Three-dimensional nonequilibrium steady state of active particles: symmetry breaking and clustering

Motile creatures are ubiquitous in the natural world. Spanning a broad range of length scales, they all have in common the fact that they convert energy from internal or external resources into motion. In most natural situations one such individual does not exist on its own but is part of a large group like a flock of birds, a school of fish, or a bacterial suspension. Often these groups show interesting and surprising structure formation which emerges in a self-organized fashion without any external forcing. Recently, the modeling of the dynamics of such large groups has attracted a lot of interest also among physicists with the aim to understand the simple, local mechanisms which lead to a complex, global behavior. The subject of this thesis are active particles at low Reynolds numbers in three dimensions which mimic, for example, bacteria in an aqueous environment. All particles move at a constant speed and align nematically with neighboring particles – they do not distinguish between head and tail. Large groups of active particles are investigated by means of molecular dynamics simulations in the limit of overdamped dynamics. We investigate the nonequilibrium phase diagram of these active particles in terms of density and rotational Péclet number. The latter compares the strength of the nematic alignment with the rotational diffusion. We find a phase transition from the isotropic to the nematically ordered state. Close to the transition point, traveling density waves occur which resemble solitons. In the nematic region of the phase diagram a spontaneous chiral symmetry breaking can be observed. This occurs via the formation of patterns which are characterized by a helical arrangement of the mean local orientations. We discuss their stability and study their formation. A comparison to a one-dimensional rotor model (similar to the XY -model) reveals the importance of fluctuations. Very interestingly, density waves traveling along the helix emerge. They differ, however, in nature from the ones occurring at the nematicisotropic transition. In the second part of the thesis, the active particles are immersed in a surrounding, mildly turbulent fluid (R 20) to mimic the conditions of plankton in the ocean. The fluid flow field is modeled by means of kinematic simulations to ensure reasonable computational times. However, for comparison, a number of simulations of the self-propelled particles are also performed using the result of state-of-the-art direct numerical simulations. We find a remarkably good agreement between these two methods. The particles show a turbulence-induced clustering in the form of smallscale patches in a specific region of the phase diagram. The strongest clustering occurs if the integral length scale of the vorticity of the turbulent field is equal to half of the nematic interaction range and the Kolmogorov time scale matches the time scale of nematic alignment. Finally, we discuss the implications of our results onto the famous “paradox of the plankton”

Phytoplankton dynamics and bio-optical variables associated with Harmful Algal Blooms in aquaculture zones

The surveillance of Harmful Algal Blooms (HABs) in aquaculture zones is a crucial component in monitoring and mitigation of adverse effects caused by accumulation of high biomass of algal cells and/or associated toxins. Integrated findings of this thesis strongly stress the significance of synoptic bio-optical and conventional measures for efficient surveillance of HABs and their environmental triggers over required spatio-temporal scales, here shown for a case study in the Ebro Delta, NW Mediterranean. In particular, the installation of an environmental observatory in the Ebro Delta aquaculture area, and the capability of a radiometric sensor system as key component are highly motivated by study results. Yet it was clearly shown that for the interpretation of bio-optical data, detailed knowledge on bloom characteristics is crucial. By such effective coverage of bloom dynamics, combined with insights on environmental scenarios that promote the proliferation of certain taxa, public and private responses can be optimised. In a future scenario, this knowledge can be transferred to predictive models of HABs. In this sense, these future steps may advance towards preventive measures rather than mitigation actions to deal with this environmental hazard

Marine biology. Volume III - Ecology of invertebrates

Marine invertebrate ecology - sampling techniques, food intake, quality of food, seasonal aspects of food and breeding, algal mutualism, plankton, vertical migration, and bentho

Characterizing local biological hotspots in the Gulf of Maine using remote sensing data

Researchers increasingly advocate the use of ecosystem-based management (EBM) for managing complex marine ecosystems. This approach requires managers to focus on processes and cross-scale interactions, rather than individual components. However, they often lack appropriate tools and data sources to pursue this change in management approach. One method that has been proposed to understand the ecological complexity inherent in marine ecosystems is the study of biological hotspots. Biological hotspots are locations where organisms from different trophic levels aggregate to feed on abundant supplies, and they are considered a first step toward understanding the processes driving spatial and temporal heterogeneity in marine systems. Biological hotspots are supported by phytoplankton aggregations, which are characterized by high spatial and temporal variability. As a result, methods developed to locate biological hotspots in relatively stable terrestrial systems are not well suited for more dynamic marine ecosystems. The main objective of this thesis is thus to identify and characterize local-scale biological hotspots in the western side of the Gulf of Maine. The first chapter describes a new methodological framework with the steps needed to locate these types of hotspots in marine ecosystems using remote sensing datasets. Then, in the second chapter these hotspots are characterized using a novel metric that uses time series information and spatial statistics to account for both the temporal variability and spatial structure of these marine aggregations. This metric redefines biological hotspots as areas with a high probability of exhibiting positive anomalies of productivity compared to the expected regional seasonal pattern. Finally, the third chapter compares the resulting biological hotspots to fishery-dependent abundance indices of surface and benthic predators to determine the effect of the location and magnitude of phytoplankton aggregations on the rest of the ecosystem. Analyses indicate that the spatial scale and magnitude of biological hotspots in the Gulf of Maine depend on the location and time of the year. Results also show that these hotspots change over time in response to both short-term oceanographic processes and long-term climatic cycles. Finally, the new metric presented here facilitates the spatial comparison between different trophic levels, thus allowing interdisciplinary ecosystem-wide studies

