Dynamics of a large submersed plant bed in upper Chesapeake Bay

A large SAV bed in upper Chesapeake Bay has experienced several abrupt shifts over the past half-century, beginning with near-complete loss after a record-breaking flood in 1972, followed by an unexpected, rapid resurgence in the early 2000’s, then partial decline in 2011 following another major flood event. Together, these trends and events provide a unique opportunity to study a recovering SAV ecosystem from several different perspectives. First, I analyzed and synthesized existing time series datasets to make inferences about what factors prompted the recovery. Next, I analyzed existing datasets, together with field samples and a simple hydrodynamic model to investigate mechanisms of SAV bed loss and resilience to storm events. Finally, I conducted field deployments and experiments to explore how the bed affects internal physical and biogeochemical processes and what implications those effects have for the dynamics of the system. I found that modest reductions in nutrient loading, coupled with several consecutive dry years likely facilitated the SAV resurgence. Furthermore, positive feedback processes may have played a role in the sudden nature of the recovery because they could have reinforced the state of the bed before and after the abrupt shift. I also found that scour and poor water clarity associated with sediment deposition during the 2011 flood event were mechanisms of plant loss. However, interactions between the bed, water flow, and waves served as mechanisms of resilience because these processes created favorable growing conditions (i.e., clear water, low flow velocities) in the inner core of the bed. Finally, I found that that interactions between physical and biogeochemical processes led to low nutrient concentrations inside the bed relative to outside the bed, which created conditions that precluded algal growth and reinforced vascular plant dominance. This work demonstrates that positive feedbacks play a central role in SAV resilience to both chronic eutrophication as well as acute storm events. Furthermore, I show that analysis of long-term ecological monitoring data, together with field measurements and experiments, can be an effective approach for understanding the mechanisms underlying ecosystem dynamics.

Climate Change Influences Carrying Capacity in a Coastal Embayment Dedicated to Shellfish Aquaculture

A spatially explicit coupled hydrodynamic-biogeochemical model was developed to study a coastal ecosystem under the combined effects of mussel aquaculture, nutrient loading and climate change. The model was applied to St Peter's Bay (SPB), Prince Edward Island, Eastern Canada. Approximately 40 % of the SPB area is dedicated to mussel (Mytilus edulis) longline culture. Results indicate that the two main food sources for mussels, phytoplankton and organic detritus, are most depleted in the central part of the embayment. Results also suggest that the system is near its ultimate capacity, a state where the energy cycle is restricted to nitrogen-phytoplankton-detritus-mussels with few resources left to be transferred to higher trophic levels. Annually, mussel meat harvesting extracts nitrogen (N) resources equivalent to 42 % of river inputs or 46.5 % of the net phytoplankton primary production. Under such extractive pressure, the phytoplankton biomass is being curtailed to 1980's levels when aquaculture was not yet developed and N loading was half the present level. Current mussel stocks also decrease bay-scale sedimentation rates by 14 %. Finally, a climate change scenario (year 2050) predicted a 30 % increase in mussel production, largely driven by more efficient utilization of the phytoplankton spring bloom. However, the predicted elevated summer temperatures (> 25 A degrees C) may also have deleterious physiological effects on mussels and possibly increase summer mortality levels. In conclusion, cultivated bivalves may play an important role in remediating the negative impacts of land-derived nutrient loading. Climate change may lead to increases in production and ecological carrying capacity as long as the cultivated species can tolerate warmer summer conditions.

