Coarsening Dynamics of Granular Heaplets in Tapped Granular Layers

A semi-continuum model is introduced to study the dynamics of the formation of granular heaplets in tapped granular layers. By taking into account the energy dissipation of collisions and screening effects due to avalanches, this model is able to reproduce qualitatively the pattern of these heaplets. Our simulations show that the granular heaplets are characterised by an effective surface tension which depends on the magnitude of the tapping intensity. Also, we observe that there is a coarsening effect in that the average size of the heaplets, V grows as the number of taps k increases. The growth law at intermediate times can be fitted by a scaling function V ~ k^z but the range of validity of the power law is limited by size effects. The growth exponent z appears to diverge as the tapping intensity is increased.Comment: 4 pages, 4 figure

Internet data packet transport: from global topology to local queueing dynamics

We study structural feature and evolution of the Internet at the autonomous systems level. Extracting relevant parameters for the growth dynamics of the Internet topology, we construct a toy model for the Internet evolution, which includes the ingredients of multiplicative stochastic evolution of nodes and edges and adaptive rewiring of edges. The model reproduces successfully structural features of the Internet at a fundamental level. We also introduce a quantity called the load as the capacity of node needed for handling the communication traffic and study its time-dependent behavior at the hubs across years. The load at hub increases with network size $N$ as $\sim N^{1.8}$. Finally, we study data packet traffic in the microscopic scale. The average delay time of data packets in a queueing system is calculated, in particular, when the number of arrival channels is scale-free. We show that when the number of arriving data packets follows a power law distribution, $\sim n^{-\lambda}$, the queue length distribution decays as $n^{1-\lambda}$ and the average delay time at the hub diverges as $\sim N^{(3-\lambda)/(\gamma-1)}$ in the $N \to \infty$ limit when $2 < \lambda < 3$, $\gamma$ being the network degree exponent.Comment: 5 pages, 4 figures, submitted to International Journal of Bifurcation and Chao

Chemical Ecology of Marine Cyanobacterial Secondary Metabolites: a Mini-review

More than 300 nitrogen-containing secondary metabolites have been reported from the procaryotic marinecyanobacteria. A majority of these compounds are of the polypeptide or mixed polyketide-polypeptidestructural class and they are a potential source of novel pharmaceuticals. In spite of the chemical richnessof marine cyanobacteria, not much is known regarding their ecological functions. To date only a handful ofmarine cyanobacterial compounds have been examined for their involvement in predator-prey interactions.This mini-review surveys the various chemical ecology studies conducted on marine cyanobacterialcompounds. From these ecological studies, many marine cyanobacterial compounds are known to deterfeeding by several species of marine predators. Such chemical defense may be crucial in maintaining thepopulation of marine cyanobacterial bloom in nature. In addition, a series of ecological studies from ourlaboratory revealed the anti-settlement properties of a number of benthic marine cyanobacterialcompounds. These studies suggested marine cyanobacteria as a potential source of natural antifoulants forthe control of fouling organisms

Chemical Ecology of Marine Cyanobacterial Secondary Metabolites: a Mini-review

More than 300 nitrogen-containing secondary metabolites have been reported from the procaryotic marinecyanobacteria. A majority of these compounds are of the polypeptide or mixed polyketide-polypeptidestructural class and they are a potential source of novel pharmaceuticals. In spite of the chemical richnessof marine cyanobacteria, not much is known regarding their ecological functions. To date only a handful ofmarine cyanobacterial compounds have been examined for their involvement in predator-prey interactions.This mini-review surveys the various chemical ecology studies conducted on marine cyanobacterialcompounds. From these ecological studies, many marine cyanobacterial compounds are known to deterfeeding by several species of marine predators. Such chemical defense may be crucial in maintaining thepopulation of marine cyanobacterial bloom in nature. In addition, a series of ecological studies from ourlaboratory revealed the anti-settlement properties of a number of benthic marine cyanobacterialcompounds. These studies suggested marine cyanobacteria as a potential source of natural antifoulants forthe control of fouling organisms

The effects of different indole-3-butyric acid (IBA) concentrations, two light regimes of in vitro rooting and acclimatization of in vitro teak (Tectona grandis L.f) plantlets

Effects of different indole-3-butyric (IBA) concentrations (0, 0.5, 1.0, 2.0, 3.0 and 5.0 mg/l), two light regimes of in vitro rooting and acclimatization on in vitro teak (Tectona grandis L.f) were investigated. Shoots incubated in the light produced higher mean number of roots (2.0) and mean root length of 15.0 and 4.5 mm when supplemented with low IBA concentrations of 0.5 and 1.0 mg/l, respectively. Conversely, when shoots were incubated in the dark, higher mean number of roots (8.0 and 3.0) and mean root lengths (14.0 and 8.8 mm) were produced when supplemented with higher IBA concentrations of 2.0 and 3.0 mg/l, respectively. IBA was found necessary for root induction and growth in light and dark where 2.0 mg/l was optimum as it recorded high mean number of root (6.0 and 8.0) with mean root lengths of 11.8 and 14.0 mm, respectively. High survival percentage of 80% was recorded for those plantlets raised in "jiffy-7" but survival reduced to 40% when grown in the autoclaved soil after one week

