Flow around a hemisphere-cylinder at high angle of attack and low Reynolds number. Part II: POD and DMD applied to reduced domains

Three-dimensional direct numerical simulations (DNS) have been performed on a finite-size hemispherecylinder model at angle of attack AoA = 20◦ and Reynolds numbers Re = 350 and 1000. Under these conditions, massive separation exists on the nose and lee-side of the cylinder, and at both Reynolds numbers the flow is found to be unsteady. Proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD) are employed in order to study the primary instability that triggers unsteadiness at Re = 350. The dominant coherent flow structures identified at the lower Reynolds number are also found to exist at Re = 1000; the question is then posed whether the flow oscillations and structures found at the two Reynolds numbers are related. POD and DMD computations are performed using different subdomains of the DNS computational domain. Besides reducing the computational cost of the analyses, this also permits to isolate spatially localized oscillatory structures from other, more energetic structures present in the flow. It is found that POD and DMD are in general sensitive to domain truncation and noneducated choices of the subdomain may lead to inconsistent results. Analyses at Re = 350 show that the primary instability is related to the counter rotating vortex pair conforming the three-dimensional afterbody wake, and characterized by the frequency St ≈ 0.11, in line with results in the literature. At Re = 1000, vortex-shedding is present in the wake with an associated broadband spectrum centered around the same frequency. The horn/leeward vortices at the cylinder lee-side, upstream of the cylinder base, also present finite amplitude oscillations at the higher Reynolds number. The spatial structure of these oscillations, described by the POD modes, is easily differentiated from that of the wake oscillations. Additionally, the frequency spectra associated with the lee-side vortices presents well defined peaks, corresponding to St ≈ 0.11 and its few harmonics, as opposed to the broadband spectrum found at the wake.

A rede de marcação e recaptura: o caso de borboletas do gênero heliconius

(The Mark and Recapture Network: a Heliconius case study). The current pace of habitat destruction, especially in tropical landscapes, has increased the need for understanding minimum patch requirements and patch distance as tools for conserving species in forest remnants. Mark recapture and tagging studies have been instrumental in providing parameters for functional models. Because of their popularity, ease of manipulation and well known biology, butterflies have become model in studies of spatial structure. Yet, most studies on butterflies movement have focused on temperate species that live in open habitats, in which forest patches are barrier to movement. This study aimed to view and review data from mark-recapture as a network in two species of butterfly (Heliconius erato and Heliconius melpomene). A work of marking and recapture of the species was carried out in an Atlantic forest reserve located about 20km from the city of Natal (RN). Mark recapture studies were conducted in 3 weekly visits during January-February and July-August in 2007 and 2008. Captures were more common in two sections of the dirt road, with minimal collection in the forest trail. The spatial spread of captures was similar in the two species. Yet, distances between recaptures seem to be greater for Heliconius erato than for Heliconius melpomene. In addition, the erato network is more disconnected, suggesting that this specie has shorter traveling patches. Moving on to the network, both species have similar number of links (N) and unweighed vertices (L). However, melpomene has a weighed network 50% more connections than erato. These network metrics suggest that erato has more compartmentalized network and restricted movement than melpomene. Thus, erato has a larger number of disconnected components, nC, in the network, and a smaller network diameter. The frequency distribution of network connectivity for both species was better explained by a Power-law than by a random, Poissom distribution, showing that the Power-law provides a better fit than the Poisson for both species. Moreover, the Powerlaw erato is much better adjusted than in melpomene, which should be linked to the small movements that erato makes in the network

Investigations of Cloud Microphysical Response to Mixing Using Digital Holography