Small-scale variability of the current in the Strait of Bonifacio

Current dynamics in the Strait of Bonifacio (south Corsica) were investigated at a small scale during the STELLAMARE1 multidisciplinary cruise in summer 2012, using in situ measurements and modeling data. The Strait of Bonifacio is a particularly sensitive marine area in which specific conservation measures have been taken to preserve the natural environment and wild species. Good knowledge of the hydrodynamics in this area is essential to optimize the Marine Protected Area's management rules. Therefore, we used a high-resolution model (400 m) based on the MARS3D code to investigate the main flux exchanges and to formulate certain hypotheses about the formation of possible eddy structures. The aim of the present paper is first to synthetize the results obtained by combining Acoustic Doppler Current Profiler data, hydrological parameters, Lagrangian drifter data, and satellite observations such as MODIS OC5 chlorophyll a data or Metop-A AVHRR Sea Surface Temperature (SST) data. These elements are then used to validate the presence of the mesoscale eddies simulated by the model and their recurrence outside the cruise period. To complete the analysis, the response of the 3D hydrodynamical model was evaluated under two opposing wind systems and certain biases were detected. Strong velocities up to 1 m s(-1) were recorded in the east part due to the Venturi effect; a complementary system of vortices governed by Coriolis effect and west wind was observed in the west part, and horizontal stratification in the central part has been identified under typical wind condition.

Phytoplankton versus macrophyte contribution to primary production and biogeochemical cycles of a coastal mesotidal system. A modelling approach

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean. The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay.

Variational ensemble Kalman filtering applied to data assimilation problems in computational fluid dynamics

One challenge on data assimilation (DA) methods is how the error covariance for the model state is computed. Ensemble methods have been proposed for producing error covariance estimates, as error is propagated in time using the non-linear model. Variational methods, on the other hand, use the concepts of control theory, whereby the state estimate is optimized from both the background and the measurements. Numerical optimization schemes are applied which solve the problem of memory storage and huge matrix inversion needed by classical Kalman filter methods. Variational Ensemble Kalman filter (VEnKF), as a method inspired the Variational Kalman Filter (VKF), enjoys the benefits from both ensemble methods and variational methods. It avoids filter inbreeding problems which emerge when the ensemble spread underestimates the true error covariance. In VEnKF this is tackled by resampling the ensemble every time measurements are available. One advantage of VEnKF over VKF is that it needs neither tangent linear code nor adjoint code. In this thesis, VEnKF has been applied to a two-dimensional shallow water model simulating a dam-break experiment. The model is a public code with water height measurements recorded in seven stations along the 21:2 m long 1:4 m wide flume’s mid-line. Because the data were too sparse to assimilate the 30 171 model state vector, we chose to interpolate the data both in time and in space. The results of the assimilation were compared with that of a pure simulation. We have found that the results revealed by the VEnKF were more realistic, without numerical artifacts present in the pure simulation. Creating a wrapper code for a model and DA scheme might be challenging, especially when the two were designed independently or are poorly documented. In this thesis we have presented a non-intrusive approach of coupling the model and a DA scheme. An external program is used to send and receive information between the model and DA procedure using files. The advantage of this method is that the model code changes needed are minimal, only a few lines which facilitate input and output. Apart from being simple to coupling, the approach can be employed even if the two were written in different programming languages, because the communication is not through code. The non-intrusive approach is made to accommodate parallel computing by just telling the control program to wait until all the processes have ended before the DA procedure is invoked. It is worth mentioning the overhead increase caused by the approach, as at every assimilation cycle both the model and the DA procedure have to be initialized. Nonetheless, the method can be an ideal approach for a benchmark platform in testing DA methods. The non-intrusive VEnKF has been applied to a multi-purpose hydrodynamic model COHERENS to assimilate Total Suspended Matter (TSM) in lake Säkylän Pyhäjärvi. The lake has an area of 154 km2 with an average depth of 5:4 m. Turbidity and chlorophyll-a concentrations from MERIS satellite images for 7 days between May 16 and July 6 2009 were available. The effect of the organic matter has been computationally eliminated to obtain TSM data. Because of computational demands from both COHERENS and VEnKF, we have chosen to use 1 km grid resolution. The results of the VEnKF have been compared with the measurements recorded at an automatic station located at the North-Western part of the lake. However, due to TSM data sparsity in both time and space, it could not be well matched. The use of multiple automatic stations with real time data is important to elude the time sparsity problem. With DA, this will help in better understanding the environmental hazard variables for instance. We have found that using a very high ensemble size does not necessarily improve the results, because there is a limit whereby additional ensemble members add very little to the performance. Successful implementation of the non-intrusive VEnKF and the ensemble size limit for performance leads to an emerging area of Reduced Order Modeling (ROM). To save computational resources, running full-blown model in ROM is avoided. When the ROM is applied with the non-intrusive DA approach, it might result in a cheaper algorithm that will relax computation challenges existing in the field of modelling and DA.

