Structural Analysis of Highly Relaxed GaSb Grown on GaAs Substrates with Periodic Interfacial Array of 90° Misfit Dislocations

We report structural analysis of completely relaxed GaSb epitaxial layers deposited monolithically on GaAs substrates using interfacial misfit (IMF) array growth mode. Unlike the traditional tetragonal distortion approach, strain due to the lattice mismatch is spontaneously relieved at the heterointerface in this growth. The complete and instantaneous strain relief at the GaSb/GaAs interface is achieved by the formation of a two-dimensional Lomer dislocation network comprising of pure-edge (90°) dislocations along both [110] and [1-10]. In the present analysis, structural properties of GaSb deposited using both IMF and non-IMF growths are compared. Moiré fringe patterns along with X-ray diffraction measure the long-range uniformity and strain relaxation of the IMF samples. The proof for the existence of the IMF array and low threading dislocation density is provided with the help of transmission electron micrographs for the GaSb epitaxial layer. Our results indicate that the IMF-grown GaSb is completely (98.5%) relaxed with very low density of threading dislocations (105 cm−2), while GaSb deposited using non-IMF growth is compressively strained and has a higher average density of threading dislocations (>109 cm−2)

The Effect of Structural Complexity, Prey Density, and “Predator-Free Space” on Prey Survivorship at Created Oyster Reef Mesocosms

Interactions between predators and their prey are influenced by the habitat they occupy. Using created oyster (Crassostrea virginica) reef mesocosms, we conducted a series of laboratory experiments that created structure and manipulated complexity as well as prey density and “predator-free space” to examine the relationship between structural complexity and prey survivorship. Specifically, volume and spatial arrangement of oysters as well as prey density were manipulated, and the survivorship of prey (grass shrimp, Palaemonetes pugio) in the presence of a predator (wild red drum, Sciaenops ocellatus) was quantified. We found that the presence of structure increased prey survivorship, and that increasing complexity of this structure further increased survivorship, but only to a point. This agrees with the theory that structural complexity may influence predator-prey dynamics, but that a threshold exists with diminishing returns. These results held true even when prey density was scaled to structural complexity, or the amount of “predator-free space” was manipulated within our created reef mesocosms. The presence of structure and its complexity (oyster shell volume) were more important in facilitating prey survivorship than perceived refugia or density-dependent prey effects. A more accurate indicator of refugia might require “predator-free space” measures that also account for the available area within the structure itself (i.e., volume) and not just on the surface of a structure. Creating experiments that better mimic natural conditions and test a wider range of “predator-free space” are suggested to better understand the role of structural complexity in oyster reefs and other complex habitats

A survey of visualization tools for biological network analysis

The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing

Selective area epitaxy of ultra-high density InGaN quantum dots by diblock copolymer lithography

Highly uniform InGaN-based quantum dots (QDs) grown on a nanopatterned dielectric layer defined by self-assembled diblock copolymer were performed by metal-organic chemical vapor deposition. The cylindrical-shaped nanopatterns were created on SiNx layers deposited on a GaN template, which provided the nanopatterning for the epitaxy of ultra-high density QD with uniform size and distribution. Scanning electron microscopy and atomic force microscopy measurements were conducted to investigate the QDs morphology. The InGaN/GaN QDs with density up to 8 × 1010 cm-2 are realized, which represents ultra-high dot density for highly uniform and well-controlled, nitride-based QDs, with QD diameter of approximately 22-25 nm. The photoluminescence (PL) studies indicated the importance of NH3 annealing and GaN spacer layer growth for improving the PL intensity of the SiNx-treated GaN surface, to achieve high optical-quality QDs applicable for photonics devices

Persistence Increases with Diversity and Connectance in Trophic Metacommunities

We are interested in understanding if metacommunity dynamics contribute to the persistence of complex spatial food webs subject to colonization-extinction dynamics. We study persistence as a measure of stability of communities within discrete patches, and ask how do species diversity, connectance, and topology influence it in spatially structured food webs.We answer this question first by identifying two general mechanisms linking topology of simple food web modules and persistence at the regional scale. We then assess the robustness of these mechanisms to more complex food webs with simulations based on randomly created and empirical webs found in the literature. We find that linkage proximity to primary producers and food web diversity generate a positive relationship between complexity and persistence in spatial food webs. The comparison between empirical and randomly created food webs reveal that the most important element for food web persistence under spatial colonization-extinction dynamics is the degree distribution: the number of prey species per consumer is more important than their identity.With a simple set of rules governing patch colonization and extinction, we have predicted that diversity and connectance promote persistence at the regional scale. The strength of our approach is that it reconciles the effect of complexity on stability at the local and the regional scale. Even if complex food webs are locally prone to extinction, we have shown their complexity could also promote their persistence through regional dynamics. The framework we presented here offers a novel and simple approach to understand the complexity of spatial food webs