Publications
196 results found
Kehl C, Nooteboom PD, Kaandorp MLA, et al., 2023, Efficiently simulating Lagrangian particles in large-scale ocean flows — Data structures and their impact on geophysical applications, Computers and Geosciences, Vol: 175, ISSN: 0098-3004
Studying oceanography by using Lagrangian simulations has been adopted for a range of scenarios, such as the determining the fate of microplastics in the ocean, simulating the origin locations of microplankton used for palaeoceanographic reconstructions, and for studying the impact of fish aggregation devices on the migration behaviour of tuna. These simulations are complex and represent a considerable runtime effort to obtain trajectory results, which is the prime motivation for enhancing the performance of Lagrangian particle simulators. This paper assesses established performance enhancing techniques from Eulerian simulators in light of computational conditions and demands of Lagrangian simulators. A performance enhancement strategy specifically targeting physics-based Lagrangian particle simulations is outlined to address the performance gaps, and techniques for closing the performance gap are presented and implemented. Realistic experiments are derived from three specific oceanographic application scenarios, and the suggested performance-enhancing techniques are benchmarked in detail, so to allow for a good attribution of speed-up measurements to individual techniques. The impacts and insights of the performance enhancement strategy are further discussed for Lagrangian simulations in other geoscience applications. The experiments show that I/O-enhancing techniques, such as dynamic loading and buffering, lead to considerable speed-up on-par with an idealised parallelisation of the process over 20 nodes. Conversely, while the cache-efficient structure-of-arrays collection yields a visible speed-up, other alternative data structures fail in fulfilling the theoretically-expected performance increase. This insight demonstrates the importance of good data alignment in memory and caches for Lagrangian physics simulations.
Guerrini F, Lobelle D, Mari L, et al., 2023, Modeling carbon export mediated by biofouled microplastics in the Mediterranean Sea, Limnology and Oceanography
Marine microplastics can be colonized by biofouling microbial organisms, leading to a decrease in microplastics' buoyancy. The sinking of biofouled microplastics could therefore represent a novel carbon export pathway within the ocean carbon cycle. Here, we model how microplastics are biofouled by diatoms, their consequent vertical motion due to buoyancy changes, and the interactions between particle-attached diatoms and carbon pools within the water column. We initialize our Lagrangian framework with biogeochemical data from NEMO-MEDUSA-2.0 and estimate the amount of organic carbon exported below 100 m depth starting from different surface concentrations of 1-mm microplastics. We focus on the Mediterranean Sea that is characterized by some of the world's highest microplastics concentrations and is a hotspot for biogeochemical changes induced by rising atmospheric carbon dioxide levels. Our results show that the carbon export caused by sinking biofouled microplastics is proportional to the concentration of microplastics in the sea surface layer, at least at modeled concentrations. We estimate that, while current concentrations of microplastics can modify the natural biological carbon export by < 1%, future concentrations projected under business-as-usual pollution scenarios may lead to carbon exports up to 5% larger than the baseline (1998–2012) by 2050. Areas characterized by high primary productivity, that is, the Western and Central Mediterranean, are those where microplastics-mediated carbon export results to be the highest. While highlighting the potential and quantitatively limited occurrence of this phenomenon in the Mediterranean Sea, our results call for further investigation of a microplastics-related carbon export pathway in the global ocean.
