Parallel bandwidth characteristics calculations for thin avalanche photodiodes on a SGI Origin 2000 supercomputer

An important factor for high-speed optical communication is the availability of ultrafast and low-noise photodetectors. Among the semiconductor photodetectors that are commonly used in today’s long-haul and metro-area fiber-optic systems, avalanche photodiodes (APDs) are often preferred over p-i-n photodiodes due to their internal gain, which significantly improves the receiver sensitivity and alleviates the need for optical pre-amplification. Unfortunately, the random nature of the very process of carrier impact ionization, which generates the gain, is inherently noisy and results in fluctuations not only in the gain but also in the time response. Recently, a theory characterizing the autocorrelation function of APDs has been developed by us which incorporates the dead-space effect, an effect that is very significant in thin, high-performance APDs. The research extends the time-domain analysis of the dead-space multiplication model to compute the autocorrelation function of the APD impulse response. However, the computation requires a large amount of memory space and is very time consuming. In this research, we describe our experiences in parallelizing the code in MPI and OpenMP using CAPTools. Several array partitioning schemes and scheduling policies are implemented and tested. Our results show that the code is scalable up to 64 processors on a SGI Origin 2000 machine and has small average errors.

Simulating the evacuation of very large populations in large domains using a parallel implementation of the buildingEXODUS evacuation model

Computer egress simulation has potential to be used in large scale incidents to provide live advice to incident commanders. While there are many considerations which must be taken into account when applying such models to live incidents, one of the first concerns the computational speed of simulations. No matter how important the insight provided by the simulation, numerical hindsight will not prove useful to an incident commander. Thus for this type of application to be useful, it is essential that the simulation can be run many times faster than real time. Parallel processing is a method of reducing run times for very large computational simulations by distributing the workload amongst a number of CPUs. In this paper we examine the development of a parallel version of the buildingEXODUS software. The parallel strategy implemented is based on a systematic partitioning of the problem domain onto an arbitrary number of sub-domains. Each sub-domain is computed on a separate processor and runs its own copy of the EXODUS code. The software has been designed to work on typical office based networked PCs but will also function on a Windows based cluster. Two evaluation scenarios using the parallel implementation of EXODUS are described; a large open area and a 50 story high-rise building scenario. Speed-ups of up to 3.7 are achieved using up to six computers, with high-rise building evacuation simulation achieving run times of 6.4 times faster than real time.

Multilevel refinement for combinatorial optimisation: boosting metaheuristic performance

The multilevel paradigm as applied to combinatorial optimisation problems is a simple one, which at its most basic involves recursive coarsening to create a hierarchy of approximations to the original problem. An initial solution is found, usually at the coarsest level, and then iteratively refined at each level, coarsest to finest, typically by using some kind of heuristic optimisation algorithm (either a problem-specific local search scheme or a metaheuristic). Solution extension (or projection) operators can transfer the solution from one level to another. As a general solution strategy, the multilevel paradigm has been in use for many years and has been applied to many problem areas (for example multigrid techniques can be viewed as a prime example of the paradigm). Overview papers such as [] attest to its efficacy. However, with the exception of the graph partitioning problem, multilevel techniques have not been widely applied to combinatorial problems and in this chapter we discuss recent developments. In this chapter we survey the use of multilevel combinatorial techniques and consider their ability to boost the performance of (meta)heuristic optimisation algorithms.

Determination of micelle/water partition coefficients and associated thermodynamic data for dialkyl phthalate esters

Micelle/water partition coefficients for three dialkyl phthalate esters - dimethyl phthalate ester (DMP), diethyl phthalate ester (DEP) and dipropyl phthalate ester (DPP) were obtained by micellar liquid chromatography (MLC). Experiments were conducted over a temperature range which led to calculation of a Gibbs free energy, enthalpy and entropy of transfer for the phthalate esters. In addition, small angle neutron scattering (SANS) experiments were conducted with no substantial change observed in micelle size before and after phthalate ester incorporation. Overall, a novel method for obtaining thermodynamic information, based on partitioning data, has been developed for dialkyl phthalate esters using micellar liquid chromatography.