Cloud edge mixing plays an important role in the life cycle and development of clouds. Entrainment of subsaturated air affects the cloud at the microscale, altering the number density and size distribution of its droplets. The resulting effect is determined by two timescales: the time required for the mixing event to complete, and the time required for the droplets to adjust to their new environment. If mixing is rapid, evaporation of droplets is uniform and said to be homogeneous in nature. In contrast, slow mixing (compared to the adjustment timescale) results in the droplets adjusting to the transient state of the mixture, producing an inhomogeneous result. Studying this process in real clouds involves the use of airborne optical instruments capable of measuring clouds at the `single particle' level. Single particle resolution allows for direct measurement of the droplet size distribution. This is in contrast to other `bulk' methods (i.e. hot-wire probes, lidar, radar) which measure a higher order moment of the distribution and require assumptions about the distribution shape to compute a size distribution. The sampling strategy of current optical instruments requires them to integrate over a path tens to hundreds of meters to form a single size distribution. This is much larger than typical mixing scales (which can extend down to the order of centimeters), resulting in difficulties resolving mixing signatures. The Holodec is an optical particle instrument that uses digital holography to record discrete, local volumes of droplets. This method allows for statistically significant size distributions to be calculated for centimeter scale volumes, allowing for full resolution at the scales important to the mixing process. The hologram also records the three dimensional position of all particles within the volume, allowing for the spatial structure of the cloud volume to be studied. Both of these features represent a new and unique view into the mixing problem. In this dissertation, holographic data recorded during two different field projects is analyzed to study the mixing structure of cumulus clouds. Using Holodec data, it is shown that mixing at cloud top can produce regions of clear but humid air that can subside down along the edge of the cloud as a narrow shell, or advect down shear as a `humid halo'. This air is then entrained into the cloud at lower levels, producing mixing that appears to be very inhomogeneous. This inhomogeneous-like mixing is shown to be well correlated with regions containing elevated concentrations of large droplets. This is used to argue in favor of the hypothesis that dilution can lead to enhanced droplet growth rates. I also make observations on the microscale spatial structure of observed cloud volumes recorded by the Holodec.

Effects in ultrafast laser micromachining PMMA-based optical fibre grating

Ultrafast laser owns extreme small beam size and high pulse intensity which enable spatial localised modification either on the surface or in the bulk of materials. Therefore, ultrafast laser has been widely used to micromachine optical fibres to alter optical structures. In order to do the precise control of the micromachining process to achieve the desired structure and modification, investigations on laser parameters control should be carried out to make better understanding of the effects in the laser micromachining process. These responses are important to laser machining, most of which are usually unknown during the process. In this work, we report the real time monitored results of the reflection of PMMA based optical fibre Bragg gratings (POFBGs) during excimer ultraviolet laser micromachining process. Photochemical and thermal effects have been observed during the process. The UV radiation was absorbed by the PMMA material, which consequently induced the modifications in both spatial structure and material properties of the POFBG. The POFBG showed a significant wavelength blue shift during laser micromachining. Part of it attributed to UV absorption converted thermal energy whilst the other did not disappear after POFBG cooling off, which attributed to UV induced photodegradation in POF.

Comparison of small remotely operated vehicles and diver-operated video of circalittoral benthos

Underwater video transect methods using small remotely operated vehicles (ROVs) and diveroperated video (DOV) are commonly used in benthic biodiversity assessments. Constraints posed by deeper waters have made surveys of the circalittoral zone ([30 m depth), a particularly challenging problem. Here we compare benthic diversity metrics and cluster analyses obtained with ROV and DOV between 45 and 65 m depth off southwest Iberia, across local (tens to hundreds of meters) and regional scales (tens of kilometers). Results showed no difference between methods in terms of the benthic species richness, taxonomic distinctness, and beta diversity, but only minor differences in the spatial structure depicted at the regional level. At the local scale, DOV performed better at discriminating patterns likely because of the divers visual acuity. We found that small ROV and DOV are reliable and comparable methods for the study of circalittoral benthic assemblages and can be used in a complimentary way to detect the greatest amount of variation in benthic ecosystems. Our study facilitates the understanding of capabilities and limitations of two underwater video methods and provides important insight into choice of the most appropriate technique.