Onink V, Kaandorp MLA, van Sebille E, et al., 2022, Influence of Particle Size and Fragmentation on Large-Scale Microplastic Transport in the Mediterranean Sea, ENVIRONMENTAL SCIENCE & TECHNOLOGY, Vol: 56, Pages: 15528-15540, ISSN: 0013-936X
Ypma SL, Bohte Q, Forryan A, et al., 2022, Detecting the most effective cleanup locations using network theory to reduce marine plastic debris: a case study in the Galapagos Marine Reserve, OCEAN SCIENCE, Vol: 18, Pages: 1477-1490, ISSN: 1812-0784
Nooteboom PD, Scutt Phillips J, Kehl C, et al., 2022, Modelling of tuna around fish aggregating devices: the importance of ocean flow and prey
<jats:title>Abstract</jats:title><jats:p>Catch and distribution of tuna in the ocean are typically investigated with ocean basin-scale models. Due to their large scale, such models must greatly simplify tuna behaviour occurring at a scale below ∼100 km, despite interactions at this level potentially being important to both catch and distribution of tuna. For example, the associative behaviour of tuna with man-made floating objects, that are deployed by fishers to improve their catch rates (Fish Aggregating Devices; FADs), are usually ignored or simplified. Here we present a model that can be used to investigate the influence of tuna dynamics below the ∼100 km scale on larger scales. It is an Agent-Based Model (ABM) of a hypothetical, tuna-like species, that includes their interactions with each other, free-floating FADs and prey. In this ABM, both tuna and FADs are represented by Lagrangian particles that are advected by an ocean flow field, with tuna also exhibiting active swimming based on internal states such as stomach fullness. We apply the ABM in multiple configurations of idealised flow and prey fields, alongside differing interaction strengths between agents. When tuna swimming behaviour is influenced equally by prey and FADs, we find that the model simulations compare well with observations at the ≲ 100 km scale. For instance, compared to observations, tuna particles have a similar stomach fullness when associated or non-associated to a FAD, tuna colonize at similar timescales at FADs after their deployment and tuna particles exhibit similar variations in continuous residence times. However, we find large differences in emergent dynamics such as residence and catch among different flow configurations, because the flow determines the time scale at which tuna encounter FADs. These findings are discussed in the context of directing future research, and an improved interpretation of tuna catch and other data for the sustainable managem
Gomez-Navarro L, Van Sebille E, MORALES MÁRQUEZ V, et al., 2022, The effect of model tidal forcing on virtual particle dispersion and accumulation at the ocean surface
Nooteboom PD, Baatsen M, Bijl PK, et al., 2022, Improved Model-Data Agreement With Strongly Eddying Ocean Simulations in the Middle-Late Eocene, PALEOCEANOGRAPHY AND PALEOCLIMATOLOGY, Vol: 37, ISSN: 2572-4517
Christensen AK, Piggott MD, van Sebille E, et al., 2022, Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer., PLoS Comput Biol, Vol: 18
Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Spatial patchiness is a critical factor underlying these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a fully 3D direct numerical simulation of convective mixed layer turbulence, with an individual-based microbial model to test the key hypothesis that the coupling of gyrotactic motility and turbulence drives intense microscale patchiness. The fluid model simulates turbulent convection caused by heat loss through the fluid surface, for example during the night, during autumnal or winter cooling or during a cold-air outbreak. We find that under such conditions, turbulence-driven patchiness is depth-structured and requires high motility: Near the fluid surface, intense convective turbulence overpowers motility, homogenising motile and non-motile microbes approximately equally. At greater depth, in conditions analogous to a thermocline, highly motile microbes can be over twice as patch-concentrated as non-motile microbes, and can substantially amplify their swimming velocity by efficiently exploiting fast-moving packets of fluid. Our results substantiate the predictions of earlier studies, and demonstrate that turbulence-driven patchiness is not a ubiquitous consequence of motility but rather a delicate balance of motility and turbulent intensity.
Ypma SL, Bohte Q, Forryan A, et al., 2022, Detecting most effective cleanup locations using network theory to reduce marine plastic debris: A case study in the Galapagos Marine Reserve
<jats:p>Abstract. The Galapagos Marine Reserve was established in 1986 to ensure protection of the islands' unique biodiversity. Unfortunately, the islands are polluted by marine plastic debris and the island authorities face the challenge to effectively remove plastic from its shorelines due to limited resources. To optimise efforts, we have identified the most effective cleanup locations on the Galapagos Islands using network theory. A network is constructed from a Lagrangian simulation describing the flow of macroplastic between the various islands within the Galapagos Marine Reserve, where the nodes represent locations along the coastline and the edges the likelihood for plastic to travel from one location and beach at another. We have found four network centralities that provide the best coastline ranking to optimise the cleanup effort based on various impact metrics. In particular locations with a high retention rate are favourable for cleanup. The results indicate that using the most effective centrality for finding cleanup locations is a good strategy for heavily polluted regions if the distribution of marine plastic debris on the coastlines is unknown and limited cleanup resources are available. </jats:p>
