Nucleosynthesis in the accretion disks of type II collapsars

We investigate nucleosynthesis inside the gamma-ray burst (GRB) accretion disks formed by the Type II collapsars. In these collapsars, the core collapse of massive stars first leads to the formation of a proto-neutron star. After that, an outward moving shock triggers a successful supernova. However, the supernova ejecta lacks momentum and within a few seconds the newly formed neutron star gets transformed to a stellar mass black hole via massive fallback. The hydrodynamics of such an accretion disk formed from the fallback material of the supernova ejecta has been studied extensively in the past. We use these well-established hydrodynamic models for our accretion disk in order to understand nucleosynthesis, which is mainly advection dominated in the outer regions. Neutrino cooling becomes important in the inner disk where the temperature and density are higher. The higher the accretion rate (M) over dot is, the higher the density and temperature are in the disks. We deal with accretion disks with relatively low accretion rates: 0.001 M-circle dot s(-1) less than or similar to (M) over dot less than or similar to 0.01 M-circle dot s(-1) and hence these disks are predominantly advection dominated. We use He-rich and Si-rich abundances as the initial condition of nucleosynthesis at the outer disk, and being equipped with the disk hydrodynamics and the nuclear network code, we study the abundance evolution as matter inflows and falls into the central object. We investigate the variation in the nucleosynthesis products in the disk with the change in the initial abundance at the outer disk and also with the change in the mass accretion rate. We report the synthesis of several unusual nuclei like P-31, K-39, Sc-43, Cl-35 and various isotopes of titanium, vanadium, chromium, manganese and copper. We also confirm that isotopes of iron, cobalt, nickel, argon, calcium, sulphur and silicon get synthesized in the disk, as shown by previous authors. Much of these heavy elements thus synthesized are ejected from the disk via outflows and hence they should leave their signature in observed data.

Assessing resilience and state-transition models with historical records of cheatgrass Bromus tectorum invasion in North American sagebrush-steppe

1. Resilience-based approaches are increasingly being called upon to inform ecosystem management, particularly in arid and semi-arid regions. This requires management frameworks that can assess ecosystem dynamics, both within and between alternative states, at relevant time scales. 2. We analysed long-term vegetation records from two representative sites in the North American sagebrush-steppe ecosystem, spanning nine decades, to determine if empirical patterns were consistent with resilience theory, and to determine if cheatgrass Bromus tectorum invasion led to thresholds as currently envisioned by expert-based state-and-transition models (STM). These data span the entire history of cheatgrass invasion at these sites and provide a unique opportunity to assess the impacts of biotic invasion on ecosystem resilience. 3. We used univariate and multivariate statistical tools to identify unique plant communities and document the magnitude, frequency and directionality of community transitions through time. Community transitions were characterized by 37-47% dissimilarity in species composition, they were not evenly distributed through time, their frequency was not correlated with precipitation, and they could not be readily attributed to fire or grazing. Instead, at both sites, the majority of community transitions occurred within an 8-10year period of increasing cheatgrass density, became infrequent after cheatgrass density peaked, and thereafter transition frequency declined. 4. Greater cheatgrass density, replacement of native species and indication of asymmetry in community transitions suggest that thresholds may have been exceeded in response to cheatgrass invasion at one site (more arid), but not at the other site (less arid). Asymmetry in the direction of community transitions also identified communities that were at-risk' of cheatgrass invasion, as well as potential restoration pathways for recovery of pre-invasion states. 5. Synthesis and applications. These results illustrate the complexities associated with threshold identification, and indicate that criteria describing the frequency, magnitude, directionality and temporal scale of community transitions may provide greater insight into resilience theory and its application for ecosystem management. These criteria are likely to vary across biogeographic regions that are susceptible to cheatgrass invasion, and necessitate more in-depth assessments of thresholds and alternative states, than currently available.