The 'rotiferologist' effect and other global correlates of species richness in monogonont rotifers

Global biodiversity patterns are often driven by diff erent environmental variables at diff erent scales. However, it is still controversial whether there are general trends, whether similar processes are responsible for similar patterns, and/or whether confounding eff ects such as sampling bias can produce misleading results. Our aim is twofold: 1) assessing the global correlates of diversity in a group of microscopic animals little analysed so far, and 2) inferring the infl uence of sampling intensity on biodiversity analyses. As a case study, we choose rotifers, because of their high potential for dispersal across the globe. We assembled and analysed a new worldwide dataset of records of monogonont rotifers, a group of microscopic aquatic animals, from 1960 to 1992. Using spatially explicit models, we assessed whether the diversity patterns conformed to those commonly obtained for larger organisms, and whether they still held true after controlling for sampling intensity, variations in area, and spatial structure in the data. Our results are in part analogous to those commonly obtained for macroorganisms (habitat heterogeneity and precipitation emerge as the main global correlates), but show some divergence (potential absence of a latitudinal gradient and of a large-scale correlation with human population). Moreover, the eff ect of sampling eff ort is remarkable, accounting for 50% of the variability; this strong eff ect may mask other patterns such as latitudinal gradients. Our study points out that sampling bias should be carefully considered when drawing conclusions from large-scale analyses, and calls for further faunistic work on microorganisms in all regions of the world to better understand the generality of the processes driving global patterns in biodiversity.

European lampreys: new insights on postglacial colonization, gene flow and speciation.

Ice ages are known to be the most dominant palaeoclimatic feature occurring on Earth, producing severe climatic oscillations and consequently shaping the distribution and the population structure of several species. Lampreys constitute excellent models to study the colonization of freshwater systems, as they commonly appear in pairs of closely related species of anadromous versus freshwater resident adults, thus having the ability to colonize new habitats, through the anadromous species, and establish freshwater resident derivates. We used 10 microsatellite loci to investigate the spatial structure, patterns of gene flow and migration routes of Lampetra populations in Europe. We sampled 11 populations including the migratory L. fluviatilis and four resident species, L. planeri, L. alavariensis, L. auremensis and L. lusitanica, the last three endemic to the Iberian Peninsula. In this southern glacial refugium almost all sampled populations represent a distinct genetic cluster, showing high levels of allopatric differentiation, reflecting long periods of isolation. As result of their more recent common ancestor, populations from northern Europe are less divergent among them, they are represented by fewer genetic clusters, and there is evidence of strong recent gene flow among populations. These previously glaciated areas from northern Europe may have been colonized from lampreys expanding out of the Iberian refugia. The pair L. fluviatilis/L. planeri is apparently at different stages of speciation in different locations, showing evidences of high reproductive isolation in the southern refugium, and low differentiation in the north.

Benthic macrofauna structure in the northeast area of Todos os Santos Bay, Bahia State, Brazil: patterns of spatial and seasonal distribution

Structure of intertidal and subtidal benthic macrofauna in the northeastern region of Todos os Santos Bay (TSB), northeast Brazil, was investigated during a period of two years. Relationships with environmental parameters were studied through uni-and multivariate statistical analyses, and the main distributional patterns shown to be especially related to sediment type and content of organic fractions (Carbon, Nitrogen, Phosphorus), on both temporal and spatial scales. Polychaete annelids accounted for more than 70% of the total fauna and showed low densities, species richness and diversity, except for the area situated on the reef banks. These banks constitute a peculiar environment in relation to the rest of the region by having coarse sediments poor in organic matter and rich in biodetritic carbonates besides an abundant and diverse fauna. The intertidal region and the shallower area nearer to the oil refinery RLAM, with sediments composed mainly of fine sand, seem to constitute an unstable system with few highly dominant species, such as Armandia polyophthalma and Laeonereis acuta. In the other regions of TSB, where muddy bottoms predominated, densities and diversity were low, especially in the stations near the refinery. Here the lowest values of the biological indicators occurred together with the highest organic compound content. In addition, the nearest sites (stations 4 and 7) were sometimes azoic. The adjacent Caboto, considered as a control area at first, presented low density but intermediate values of species diversity, which indicates a less disturbed environment in relation to the pelitic infralittoral in front of the refinery. The results of the ordination analyses evidenced five homogeneous groups of stations (intertidal; reef banks; pelitic infralittoral; mixed sediments; Caboto) with different specific patterns, a fact which seems to be mainly related to granulometry and chemical sediment characteristics.