Bergmann M, Collard F, Fabres J, et al., 2022, Plastic pollution in the Arctic (vol 3, pg 323, 2022), NATURE REVIEWS EARTH & ENVIRONMENT, Vol: 3, Pages: 420-420
Valles-Casanova I, Fraile-Nuez E, Martin-Rey M, et al., 2022, Water Mass Transports and Pathways in the North Brazil-Equatorial Undercurrent Retroflection, JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS, Vol: 127, ISSN: 2169-9275
Fischer R, Lobelle D, Kooi M, et al., 2022, Modelling submerged biofouled microplastics and their vertical trajectories, BIOGEOSCIENCES, Vol: 19, Pages: 2211-2234, ISSN: 1726-4170
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- Citations: 5
Bergmann M, Collard F, Fabres J, et al., 2022, Plastic pollution in the Arctic, NATURE REVIEWS EARTH & ENVIRONMENT, Vol: 3, Pages: 323-337
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- Citations: 23
Bertoncelj V, Stocchi P, Holzhauser C, et al., 2022, Assessing hydrodynamic processes of nearshore coral reefs: numerical modeling and field observations around the island of Cura&#231;ao
<jats:p>&lt;p&gt;The state of coral reef ecosystems is highly dependent on the availability and ratio of essential resources such as oxygen, minerals and nutrients, and the presence of pollutants, pathogens and other possible stressors. The distribution of these inputs is dynamic and depends on many factors, including the nearshore hydrodynamic processes. These are unique processes, consisting of tidal pumping, nearshore circulation, and wave action. Furthermore, these processes are highly influenced by complex reef bathymetry and the physical roughness of the reef. The latter has a crucial role in the boundary layer characteristics, which influences uptake by reef organisms at smaller spatial scales.&lt;/p&gt;&lt;p&gt;The understanding of distribution and transport of particulate and dissolved substances is challenging as field surveys are difficult to perform and there is a large variety of coral shapes. However, assessing the hydrodynamic processes is a necessary first step in order to link the sources and sinks of substances with the coral health and growth. Within the interdisciplinary research program SEALINK, we aim to assess the distribution and pathways of substances around the island of Cura&amp;#231;ao. Field observations on selected sites along the coast of Cura&amp;#231;ao include current and wave measurements with Acoustic Doppler Current Profilers and flow visualization with fluorescent dye.&lt;/p&gt;&lt;p&gt;We will present preliminary results from the field campaign showing velocity fields and wave transformation on different stations along the cross-shore transects on the reef platform. Using a combination of field observations and 3D non-hydrostatic Computational Fluid Dynamics models, we investigate the mixing mechanisms and local energy balance at scales of O(10 m) on the selected reef quadrants. This serves as a basis for a further analysis wit
Kaandorp M, Lobelle D, Kehl C, et al., 2022, A global 3D map of marine plastic litter: a data assimilated modelling framework &#160;
<jats:p>&lt;p&gt;Estimates of plastic quantities entering our oceans are not yet consistent with observed concentrations in the marine environment. This has led to the often-quoted statement that 99% of the marine plastics are missing. Here, we present a framework where the global transport of marine plastics is modelled over long time scales, in which the effects of different sources and sinks is investigated. Data assimilation techniques are used to inform unknown parameters regarding these sources and sinks, enabling us to quantify their role on the global plastic mass budget.&lt;/p&gt;&lt;p&gt;State-of-the-art numerical models are included in the framework to capture for the first time the combined effect of marine plastic beaching, resuspension, biofouling, turbulent mixing, and fragmentation. The relative importance of different marine plastic sources is investigated, such as mismanaged coastal plastic waste, riverine outflow, and fishing activity. Unknown parameters are found by means of calibration to a large set of observational data of plastic concentrations in the ocean surface water, water column, ocean floor, and on coastlines.&lt;/p&gt;&lt;p&gt;We show that with this framework, the global marine plastic mass budget can be closed. An overview is given of which environmental reservoirs are likely to contain most of the plastic mass, which sources are contributing to most of the pollution, and what the residence times of litter in the marine environment is. With the model calibration approach, we additionally get a better insight in the physics governing the transport of marine litter.&amp;#160;&lt;/p&gt;</jats:p>