A divide and conquer strategy for scaling weather simulations with multiple regions of interest

Accurate and timely prediction of weather phenomena, such as hurricanes and flash floods, require high-fidelity compute intensive simulations of multiple finer regions of interest within a coarse simulation domain. Current weather applications execute these nested simulations sequentially using all the available processors, which is sub-optimal due to their sub-linear scalability. In this work, we present a strategy for parallel execution of multiple nested domain simulations based on partitioning the 2-D processor grid into disjoint rectangular regions associated with each domain. We propose a novel combination of performance prediction, processor allocation methods and topology-aware mapping of the regions on torus interconnects. Experiments on IBM Blue Gene systems using WRF show that the proposed strategies result in performance improvement of up to 33% with topology-oblivious mapping and up to additional 7% with topology-aware mapping over the default sequential strategy.

Certificate-less on-demand public key management (CLPKM) for self-organized MANETs

In this paper, we have proposed a novel certificate-less on-demand public key management (CLPKM) protocol for self-organized MANETs. The protocol works on flat network architecture, and distinguishes between authentication layer and routing layer of the network. We put an upper limit on the length of verification route and use the end-to-end trust value of a route to evaluate its strength. The end-to-end trust value is used by the protocol to select the most trusted verification route for accomplishing public key verification. Also, the protocol uses MAC function instead of RSA certificates to perform public key verification. By doing this, the protocol saves considerable computation power, bandwidth and storage space. The saved storage space is utilized by the protocol to keep a number of pre-established routes in the network nodes, which helps in reducing the average verification delay of the protocol. Analysis and simulation results confirm the effectiveness of the proposed protocol.

Performance analysis of beacon-less IEEE 802.15.4 multi-hop networks

We develop an approximate analytical technique for evaluating the performance of multi-hop networks based on beacon-less CSMA/CA as standardised in IEEE 802.15.4, a popular standard for wireless sensor networks. The network comprises sensor nodes, which generate measurement packets, and relay nodes which only forward packets. We consider a detailed stochastic process at each node, and analyse this process taking into account the interaction with neighbouring nodes via certain unknown variables (e.g., channel sensing rates, collision probabilities, etc.). By coupling these analyses of the various nodes, we obtain fixed point equations that can be solved numerically to obtain the unknown variables, thereby yielding approximations of time average performance measures, such as packet discard probabilities and average queueing delays. Different analyses arise for networks with no hidden nodes and networks with hidden nodes. We apply this approach to the performance analysis of tree networks rooted at a data sink. Finally, we provide a validation of our analysis technique against simulations.

On the absence of shear cracking and grain boundary cavitation in secondary tensile regions of Ti-6Al-4V-0.1B alloy during hot (alpha plus beta)-compression

Deformation instabilities, such as shear cracking and grain boundary cavitation, which are observed in the secondary tensile region of Ti-6Al-4V alloy during compressive deformation in the (+)-phase field, do not form in Ti-6Al-4V-0.1B alloy when processed under the same conditions. This has been attributed to the microstructural modifications, e.g. the absence of grain boundary and adjacent grain boundary retained layers and a lower proportion of 90(o)-misoriented -colonies that occur with boron addition.

Note on high aspect-ratio SU-8 micromechanical structures using mask-less direct laser writing

We report high aspect-ratio micromechanical structures made of SU-8 polymer, which is a negative photoresist. Mask-less direct writing with 405 nm laser is used to pattern spin-cast SU-8 films of thickness of more than 600 um. As compared with X-ray lithography, which helps pattern material to give aspect ratios of 1:50 or higher, laser writing is a less expensive and more accessible alternative. In this work, aspect ratios up to 1:30 were obtained on narrow pillars and cantilever structures. Deep vertical patterning was achieved in multiple exposures of the surface with varying dosages given at periodic intervals of sufficient duration. It was found that a time lag between successive exposures at the same location helps the material recover from the transient changes that occur during exposure to the laser. This gives vertical sidewalls to the resulting structures. The time-lags and dosages were determined by conducting several trials. The micromechanical structures obtained with laser writing are compared with those obtained with traditional UV lithography as well as e-beam lithography. Laser writing gives not only high aspect ratios but also narrow gaps whereas e-beam can only give narrow gaps over very small depths. Unlike traditional UV lithography, laser writing does not need a mask. Furthermore, there is no adjustment for varying the dosage in traditional UV lithography. A drawback of this method compared to UV lithography is that the writing time increases. Some test structures as well as a compliant microgripper are fabricated.

Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

Protein functional annotation relies on the identification of accurate relationships, sequence divergence being a key factor. This is especially evident when distant protein relationships are demonstrated only with three-dimensional structures. To address this challenge, we describe a computational approach to purposefully bridge gaps between related protein families through directed design of protein-like ``linker'' sequences. For this, we represented SCOP domain families, integrated with sequence homologues, as multiple profiles and performed HMM-HMM alignments between related domain families. Where convincing alignments were achieved, we applied a roulette wheel-based method to design 3,611,010 protein-like sequences corresponding to 374 SCOP folds. To analyze their ability to link proteins in homology searches, we used 3024 queries to search two databases, one containing only natural sequences and another one additionally containing designed sequences. Our results showed that augmented database searches showed up to 30% improvement in fold coverage for over 74% of the folds, with 52 folds achieving all theoretically possible connections. Although sequences could not be designed between some families, the availability of designed sequences between other families within the fold established the sequence continuum to demonstrate 373 difficult relationships. Ultimately, as a practical and realistic extension, we demonstrate that such protein-like sequences can be ``plugged-into'' routine and generic sequence database searches to empower not only remote homology detection but also fold recognition. Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. (C) 2013 Elsevier Ltd. All rights reserved.

Reduced graphene oxide induced phase miscibility in polystyrene-poly(vinyl methyl ether) blends

Graphene oxide and reduced graphene oxide (r-GO) were synthesized by wet chemistry and the effect of r-GO in PS-PVME blends was investigated here with respect to phase miscibility, intermolecular cooperativity in the glass transition region and concentration fluctuation variance by shear rheology and dielectric spectroscopy. The spinodal decomposition temperature (T-s) and correlation length were evaluated from isochronal temperature scans in shear rheology. The r-GO is shown to induce miscibility in the blends, which may lead to increased local heterogeneity in the blends, though the length of cooperatively re-arranged regions (xi) at T-g is more or less unaltered. The evolution of the phase morphology as a function of temperature was assessed using polarized optical microscopy (POM). In the case of the 60/40 PS-PVME blends with 0.25 wt% r-GO, apart from significant refinement in the morphology, retention of the interconnected ligaments of PVME was observed, even in the late stages of phase separation suggesting that the coarsening of the phase morphology has been slowed down in the presence of r-GO. This phenomenon was also supported by AFM. Surface enrichment of PVME, owing to its lower surface tension, in the demixed samples was supported by XPS scans. The interconnected network of PVME has resulted in significantly higher permittivity in the bi-phasic blends, although the concentration of r-GO is below the percolation threshold.

On the systematic position of some Asian enigmatic genera of Asclepiadoideae (Apocynaceae)

