proton asymmetry at a given temperature. Interestingly, the measured η/s values are comparable to that of the high-temperature quark-gluon plasma, pointing towards the fact that strong fluidity may be the universal feature of the strong interaction of many-body quantum systems.

Analysis of dispersion and absorption characteristics of shear waves in sinusoidally corrugated elastic medium with void pores.

This theoretical work reports the dispersion and absorption characteristics of horizontally polarized shear wave (SH-wave) in a corrugated medium with void pores sandwiched between two dissimilar half-spaces. The dispersion and absorption equations have been derived in a closed form using the method of separation of variables. It has been established that there are two different kinds of wavefronts propagating in the proposed media. One of the wavefronts depends on the modulus of rigidity of elastic matrix of the medium and satisfies the dispersion equation of SH-waves. The second wavefront depends on the changes in volume fraction of the pores. Numerical computation of the obtained relations has been performed and the results are depicted graphically. The influence of corrugation, sandiness on the phase velocity and the damped velocity of SH-wave has been studied extensively.

Design and Development of ChemInfoCloud: An Integrated Cloud Enabled Platform for Virtual Screening.

The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

MegaMiner: A Tool for Lead Identification Through Text Mining Using Chemoinformatics Tools and Cloud Computing Environment.

Virtual screening is an indispensable tool to cope with the massive amount of data being tossed by the high throughput omics technologies. With the objective of enhancing the automation capability of virtual screening process a robust portal termed MegaMiner has been built using the cloud computing platform wherein the user submits a text query and directly accesses the proposed lead molecules along with their drug-like, lead-like and docking scores. Textual chemical structural data representation is fraught with ambiguity in the absence of a global identifier. We have used a combination of statistical models, chemical dictionary and regular expression for building a disease specific dictionary. To demonstrate the effectiveness of this approach, a case study on malaria has been carried out in the present work. MegaMiner offered superior results compared to other text mining search engines, as established by F score analysis. A single query term 'malaria' in the portlet led to retrieval of related PubMed records, protein classes, drug classes and 8000 scaffolds which were internally processed and filtered to suggest new molecules as potential anti-malarials. The results obtained were validated by docking the virtual molecules into relevant protein targets. It is hoped that MegaMiner will serve as an indispensable tool for not only identifying hidden relationships between various biological and chemical entities but also for building better corpus and ontologies.

Protein Ligand Complex Guided Approach for Virtual Screening.

The target ligand association data is a rich source of information which is not exploited enough for drug design efforts in virtual screening. A java based open-source toolkit for Protein Ligand Network Extraction (J-ProLiNE) focused on protein-ligand complex analysis with several features integrated in a distributed computing network has been developed. Sequence alignment and similarity search components have been automated to yield local, global alignment scores along with similarity and distance scores. 10000 proteins with co-crystallized ligands from pdb and MOAD databases were extracted and analyzed for revealing relationships between targets, ligands and scaffolds. Through this analysis, we could generate a protein ligand network to identify the promiscuous and selective scaffolds for multiple classes of proteins targets. Using J-ProLiNE we created a 507 x 507 matrix of protein targets and native ligands belonging to six enzyme classes and analyzed the results to elucidate the protein-protein, protein-ligand and ligand-ligand interactions. In yet another application of the J-ProLiNE software, we were able to process kinase related information stored in US patents to construct disease-gene-ligand-scaffold networks. It is hoped that the studies presented here will enable target ligand knowledge based virtual screening for inhibitor design.

ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.