RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies in the fitted component. Results: Here we present the RIBFIND server, a tool for identifying rigid bodies in protein structures. The server identifies rigid bodies in proteins by calculating spatial proximity between their secondary structural elements. Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk

Delocalization transition for the Google matrix

We study the localization properties of eigenvectors of the Google matrix, generated both from the World Wide Web and from the Albert-Barabasi model of networks. We establish the emergence of a delocalization phase for the PageRank vector when network parameters are changed. In the phase of localized PageRank, a delocalization takes place in the complex plane of eigenvalues of the matrix, leading to delocalized relaxation modes. We argue that the efficiency of information retrieval by Google-type search is strongly affected in the phase of delocalized PageRank.Comment: 4 pages, 5 figures. Research done at http://www.quantware.ups-tlse.fr

Synopsis of the genus Cinnamomum Schaeffer (Lauraceae) in India

A checklist of the genus Cinnamomum in India is presented including nomenclature, a brief description, details of the publications where the detailed description and illustration of the species appeared, phenology, distribution of the species within and outside India and IUCN threat status. A total of 45 taxa (43 species and two infraspecific taxa) have been recorded here based on available information. Twenty-four taxa are found to be endemic to India. Kerala in Peninsular India records the largest number of 24 taxa and may be considered as hotspot area for this genus. The genus possesses the greatest phytogeographical affinity to China with 13 species

Catalytic activity of niobia supported graphene oxide for esterification of oleic acid

Biodiesel has been obtained from esterification of oleic acid with methanol using niobia loaded graphene oxide (GO). Different weight percentages of niobia (1, 3, 5 and 7 wt.%) have been loaded on GO by the wet impregnation method. The synthesized materials have been characterized by XRD, FT-IR, Raman spectroscopy, TGA, BET surface area, NH3-TPD, ICP-OES, SEM and HR-TEM studies. The catalytic activity of niobia supported on GO has been tested for esterification of oleic acid with methanol for biodiesel production. The maximum yield of methyl oleate (96.4%) is obtained at the reaction conditions of 150 °C, 0.5 g of 5 wt% of niobia on GO catalyst, 1:9 molar ratio of oleic acid:methanol and time 4 h. Influence of solvents (ethanol, propanol, butanol) has been tested for comparative study with same reaction conditions. Based on the catalytic studies, niobia supported GO has good catalytic activity for esterification of oleic acid reaction with good reusability

Two-dimensional ranking of Wikipedia articles

The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists {\it ab aeterno}. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.Comment: RevTex 9 pages, data, discussion added, more data at http://www.quantware.ups-tlse.fr/QWLIB/2drankwikipedia

Lattice Forward-Secure Identity Based Encryption Scheme

Abstract Protecting secret keys is crucial for cryptography. There are some relatively insecure devices (smart cards, mobile phones etc.) which have threat of key exposure. The goal of the forward security is to protect security of past uses of key even if the current secret key is exposed. In this paper we propose lattice based forward-secure identity based encryption scheme based on LWE assumption in random oracle model. We also propose lattice based forward-secure identity based encryption scheme in the standard model

Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health.

Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance. The importance of these protein mutations has led to the development of many resources for understanding and predicting their effects. We propose that a better understanding of how these mutations affect the structure, function, and formation of multiprotein complexes provides novel opportunities for tackling them, including the development of small-molecule drugs targeted specifically to mutated PPIs.H.J. is currently funded by an Astex Pharmaceuticals Sustaining Innovation Postdoctoral Fellowship hosted at the Wellcome Trust Sanger Institute. M.A.T was supported by scholarships from Promega Corporation, as well as the College of Agricultural and Life Sciences and the Department of Biochemistry at the University of Wisconsin-Madison, USA. B.O.M was supported by the Bill and Melinda Gates Foundation. D.B.A is the recipient of a C. J. Martin Research Fellowship from the National Health and Medical Research Council of Australia (APP1072476) and is funded by the Wellcome Trust and Jack Brockhoff Foundation (JBF 4186, 2016). T.L.B. receives funding from the University of Cambridge and The Wellcome Trust for facilities and support

Synthesis, Structural and Optical Properties of PVP Encapsulated CdS Nanoparticles

Highly monodispersed CdS nanoparticles using polyvinyl pyrrolidone (PVP) as the capping agent were synthesised by chemical coprecipitation method. The surface‐modified cadmium sulfide nanoparticles were found to be remarkably stable. In the presence of PVP, cubic phase with small grain size of CdS were observed in XRD. The peaks were identified to originate from (111), (220) and (311) planes of CdS, respectively. The crystallite size of the synthesised CdS nanoparticles was about 3 nm calculated from the (111) plane of XRD pattern and it was also confirmed through HRTEM. Morphology and elemental mapping of the synthesised nanoparticles were studied by SEM and EDX analyses. Increase in the band gap with decrease in the particle size was observed from the reflectance mode UV spectrum, which confirms the quantum confinement effect. From the photoluminescence studies, enhanced near‐band‐edge blue light emission and significantly reduced defect‐related green emission were observed. Longitudinal optical (LO) phonon modes, corresponds to pure CdS were observed in Raman spectrum