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

Positional information in developing embryos is specified by spatial gradients of transcriptional regulators. One of the classic systems for studying this is the activation of the hunchback (hb) gene in early fruit fly (Drosophila) segmentation by the maternally-derived gradient of the Bicoid (Bcd) protein. Gene regulation is subject to intrinsic noise which can produce variable expression. This variability must be constrained in the highly reproducible and coordinated events of development. We identify means by which noise is controlled during gene expression by characterizing the dependence of hb mRNA and protein output noise on hb promoter structure and transcriptional dynamics. We use a stochastic model of the hb promoter in which the number and strength of Bcd and Hb (self-regulatory) binding sites can be varied. Model parameters are fit to data from WT embryos, the self-regulation mutant hb(14F), and lacZ reporter constructs using different portions of the hb promoter. We have corroborated model noise predictions experimentally. The results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, rather than on Bcd fluctuations. The constructs and mutant, which lack self-regulation, indicate that the multiple Bcd binding sites in the hb promoter (and their strengths) also play a role in buffering noise. The model is robust to the variation in Bcd binding site number across a number of fly species. This study identifies particular ways in which promoter structure and regulatory dynamics reduce hb output noise. Insofar as many of these are common features of genes (e. g. multiple regulatory sites, cooperativity, self-feedback), the current results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development.

Spatial genetic structure of Hymenaea stigonocarpa Mart. ex Hayne assessed with chloroplast microsatellite markers

The use of chloroplast DNA markers (cpDNA) helps to elucidate questions related to ecology, evolution and genetic structure. The knowledge of inter-and intra-population genetic structure allows to design effective conservation and management strategies for tropical tree species. With the aim to help the conservation of Hymenaea stigonocarpa of the Cerrado (Brazilian savanna) in Sao Paulo State, an analysis of the spatial genetic structure (SGS) was conducted in two populations using five universal chloroplast microsatellite loci (cpSSR). The population of 68 trees of H. stigonocarpa in the Ecological Station of Itirapina (ESI) had a single haplotype, indicating a strong founder effect. In turn, the population of 47 trees of H. stigonocarpa in a contiguous area that includes the Ecological Station of Assis and the Assis State Forest (ESA), showed six haplotypes ((n) over cap (h) = 6) with a moderate haplotype diversity ((h) over cap = 0667 + 0094), revealing that it was founded by a small number of maternal lineages. The SGS analysis for the population ESA/ASF, using Moran`s I index, indicated limited seed dispersal. Considering SGS, for ex situ conservation strategies in the population ESA/ASF, seed harvesting should require a minimum distance of 750 m among seed-trees.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon

Understanding the mating patterns of populations of tree species is a key component of ex situ genetic conservation. In this study, we analysed the genetic diversity, spatial genetic structure (SGS) and mating system at the hierarchical levels of fruits and individuals as well as pollen dispersal patterns in a continuous population of Theobroma cacao in Para State, Brazil. A total of 156 individuals in a 0.56 ha plot were mapped and genotyped for nine microsatellite loci. For the mating system analyses, 50 seeds were collected from nine seed trees by sampling five fruits per tree (10 seeds per fruit). Among the 156 individuals, 127 had unique multilocus genotypes, and the remaining were clones. The population was spatially aggregated; it demonstrated a significant SGS up to 15m that could be attributed primarily to the presence of clones. However, the short seed dispersal distance also contributed to this pattern. Population matings occurred mainly via outcrossing, but selfing was observed in some seed trees, which indicated the presence of individual variation for self-incompatibility. The matings were also correlated, especially within ((r) over cap (p(m)) = 0.607) rather than among the fruits ((r) over cap (p(m)) = 0.099), which suggested that a small number of pollen donors fertilised each fruit. The paternity analysis suggested a high proportion of pollen migration (61.3%), although within the plot, most of the pollen dispersal encompassed short distances (28m). The determination of these novel parameters provides the fundamental information required to establish long-term ex situ conservation strategies for this important tropical species. Heredity (2011) 106, 973-985; doi:10.1038/hdy.2010.145; published online 8 December 2010

Integrating high and moderate spatial resolution image data to estimate forest age structure

The collection of spatial information to quantify changes to the state and condition of the environment is a fundamental component of conservation or sustainable utilization of tropical and subtropical forests, Age is an important structural attribute of old-growth forests influencing biological diversity in Australia eucalypt forests. Aerial photograph interpretation has traditionally been used for mapping the age and structure of forest stands. However this method is subjective and is not able to accurately capture fine to landscape scale variation necessary for ecological studies. Identification and mapping of fine to landscape scale vegetative structural attributes will allow the compilation of information associated with Montreal Process indicators lb and ld, which seek to determine linkages between age structure and the diversity and abundance of forest fauna populations. This project integrated measurements of structural attributes derived from a canopy-height elevation model with results from a geometrical-optical/spectral mixture analysis model to map forest age structure at a landscape scale. The availability of multiple-scale data allows the transfer of high-resolution attributes to landscape scale monitoring. Multispectral image data were obtained from a DMSV (Digital Multi-Spectral Video) sensor over St Mary's State Forest in Southeast Queensland, Australia. Local scene variance levels for different forest tapes calculated from the DMSV data were used to optimize the tree density and canopy size output in a geometric-optical model applied to a Landsat Thematic Mapper (TU) data set. Airborne laser scanner data obtained over the project area were used to calibrate a digital filter to extract tree heights from a digital elevation model that was derived from scanned colour stereopairs. The modelled estimates of tree height, crown size, and tree density were used to produce a decision-tree classification of forest successional stage at a landscape scale. The results obtained (72% accuracy), were limited in validation, but demonstrate potential for using the multi-scale methodology to provide spatial information for forestry policy objectives (ie., monitoring forest age structure).

Fine-scale spatial genetic structure and gene dispersal in Silene latifolia.

Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F(ST)=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5-30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.

Spatial variation of dung beetle assemblages associated with forest structure in remnants of southern Brazilian Atlantic Forest

ABSTRACT The Brazilian Atlantic Forest is one of the world's biodiversity hotspots, and is currently highly fragmented and disturbed due to human activities. Variation in environmental conditions in the Atlantic Forest can influence the distribution of species, which may show associations with some environmental features. Dung beetles (Coleoptera: Scarabaeinae) are insects that act in nutrient cycling via organic matter decomposition and have been used for monitoring environmental changes. The aim of this study is to identify associations between the spatial distribution of dung beetle species and Atlantic Forest structure. The spatial distribution of some dung beetle species was associated with structural forest features. The number of species among the sampling sites ranged widely, and few species were found in all remnant areas. Principal coordinates analysis indicated that species composition, abundance and biomass showed a spatially structured distribution, and these results were corroborated by permutational multivariate analysis of variance. The indicator value index and redundancy analysis showed an association of several dung beetle species with some explanatory environmental variables related to Atlantic Forest structure. This work demonstrated the existence of a spatially structured distribution of dung beetles, with significant associations between several species and forest structure in Atlantic Forest remnants from Southern Brazil.