Macroecology of Calanus finmarchicus and C. helgolandicus in the North Atlantic Ocean and adjacent seas

Global climate change is expected to modify the spatial distribution of marine organisms. However, projections of future changes should be based on robust information on the ecological niche of species. This paper presents a macroecological study of the environmental tolerance and ecological niche (sensu Hutchinson 1957, i.e. the field of tolerance of a species to the principal factors of its environment) of Calanus finmarchicus and C. helgolandicus in the North Atlantic Ocean and adjacent seas. Biological data were collected by the Continuous Plankton Recorder (CPR) Survey, which samples plankton in the North Atlantic and adjacent seas at a standard depth of 7 m. Eleven parameters were chosen including bathymetry, temperature, salinity, nutrients, mixed-layer depth and an index of turbulence compiled from wind data and chlorophyll a concentrations (used herein as an index of available food). The environmental window and the optimum level were determined for both species and for each abiotic factor and chlorophyll concentration. The most important parameters that influenced abundance and spatial distribution were temperature and its correlates such as oxygen and nutrients. Bathymetry and other water-column-related parameters also played an important role. The ecological niche of C. finmarchicus was larger than that of C. helgolandicus and both niches were significantly separated. Our results have important implications in the context of global climate change. As temperature (and to some extent stratification) is predicted to continue to rise in the North Atlantic sector, changes in the spatial distribution of these 2 Calanus species can be expected. Application of this approach to the 1980s North Sea regime shift provides evidence that changes in sea temperature alone could have triggered the substantial and rapid changes identified in the dynamic regimes of these ecosystems. C. finmarchicus appears to be a good indicator of the Atlantic Polar Biome (mainly the Atlantic Subarctic and Arctic provinces) while C. helgolandicus is an indicator of more temperate waters (Atlantic Westerly Winds Biome) in regions characterised by more pronounced spatial changes in bathymetry.

The Nematode-Copepod Ratio And Its Use In Pollution Ecology

The nematode/copepod ratio is critically examined with a view to adding some precision to its proposed use in pollution ecology. At two unpolluted intertidal sites, differing markedly in sediment grade, the metabolic requirements of copepods are shown to be equivalent to the requirements of that fraction of the nematode population which feeds in the same way. The partitioning of this total energy requirement among individuals depends on the distribution of individual metabolic body sizes and the relative rates of metabolism. The distribution of body sizes is constrained by the sediment granulometry, which affects nematodes and copepods differently. These considerations enable precise predictions of the nematode/copepod ratios expected in unpolluted situations, against which observed ratios can be compared.

Competition Drives Clumpy Species Coexistence in Estuarine Phytoplankton

Understanding the mechanisms that maintain biodiversity is a fundamental problem in ecology. Competition is thought to reduce diversity, but hundreds of microbial aquatic primary producers species coexist and compete for a few essential resources (e.g., nutrients and light). Here, we show that resource competition is a plausible mechanism for explaining clumpy distribution on individual species volume (a proxy for the niche) of estuarine phytoplankton communities ranging from North America to South America and Europe, supporting the Emergent Neutrality hypothesis. Furthermore, such a clumpy distribution was also observed throughout the Holocene in diatoms from a sediment core. A Lotka-Volterra competition model predicted position in the niche axis and functional affiliation of dominant species within and among clumps. Results support the coexistence of functionally equivalent species in ecosystems and indicate that resource competition may be a key process to shape the size structure of estuarine phytoplankton, which in turn drives ecosystem functioning.

Scale-dependent response diversity of seabirds to prey in the North Sea

Functional response diversity is defined as the diversity of responses to environmental change among species that contribute to the same ecosystem function. Because different ecological processes dominate on different spatial and temporal scales, response diversity is likely to be scale dependent. Using three extensive data sets on seabirds, pelagic fish, and zooplankton, we investigate the strength and diversity in the response of seabirds to prey in the North Sea over three scales of ecological organization. Two-stage analyses were used to partition the variance in the abundance of predators and prey among the different scales of investigation: variation from year to year, variation among habitats, and variation on the local patch scale. On the year-to-year scale, we found a strong and synchronous response of seabirds to the abundance of prey, resulting in low response diversity. Conversely, as different seabird species were found in habitats dominated by different prey species, we found a high diversity in the response of seabirds to prey on the habitat scale. Finally, on the local patch scale, seabirds were organized in multispecies patches. These patches were weakly associated with patches of prey, resulting in a weak response strength and a low response diversity. We suggest that ecological similarities among seabird species resulted in low response diversity on the year-to-year scale. On the habitat scale, we suggest that high response diversity was due to interspecific competition and niche segregation among seabird species. On the local patch scale, we suggest that facilitation with respect to the detection and accessibility of prey patches resulted in overlapping distribution of seabirds but weak associations with prey. The observed scale dependencies in response strength and diversity have implications for how the seabird community will respond to different environmental disturbances.