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

pH is a ubiquitous regulator of biological activity, including protein‐folding, protein‐protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH‐dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi‐site λ‐dynamics (CPHMD MSλD ). In the CPHMD MSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi‐site λ‐dynamics, and designed novel biasing potentials to ensure that the physical end‐states are predominantly sampled. We show that explicit solvent CPHMD MSλD simulations model realistic pH‐dependent properties of proteins such as the Hen‐Egg White Lysozyme (HEWL), binding domain of 2‐oxoglutarate dehydrogenase (BBL) and N‐terminal domain of ribosomal protein L9 (NTL9), and the p K a predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 p K a units. With the recent development of the explicit solvent CPHMD MSλD framework for nucleic acids, accurate modeling of pH‐dependent properties of both major class of biomolecules—proteins and nucleic acids is now possible. Proteins 2014; 82:1319–1331. © 2013 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107513/1/prot24499-sup-0002-suppinfo02.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/107513/2/prot24499-sup-0001-suppinfo01.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/107513/3/prot24499.pd

Diversity, Distribution and Biological Activity of Soft Corals (Octocorallia, Alcyonacea) in Singapore

The Southern Islands of Singapore are known to contain coral reefs which are high in biodiversity. However, the diversity of soft corals had received little attention to date. This study was conducted to determine the soft coral diversity in Singapore reefs as well as to conduct preliminary bioactivity tests on the organic extracts from these soft corals. A 100-meter line transect was used to survey soft corals at a 3m depth at ten different sample sites. Sclerites from samples were used to identify the soft corals to the generic level. This study uncovered the following genera of soft corals: Carijoa spp., Cladiella spp., Sinularia spp., Lobophytum spp., Sarcophyton spp., Stereonephthya spp., and Nephthea spp. In addition, an unidentified genus of soft coral was observed at Kusu Island. Cladiella spp. yielded the highest number of colonies, and Sarcophyton spp. had the highest coverage in terms of total colony diameter. The brine shrimp (Artemia salina) toxicity assay was carried out to screen for toxicity of the soft coral extracts at concentrations of 10, 100, and 1000 ppm. Results showed high levels of toxicity in extracts of Sarcophyton spp. and Cladiella spp., indicating that these soft corals are potentially good sources of bioactive compounds for drug discovery

The Quirky Collider Signals of Folded Supersymmetry

We investigate the collider signals associated with scalar quirks ("squirks") in folded supersymmetric models. As opposed to regular superpartners in supersymmetric models these particles are uncolored, but are instead charged under a new confining group, leading to radically different collider signals. Due to the new strong dynamics, squirks that are pair produced do not hadronize separately, but rather form a highly excited bound state. The excited ``squirkonium'' loses energy to radiation before annihilating back into Standard Model particles. We calculate the branching fractions into various channels for this process, which is prompt on collider time-scales. The most promising annihilation channel for discovery is W+photon which dominates for squirkonium near its ground state. We demonstrate the feasibility of the LHC search, showing that the mass peak is visible above the SM continuum background and estimate the discovery reach.Comment: 6 pages, 4 figure

Fluctuation-driven dynamics of the Internet topology

We study the dynamics of the Internet topology based on the empirical data on the level of the autonomous systems. It is found that the fluctuations occurring in the stochastic process of connecting and disconnecting edges are important features of the Internet dynamics. The network's overall growth can be described approximately by a single characteristic degree growth rate $g_{\rm eff} \approx 0.016$ and the fluctuation strength $\sigma_{\rm eff} \approx 0.14$, together with the vertex growth rate $\alpha \approx 0.029$. A stochastic model which incorporate these values and an adaptation rule newly introduced reproduces several features of the real Internet topology such as the correlations between the degrees of different vertices.Comment: Final version appeared in Phys. Rev. Let

Perturbation: the Catastrophe Causer in Scale-Free Networks

A new model about cascading occurrences caused by perturbation is established to search after the mechanism because of which catastrophes in networks occur. We investigate the avalanche dynamics of our model on 2-dimension Euclidean lattices and scale-free networks and find out the avalanche dynamic behaviors is very sensitive to the topological structure of networks. The experiments show that the catastrophes occur much more frequently in scale-free networks than in Euclidean lattices and the greatest catastrophe in scale-free networks is much more serious than that in Euclidean lattices. Further more, we have studied how to reduce the catastrophes' degree, and have schemed out an effective strategy, called targeted safeguard-strategy for scale-free networks.Comment: 4 pages, 6 eps figure