If you build it, will they come? Evolution towards the application of multi-dimensional GIS to fisheries-oceanography

The development of new technologies in science is a balance between existence and use. There are three versions of this duality – something is built and users come, something is built and users don’t come, and, finally, potential users show up but the ballpark has not yet been built. In each instance there is a combination of three factors at work. The first is a scientific need for a type of data or analysis. The second is a technology or technique developed to meet the need; and the third is a perception that using the technology is somehow "better" that the existing tools and that the tool is easy to use. This work examines closely the development of a tool within oceanography – the Stommel diagram for displaying the time and space spectra of oceanographic phenomena – and the spread of the use of the diagram to other disciplines. The diagram was the product of a number of elements - the mind of a truly original oceanographer, the development of equipment able to collect the detailed temporal and spatial data used to create the plot, and the rise of "big oceanography", which led Stommel to argue graphically for taking care in the design of expeditions. Understanding the spread of the Stommel plot provides a viewpoint for examining the unexpectedly slow development of multi-dimensional geographic information systems (GIS). The development of GIS’s began in the 1970's. Data structures to hold multi-dimensional data have been developed, tools for multidimensional map algebra have been created, and test applications have been developed. The current non-development of multi-dimensional GIS is examined as a background for creating and disseminating GeoModeler, a prototype of scientific GIS able to ingest and display multi-dimensional data. Taking advantage of recent technical developments, we have created a scientific GIS that can display three-dimensional oceanographic data. GeoModeler is used to visually explore and analyze the relationship between water temperature and larval walleye pollock (Theragra chalcogramma) growth in Shelikof Strait, Alaska

Characterizing local biological hotspots in the Gulf of Maine using remote sensing data

Researchers increasingly advocate the use of ecosystem-based management (EBM) for managing complex marine ecosystems. This approach requires managers to focus on processes and cross-scale interactions, rather than individual components. However, they often lack appropriate tools and data sources to pursue this change in management approach. One method that has been proposed to understand the ecological complexity inherent in marine ecosystems is the study of biological hotspots. Biological hotspots are locations where organisms from different trophic levels aggregate to feed on abundant supplies, and they are considered a first step toward understanding the processes driving spatial and temporal heterogeneity in marine systems. Biological hotspots are supported by phytoplankton aggregations, which are characterized by high spatial and temporal variability. As a result, methods developed to locate biological hotspots in relatively stable terrestrial systems are not well suited for more dynamic marine ecosystems. The main objective of this thesis is thus to identify and characterize local-scale biological hotspots in the western side of the Gulf of Maine. The first chapter describes a new methodological framework with the steps needed to locate these types of hotspots in marine ecosystems using remote sensing datasets. Then, in the second chapter these hotspots are characterized using a novel metric that uses time series information and spatial statistics to account for both the temporal variability and spatial structure of these marine aggregations. This metric redefines biological hotspots as areas with a high probability of exhibiting positive anomalies of productivity compared to the expected regional seasonal pattern. Finally, the third chapter compares the resulting biological hotspots to fishery-dependent abundance indices of surface and benthic predators to determine the effect of the location and magnitude of phytoplankton aggregations on the rest of the ecosystem. Analyses indicate that the spatial scale and magnitude of biological hotspots in the Gulf of Maine depend on the location and time of the year. Results also show that these hotspots change over time in response to both short-term oceanographic processes and long-term climatic cycles. Finally, the new metric presented here facilitates the spatial comparison between different trophic levels, thus allowing interdisciplinary ecosystem-wide studies

Seafarers, Silk, and Science: Oceanographic Data in the Making

This thesis comprises an empirical case study of scientific data production in oceanography and a philosophical analysis of the relations between newly created scientific data and the natural world. Based on qualitative interviews with researchers, I reconstruct research practices that lead to the ongoing production of digital data related to long-term developments of plankton biodiversity in the oceans. My analysis is centred on four themes: materiality, scientific representing with data, methodological continuity, and the contribution of non-scientists to epistemic processes. These are critically assessed against the background of today’s data-intensive sciences and increased automation and remoteness in oceanographic practices. Sciences of the world’s oceans have by and large been disregarded in philosophical scholarship thus far. My thesis opens this field for philosophical analysis and reveals various conditions and constraints of data practices that are largely uncontrollable by ocean scientists. I argue that the creation of useful scientific data depends on the implementation and preservation of material, methodological, and social continuities. These allow scientists to repeatedly transform visually perceived characteristics of research samples into meaningful scientific data stored in a digital database. In my case study, data are not collected but result from active intervention and subsequent manipulation and processing of newly created material objects. My discussion of scientific representing with data suggests that scientists do not extract or read any intrinsic representational relation between data and a target, but make data gradually more computable and compatible with already existing representations of natural systems. My arguments shed light on the epistemological significance of materiality, on limiting factors of scientific agency, and on an inevitable balance between changing conditions of concrete research settings and long-term consistency of data practices.European Research Counci

Proceedings of the Ocean Climate Data Workshop

The First Consultative Meeting on Responsible National Oceanographic Data Centres (RNODC's) and Climate DataServices met in February 1988 and made a number of recommendations related to improving services to meet the needs of climate programmes. Included in these discussions was a recommendation for a Workshop on Ocean Climate Data Management. This workshop will be talking about ways to establish a Global Ocean Observing System (GOOS)