Manral D, Amaral-Zettler L, van Sebille E, 2022, Lagrangian connectivity of marine plankton under thermal constraints
<jats:p>&lt;p&gt;The biogeographic distribution of marine planktonic communities in the global ocean and its drivers has been a topic of great interest in the scientific community. Some of these drivers can be abiotic: ocean currents, temperature, salinity, nutrients, and others biotic: presence of predators and competitive species. In our study, we focus on the distribution mediated by ocean currents and temperature. Combining Lagrangian modeling and network theory approaches, we estimate the pathways and timescales that establish the surface connectivity for passive i.e., freely floating plankton between stations in the Atlantic Ocean where plankton have been sampled during &lt;em&gt;Tara Oceans &amp; Tara Oceans Polar Circle&lt;/em&gt; (2009-2013) and &lt;em&gt;Tara Pacific&lt;/em&gt; (2016-2018) expeditions.&lt;/p&gt;&lt;p&gt;We obtain these estimates using a transition matrix approach derived from surface ocean simulations. Given the high rates of reproduction of many planktonic species and that only a few organisms are needed to establish connectivity, we make use of the minimum time path between different stations. To obtain plankton connectivity, two types of constraints are applied on the passive connectivity model: &lt;em&gt;thermal niche&lt;/em&gt; and &lt;em&gt;thermal adaptation rate&lt;/em&gt;, based on data for a given planktonic species from the literature. From the preliminary analysis, we find that, using minimum time paths, passive particles representative of foraminifera can connect all the stations in less than 3 years. Application of thermal niche constraints increases the minimum connectivity time between stations by approximately 10%, suggesting that plankton can keep to within their favorable thermal conditions by advecting via slightly longer paths. Main
Reijnders D, van Sebille E, Bijl P, 2022, KlimaatHelpdesk.org: Connecting citizens with climate questions to experts with answers&#160;
<jats:p>&lt;div&gt;&lt;p&gt;&lt;span&gt;When faced with a question, scientists and scholars are trained to&amp;#160;search&amp;#160;academic and informal&amp;#160;literature to find&amp;#160;the answer.&amp;#160;But where&amp;#160;can&amp;#160;the public&amp;#160;find reliable&amp;#160;answers to&amp;#160;questions about the climate crisis?&amp;#160;After all,&amp;#160;the climate crisis&amp;#160;is a topic about which our understanding&amp;#160;rapidly&amp;#160;evolves&amp;#160;across a wide array of disciplines.&amp;#160;The validity&amp;#160;and reliability&amp;#160;of&amp;#160;offered&amp;#160;information is difficult to&amp;#160;assess&amp;#160;for non-specialists, while scientific consensus is&amp;#160;sometimes deliberately undermined&amp;#160;in popular articles. Moreover,&amp;#160;civil&amp;#160;questions about&amp;#160;the&amp;#160;climate&amp;#160;crisis&amp;#160;can be very specific, pragmatic or locally applicable, so not all answers can be found on popular sources&amp;#160;that&amp;#160;commonly&amp;#160;provide only the theoretical principles or general background.&amp;#160;This raises the question how we can connect citizens with climate-related questions to understandable scientific expert&amp;#160;&lt;/span&gt;&lt;span&gt;knowledge&lt;/span&gt;&lt;span&gt;.&lt;/span&gt;&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;p&gt;&lt;span&gt;KlimaatHelpdesk.org&amp;#160;is meant to become the go-to place in the Netherlands for&amp;#160;citizens&amp;#16
Ypma S, Bohte Q, Jones J, et al., 2022, Detecting most effective coastal plastic clean-up hubs using network theory: a case study in the Galapagos Marine Reserve&#160;
<jats:p>&lt;p&gt;Over 8 tonnes of plastic are removed from the coastlines of the Galapagos Islands each year. Although the Galapagos Marine Reserve is expanding to ensure an even larger protection of its unique biodiversity, the island authorities face the challenge to effectively remove plastic from its shorelines due to limited resources. We are developing a clean-up efficacy model that will optimize for most cost-effective and least-invasive clean-up locations. Network (connectivity) theory is widely applied in ecology to study the interaction of species between spatially separated habitats. Here, we use a similar approach to discern the most effective removal hubs on the Galapagos Islands. A connectivity matrix is constructed from a Lagrangian simulation describing the flow of macroplastic between the various islands within the Galapagos Marine Reserve, where the nodes represent locations along the coastline and the edges the likelihood that plastic travels from one location and beaches at another. To measure the impact of removal, various centralities are determined, such as degree centrality, betweenness centrality (using the most likely path) and eigenvector centrality. Combining the results with other metrics such as the distance to the nearest port or tourist attractions, recommendations are made for&lt;/p&gt;&lt;ul&gt;&lt;li&gt;most effective &lt;em&gt;intervention&lt;/em&gt; removal hubs that would prevent further spread of plastic throughout the marine reserve&lt;/li&gt;&lt;li&gt;most effective &lt;em&gt;accumulation&lt;/em&gt; removal hubs that would negate the impact of plastic on wildlife&lt;/li&gt;&lt;li&gt;most suited regions for protection resulting from the existence of clusters (e.g. regions of limited connectivity)&lt;/li&gt;&l