Spatial changes in the sensitivity of Atlantic cod to climate-driven effects in the plankton

Recent strategies to sustain fish stocks have suggested a move towards an ecosystem based fisheries management (EBFM) approach. While EBFM considers the effect of fishing at the ecosystem level, it generally struggles with climate-driven environmental variability. In this study we show that the position of a fish stock within its distributional range or thermal niche (we use Icelandic and North Sea cod as examples of stocks at the centre and edge of their niche, respectively) will influence the relative importance of fishing and climate on abundance. At the warmer edge of the thermal niche of cod in the North Sea, we show a prominent influence of climate on the cod stock that is mediated through temperature effects on the plankton. In contrast, the influence of climate through its effects on plankton appears much less important at the present centre of the niche around Iceland. Recognising the potentially strong effect of climate on fish stocks, at a time of rapid global climate change, is probably an important prerequisite towards the synthesis of a cod management strategy.

Climate, plankton and cod

While a few North Atlantic cod stocks are stable, none have increased and many have declined in recent years. Although overfishing is the main cause of most observed declines, this study shows that in some regions, climate by its influence on plankton may exert a strong control on cod stocks, complicating the management of this species that often assumes a constant carrying capacity. First, we investigate the likely drivers of changes in the cod stock in the North Sea by evaluating the potential relationships between climate, plankton and cod. We do this by deriving a Plankton Index that reflects the quality and quantity of plankton food available for larval cod. We show that this Plankton Index explains 46.24% of the total variance in cod recruitment and 68.89% of the variance in total cod biomass. Because the effects of climate act predominantly through plankton during the larval stage of cod development, our results indicate a pronounced sensitivity of cod stocks to climate at the warmer, southern edge of their distribution, for example in the North Sea. Our analyses also reveal for the first time, that at a large basin scale, the abundance of Calanus finmarchicus is associated with a high probability of cod occurrence, whereas the genus Pseudocalanus appears less important. Ecosystem-based fisheries management (EBFM) generally considers the effect of fishing on the ecosystem and not the effect of climate-induced changes in the ecosystem state for the living resources. These results suggest that EBFM must consider the position of a stock within its ecological niche, the direct effects of climate and the influence of climate on the trophodynamics of the ecosystem.

Diet of auklet chicks in the Aleutian Islands, Alaska: similarity among islands, interspecies overlap, and relationships to ocean climate

Seabirds are effective samplers of the marine environment, and can be used to measure resource partitioning among species and sites via food loads destined for chicks. We examined the composition, overlap, and relationships to changing climate and oceanography of 3,216 food loads from Least, Crested, and Whiskered Auklets (Aethia pusilla, A. cristatella, A. pygmaea) breeding in Alaska during 1994–2006. Meals comprised calanoid copepods (Neocalanus spp.) and euphausiids (Thysanoessa spp.) that reflect secondary marine productivity, with no difference among Buldir, Kiska, and Kasatochi islands across 585 km of the Aleutian Islands. Meals were very similar among species (mean Least–Crested Auklet overlap C = 0.68; Least–Whiskered Auklet overlap C = 0.96) and among sites, indicating limited partitioning of prey resources for auklets feeding chicks. The biomass of copepods and euphausiids in Least and Crested Auklet food loads was related negatively to the summer (June–July–August) North Pacific Gyre Oscillation, while in Whiskered Auklet food loads, this was negatively related to the winter (December–January–February) Pacific Decadal Oscillation, both of which track basin-wide sea-surface temperature (SST) anomalies. We found a significant quadratic relationship between the biomass of calanoid copepods in Least Auklet food loads at all three study sites and summer (June–July) SST, with maximal copepod biomass between 3–6°C (r 2 = 0.71). Outside this temperature range, zooplankton becomes less available to auklets through delayed development. Overall, our results suggest that auklets are able to buffer climate-mediated bottom-up forcing of demographic parameters like productivity, as the composition of chick meals has remained constant over the course of our study.