The phylogenetic structure of Asclepiadoideae (Apocynaceae) has been elucidated at the tribal and subtribal levels in the last two decades. However, to date, the systematic positions of seven Asian genera, Cosmostigma, Graphistemma, Holostemma, Pentasachme, Raphistemma, Seshagiria and Treutlera, have not been investigated. In this study, we examine the evolutionary relationships among these seven small enigmatic Asian genera and clarify their positions in Asclepiadoideae, using a combination of plastid sequences of rbcL, rps16, trnL and trnL- F regions. Cosmostigma and Treutlera are resolved as members of the non-Hoya clade of Marsdenieae with strong support (maximum parsimony bootstrap support value BSMP = 96, maximum likelihood bootstrap support value BSML = 98, Bayesian-inferred posterior probability PP = 1.0). Pentasachme is resolved as sister of Stapeliinae to Ceropegieae with moderate support (BSMP = 64, BSML = 66, PP = 0.94). Graphistemma, Holostemma, Raphistemma and Seshagiria are all nested in the Asclepiadeae-Cynanchinae clade (BSMP = 97, BSML = 100, PP = 1.0). The study confirms the generally accepted tribal and subtribal structure of the subfamily. One exception is Eustegia minuta, which is placed here as sister to all Asclepiadeae (BSMP = 58, BSML = 76, PP = 0.99) and not as sister to the Marsdenieae + Ceropegieae clade. The weak support and conflicting position indicate the need for a placement of Eustegia as an independent tribe. In Asclepiadeae, a sister group position of Cynanchinae to the Asclepiadinae + Tylophorinae clade is favoured (BSMP = 84, BSML = 88, PP = 1.0), whereas Schizostephanus is retrieved as unresolved. Oxystelma appears as an early-branching member of Asclepiadinae with weak support (BSMP = 52, BSML = 74, PP = 0.69). Calciphila and Solenostemma are also associated with Asclepiadinae with weak support (BSMP = 37, BSML = 45, PP = 0.79), but all alternative positions are essentially without support. The position of Indian Asclepiadoideae in the family phylogeny is discussed. (c) 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 601-619.

Climate change scenarios of surface solar radiation in data sparse regions: a case study in Malaprabha River Basin, India

A variety of methods are available to estimate future solar radiation (SR) scenarios at spatial scales that are appropriate for local climate change impact assessment. However, there are no clear guidelines available in the literature to decide which methodologies are most suitable for different applications. Three methodologies to guide the estimation of SR are discussed in this study, namely: Case 1: SR is measured, Case 2: SR is measured but sparse and Case 3: SR is not measured. In Case 1, future SR scenarios are derived using several downscaling methodologies that transfer the simulated large-scale information of global climate models to a local scale ( measurements). In Case 2, the SR was first estimated at the local scale for a longer time period using sparse measured records, and then future scenarios were derived using several downscaling methodologies. In Case 3: the SR was first estimated at a regional scale for a longer time period using complete or sparse measured records of SR from which SR at the local scale was estimated. Finally, the future scenarios were derived using several downscaling methodologies. The lack of observed SR data, especially in developing countries, has hindered various climate change impact studies. Hence, this was further elaborated by applying the Case 3 methodology to a semi-arid Malaprabha reservoir catchment in southern India. A support vector machine was used in downscaling SR. Future monthly scenarios of SR were estimated from simulations of third-generation Canadian General Circulation Model (CGCM3) for various SRES emission scenarios (A1B, A2, B1, and COMMIT). Results indicated a projected decrease of 0.4 to 12.2 W m(-2) yr(-1) in SR during the period 2001-2100 across the 4 scenarios. SR was calculated using the modified Hargreaves method. The decreasing trends for the future were in agreement with the simulations of SR from the CGCM3 model directly obtained for the 4 scenarios.

Recent Seismicity in India and Adjoining Regions

In the present work, historical and instrumental seismicity data of India and its adjoining areas (within 300km from Indian political boundary) are compiled to form the earthquake catalog for the country covering the period from 1505 to 2009. The initial catalogue consisted of about 139563 earthquake events and after declustering,the total number of events obtained was 61315. Region specific earthquake magnitude scaling relations correlating different magnitude scales were achieved and a homogenous earthquake catalogue in moment magnitude (MW) scale was developed for the region. This paper also presents the results of the use of Geographic Information Systems (GIS) to prepare a digitized seismic source map of India. The latest earthquake data were superimposed on the digitized source map to get a final Seismotectonic map of India. The study area has been divided into 1225 grid points (approximately 110km×110km) and the seismicity analysis has been done to get the spatial variation of seismicity parameters ‘a’ and ‘b’ across the country. The homogenized earthquake catalogue with the event details is listed in the website http://civil.iisc.ernet.in/~sreevals/resource.htm

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.