Reijnders D, Deleersnijder E, van Sebille E, 2022, Lagrangian Ocean Ventilation: Improved Subgrid-Scale Dispersion on Neutral Surfaces
<jats:p>&lt;p&gt;Mesoscale eddies play a major role in ocean ventilation by stirring ocean tracers, such as carbon, along sloping surfaces of neutral buoyancy. To capture the effects of these turbulent eddies, coarse resolution ocean models resort to tracer diffusion parameterizations that take into account neutral surface slopes. Likewise, when studying tracer pathways in a Lagrangian framework, the effect of eddy dispersion needs to be parameterized when coarse models are used.&lt;/p&gt;&lt;p&gt;Dispersion in Lagrangian simulations is traditionally parameterized by random walks, equivalent to diffusion in Eulerian models. Beyond random walks, there is a hierarchy of stochastic parameterizations, where stochastic perturbations are added to Lagrangian particle velocities, accelerations, or hyper-accelerations. These parameterizations are referred to as the 1&lt;sup&gt;st&lt;/sup&gt;, 2&lt;sup&gt;nd&lt;/sup&gt; and 3&lt;sup&gt;rd&lt;/sup&gt; order &amp;#8216;Markov models&amp;#8217; (Markov-N&lt;em&gt;)&lt;/em&gt; respectively. Most previous studies investigate these parameterizations in two-dimensional setups, often restricted to the ocean surface. The few studies that investigated Lagrangian dispersion parameterizations on three-dimensional neutral surfaces have focused only on random walk (Markov-0) dispersion.&lt;/p&gt;&lt;p&gt;Here, we present a three-dimensional isoneutral formulation of the Markov-1 model. We also implement an anisotropic, shear-dependent formulation of Lagrangian random walk dispersion, originally formulated as a Eulerian diffusion parameterization by Le Sommer et al (2011). Random walk dispersion and Markov-1 are compared using an idealized setup as well as more realistic coarse and coarsened (50 km) ocean model out
Onink V, van Sebille E, Laufkotter C, 2022, Empirical Lagrangian parametrization for wind-driven mixing of buoyant particles at the ocean surface, GEOSCIENTIFIC MODEL DEVELOPMENT, Vol: 15, Pages: 1995-2012, ISSN: 1991-959X
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- Citations: 4
Kaandorp MLA, Ypma SL, Boonstra M, et al., 2022, Using machine learning and beach cleanup data to explain litter quantities along the Dutch North Sea coast, OCEAN SCIENCE, Vol: 18, Pages: 269-293, ISSN: 1812-0784
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- Citations: 2
Rice A, Nooteboom PD, Sebille E, et al., 2022, Limited Lateral Transport Bias During Export of Sea Surface Temperature Proxy carriers in the Mediterranean Sea, GEOPHYSICAL RESEARCH LETTERS, Vol: 49, ISSN: 0094-8276
van Duinen B, Kaandorp MLA, van Sebille E, 2022, Identifying Marine Sources of Beached Plastics Through a Bayesian Framework: Application to Southwest Netherlands, GEOPHYSICAL RESEARCH LETTERS, Vol: 49, ISSN: 0094-8276
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- Citations: 3
Nooteboom PD, Bijl PK, Kehl C, et al., 2022, Sedimentary microplankton distributions are shaped by oceanographically connected areas, EARTH SYSTEM DYNAMICS, Vol: 13, Pages: 357-371, ISSN: 2190-4979
Reijnders D, Deleersnijder E, Sebille E, 2022, Simulating Lagrangian Subgrid-Scale Dispersion on Neutral Surfaces in the Ocean, JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS, Vol: 14
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- Citations: 2
Reijnders D, Deleersnijder E, van Sebille E, 2021, Simulating Lagrangian Subgrid-Scale Dispersion on Neutral Surfaces in the Ocean
Weckhuysen B, Have IT, Meirer F, et al., 2021, Nanoscale Infrared Spectroscopy Reveals Nanoplastics at 5000 m Depth in the South Atlantic Ocean
<jats:title>Abstract</jats:title> <jats:p>Millimeter- and micrometer-sized plastics are well-documented in aquatic ecosystems, but little is known about sub-micrometer particles because conventional analytical techniques lack sufficient spatial resolution or the spectroscopic means to unambiguously identify individual nanometer-sized plastic particles. We combined the spatial resolution of atomic force microscopy with chemical information from infrared spectroscopy to detect, identify, and count nanoplastics down to 20 nm in diameter in samples from different depths in the South Atlantic Ocean. We present evidence for the presence of polyethylene terephthalate (PET) nanoplastics in different states of degradation at 5000 m. Using lab-based ageing of PET, we demonstrate that nanoplastics can form even without light or interaction with the plastisphere, and that macroscopic PET items are a plausible source of PET nanoplastics in the ocean.</jats:p>
van Duinen B, Kaandorp MLA, Van Sebille E, 2021, Identifying Marine Sources of Beached Plastics through a Bayesian Framework: Application to Southwest Netherlands
Nooteboom PD, Baatsen M, Bijl PK, et al., 2021, Strongly eddying ocean simulations required to resolve Eocene model-data mismatch
Nooteboom PD, Baatsen M, Bijl PK, et al., 2021, Strongly eddying ocean simulations required to resolve Eocene model-data mismatch
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