Physiology, ecological niches and species distribution

Although many studies have debated the theoretical links between physiology, ecological niches and species distribution, few studies have provided evidence for a tight empirical coupling between these concepts at a macroecological scale. We used an ecophysiological model to assess the fundamental niche of a key-structural marine species. We found a close relationship between its fundamental and realized niche. The relationship remains constant at both biogeographical and decadal scales, showing that changes in environmental forcing propagate from the physiological to the macroecological level. A substantial shift in the spatial distribution is detected in the North Atlantic and projections of range shift using IPCC scenarios suggest a poleward movement of the species of one degree of latitude per decade for the 21st century. The shift in the spatial distribution of this species reveals a pronounced alteration of polar pelagic ecosystems with likely implications for lower and upper trophic levels and some biogeochemical cycles.

Macrophysiology of Calanus finmarchicus in the North Atlantic Ocean

Copepods represent the major part of the dry weight of the mesozooplankton in pelagic ecosystems and therefore have a central role in the secondary production of the North Atlantic Ocean. The calanoid copepod species Calanus finmarchicus is the main large copepod in subarctic waters of the North Atlantic, dominating the dry weight of the mesozooplankton in regions such as the northern North Sea and the Norwegian Sea. The objective of this work was to investigate the relationships between both the fundamental and realised niches of C. finmarchicus in order to better understand the future influence of global climate change on the abundance, the spatial distribution and the phenology of this key-structural species. Based on standardised Principal Component Analyses (PCAs), a macroecological approach was applied to determine factors affecting the spatial distribution of C. finmarchicus and to characterise its realised niche. Second, an ecophysiological model was used to calculate the Potential Egg Production Rate (PEPR) of C. finmarchicus and the centre of its fundamental niche. Relationships between the two niches were then investigated by correlation analysis. We found a close relationship between the fundamental and realised niches of C. finmarchicus at spatial, monthly and decadal scales. While the species is at the centre of its niche in the subarctic gyre, our joint macroecological and macrophysiological analyses show that it is at the edge of its niche in the North Sea, making the species in this region more vulnerable to temperature changes.

Drivers of euphausiid species abundance and numerical abundance in the Atlantic Ocean

Mid-ocean ridges are common features of the world’s oceans but there is a lack of understanding as to how their presence affects overlying pelagic biota. The Mid-Atlantic Ridge (MAR) is a dominant feature of the Atlantic Ocean. Here, we examined data on euphausiid distribution and abundance arising from several international research programmes and from the continuous plankton recorder. We used a generalized additive model (GAM) framework to explore spatial patterns of variability in euphausiid distribution on, and at either side of, the MAR from 60°N to 55°S in conjunction with variability in a suite of biological, physical and environmental parameters. Euphausiid species abundance peaked in mid-latitudes and was significantly higher on the ridge than in adjacent waters, but the ridge did not influence numerical abundance significantly. Sea surface temperature (SST) was the most important single factor influencing both euphausiid numerical abundance and species abundance. Increases in sea surface height variance, a proxy for mixing, increased the numerical abundance of euphausiids. GAM predictions of variability in species abundance as a function of SST and depth of the mixed layer were consistent with present theories, which suggest that pelagic niche availability is related to the thermal structure of the near surface water: more deeply-mixed water contained higher euphausiid biodiversity. In addition to exposing present distributional patterns, the GAM framework enables responses to potential future and past environmental variability including temperature change to be explored.

Macrofauna along the Sudanese Red Sea coast: potential effect of mangrove clearance on community and trophic structure

Mangroves along the Sudanese Red Sea coast are under constant anthropogenic pressure. To better understand the influence of mangrove clearance on the intertidal benthic community, we investigated the composition, biodiversity and standing stock of the macrofauna communities at high-, mid- and low-water levels in three contrasting habitats: a bare sand flat, a cleared mangrove and an intact mangrove. In addition, a community-wide metric approach based on taxon-specific carbon and nitrogen isotope values was used to compare the trophic structure between the three habitats. The habitats differed significantly in terms of macrofaunal standing stock, community composition and trophic structure. The high- and mid-water levels of the intact mangroves showed a distinct macrofaunal community characterized by elevated densities and biomass, largely governed by higher decapod and gastropod abundances. Diversity was similar for cleared and intact mangroves, but much lower for the bare sand flat. Community-wide metrics indicated highest trophic diversity and community niche breadth in the intact mangroves. Differences between the cleared and intact mangroves can be partly attributed to differences in sediment characteristics resulting from mangrove clearance. These results suggest a significant impact of mangrove clearance on the macrofaunal community and trophic structure. This study calls for further investigations and management actions to protect and restore these habitats, and ensure the survival of this ecologically valuable coastal ecosystem.