From Network Structure to Dynamics and Back Again: Relating dynamical stability and connection topology in biological complex systems

The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from statistical physics and non-linear dynamics. In this paper, we look at a few examples of biological networks to see how similar questions can come up in very different contexts. We review some of our recent work that looks at how network structure (e.g., its connection topology) can dictate the nature of its dynamics, and conversely, how dynamical considerations constrain the network structure. We also see how networks occurring in nature can evolve to modular configurations as a result of simultaneously trying to satisfy multiple structural and dynamical constraints. The resulting optimal networks possess hubs and have heterogeneous degree distribution similar to those seen in biological systems.Comment: 15 pages, 6 figures, to appear in Proceedings of "Dynamics On and Of Complex Networks", ECSS'07 Satellite Workshop, Dresden, Oct 1-5, 200

Static and dynamic characteristics of protein contact networks

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding process through the lens of complex network analysis. Consequently, there is now a body of empirical studies describing topological characteristics of protein macro-molecules through their contact networks and linking these topological characteristics to protein folding. The present paper is primarily a review of this rich area. But it delves deeper into certain aspects by emphasizing short-range and long-range links, and suggests unconventional places where "power-laws" may be lurking within protein contact networks. Further, it considers the dynamical view of protein contact networks. This closer scrutiny of protein contact networks raises new questions for further research, and identifies new regularities which may be useful to parameterize a network approach to protein folding. Preliminary experiments with such a model confirm that the regularities we identified cannot be easily reproduced through random effects. Indeed, the grand challenge of protein folding is to elucidate the process(es) which not only generates the specific and diverse linkage patterns of protein contact networks, but also reproduces the dynamic behavior of proteins as they fold. Keywords: network analysis, protein contact networks, protein foldingComment: Added Appendix

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Not AvailableWetlands associated with floodplains of the Ganges and Brahmaputra river systems cover an estimated 0.2 million ha and play a vital role in the fisheries, rural economy and environment. In recent years, most wetlands in the states of Bihar, Assam and West Bengal in India have lost connectivity with their parent rivers due to natural and anthropogenic changes. These changes are causing rapid shrinkage of valuable wetlands and threatening their biodiversity and ecological function. The present study was conducted to assess the effect of river connectivity on the hydrochemistry, sediment enzyme activity, and biotic communities of these wetlands. One wetland area having link channels (open) connecting the main river, and another without link channels (closed), were selected from each of the Ganges and Brahmaputra basins for the study. Comparative analysis of open and closed, ecologically distinct wetlands of the Ganges basin revealed greater seasonal reduction in water depth and higher water conductivity (p < 0.04), nutrients (Ca+2, Mg+2, SiO3-Si), sediment microbial activity (p < 0.004), phosphorous cycling enzymes (p < 0.001), carbon cycling enzymes (p < 0.01), organic matter, conductivity, and plankton and macrozoobenthos (p < 0.01) density in the closed wetland. However, the open wetland showed higher diversity of plankton and macrozoobenthos. A profound impact of connectivity on wetland fisheries was observed in the Brahmaputra basin in Assam, where a higher percentage of catch comprised of indigenous fish species with lower fish yield was noted in the open wetland.Not Availabl

Environmental radioactivity of the St. Martin's island of Bangladesh

The activity concentration of natural and anthropogenic radionuclides in soil and rock, and in benthic algae, corals and oysters across the St. Martin's island of Bangladesh were investigated together with physicochemical parameters and texture of soil with an aim of evaluating the radioecology of the island. Soil and rock samples from the twenty-two locations of the island, eleven species of benthic algae, six species of corals and two species of oysters were analyzed. The activity of 226Ra in soil was found in the range of 7.22–103.8, in benthic algae 2.5–9.7, in coral 5.5–10 and in oyster 4.2–11.5 Bq kg-1. The activity of 232Th in soil was found in the range of 14.56–216, in benthic algae 1.3–12.6, in coral 4.4–15.6 and in oyster 3.2–8.4 Bq kg-1; and the activity of 40K in soil was in the range of 322–732, in benthic algae 17.1–45.5, in coral 21–146 and in oyster 24–32 Bq kg-1. The external radiation dose rate due to activity concentration of natural radionuclides in soil was assessed. The activity of anthropogenic 137Cs was found below detection limit.

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Not AvailableA 60-day feeding trial was conducted to evaluate the efficacy of distiller’s grain soluble (brewery waste) as a prospective ingredient to substitute expensive and high demand feed component, soybean meal for farming Labeo bata in cages installed in tropical reservoir. Two isonitrogenous and isocaloric diets comprising brewery waste (49.2 % CP) as test diet and soybean meal (44.4 % CP) as reference diet were formulated and extruded to obtain 2-mm floating pellets. The efficacy of the diets was tested in terms of survival (%), live weight gain (%), SGR (%/day), FCR, PER and ANPU and recorded 65 ± 0.2, 96 ± 8.1, 1.9 ± 0.1, 2.5 ± 0.02, 1.4 ± 0.1, 20.3 ± 2.0 and 66 ± 0.6, 112 ± 9.8, 2.2 ± 0.1, 2.2 ± 0.2, 1.6 ± 0.1 and 20 ± 2.1, respectively, for soybean and brewer’s waste-based formulated feed. The analyses of results revealed that survival, growth parameters and biochemical composition of whole body tissue did not differ significantly (p > 0.05) despite complete replacement of soybean meal by brewery waste. However, the cost estimate of diet revealed marked reduction of feed cost of Rs. 9.2/kg (33.8 %) in the test diet as compared to the reference diet. The study suggests that brewery waste could effectively replace soybean meal without effecting survival and growth of the fish. The finding thus may pave a productive way for reducing environmental pressure of disposal of an agro-industrial waste.Not Availabl