Environmental factors affecting maerl bed structure in Brittany (France)

This study used a large spatial scale approach in order to better quantify the relationships between maerl bed structure and a selection of potentially forcing physical factors. Data on maerl bed structure and morpho-sedimentary characteristics were obtained from recent oceanographic surveys using underwater video recording and grab sampling. Considering the difficulties in carrying out real-time monitoring of highly variable hydrodynamic and physicochemical factors, these were generated by three-dimensional numerical models with high spatial and temporal resolution. The BIOENV procedure indicated that variation in the percentage cover of thalli can best be explained (correlation = 0.76) by a combination of annual mean salinity, annual mean nitrate concentration and annual mean current velocity, while the variation in the proportion of living thalli can best be explained (correlation = 0.47) by a combination of depth and mud content. Linear relationships showed that the percentage cover of maerl thalli was positively correlated with nitrate concentration (R2 = 0.78, P < 0.01) and negatively correlated with salinity (R2 = 0.81, P < 0.01), suggesting a strong effect of estuarine discharge on maerl bed structure, and also negatively correlated with current velocity (R2 = 0.81, P < 0.01). When maerl beds were deeper than 10 m, the proportion of living thalli was always below 30% but when they were shallower than 10 m, it varied between 4 and 100%, and was negatively correlated with mud content (R2 = 0.53, P < 0.01). On the other hand, when mud content was below 10%, the proportion of living thalli showed a negative correlation with depth (R2 = 0.84, P < 0.01). This large spatial scale explanation of maerl bed heterogeneity provides a realistic physical characterization of these ecologically interesting benthic habitats and usable findings for their conservation and management.

Probabilistic approach of water residence time and connectivity using Markov Chains with application to tidal embayments

Markov Chain analysis was recently proposed to assess the time scales and preferential pathways into biological or physical networks by computing residence time, first passage time, rates of transfer between nodes and number of passages in a node. We propose to adapt an algorithm already published for simple systems to physical systems described with a high resolution hydrodynamic model. The method is applied to bays and estuaries on the Eastern Coast of Canada for their interest in shellfish aquaculture. Current velocities have been computed by using a 2 dimensional grid of elements and circulation patterns were summarized by averaging Eulerian flows between adjacent elements. Flows and volumes allow computing probabilities of transition between elements and to assess the average time needed by virtual particles to move from one element to another, the rate of transfer between two elements, and the average residence time of each system. We also combined transfer rates and times to assess the main pathways of virtual particles released in farmed areas and the potential influence of farmed areas on other areas. We suggest that Markov chain is complementary to other sets of ecological indicators proposed to analyse the interactions between farmed areas - e.g. depletion index, carrying capacity assessment. Markov Chain has several advantages with respect to the estimation of connectivity between pair of sites. It makes possible to estimate transfer rates and times at once in a very quick and efficient way, without the need to perform long term simulations of particle or tracer concentration.

Riffe und fazielle Entwicklung der florigemma-Bank (Korallenoolith, Oxfordium) im Süntel und östlichen Wesergebirge (NW-Deutschland

During the Sedimentation of the platform carbonate deposits of the Korallenoolith Formation (middle Oxfordian to early Kimmeridgian) small buildups ofcorals formed in the Lower Saxony Basin. These bioconstructions are restricted to particular horizons (Untere Korallenbank,ßorigenuna-Bank Member etc.) and represent patch reefs and biostromes. In this study, the development of facies, fossil assemblages, spatial distribution of fossils, and reefs of the ßorigenuna-Bank Member (upper Middle Oxfordian) in the Süntel Mts and the eastern Wesergebirge Mts is described; the formation of reefs is discussed in detail. Twelve facies types are described and interpreted. They vary between high-energy deposits as well winnowed oolites and quiet-water lagoonal mudstones. Owing to the significance of biota, micro- and macrofossils are systematically described. The reefs are preserved in growth position, are characterized by numerous corresponding features and belong to a certain reef type. According to their size, shape and framework, they represent patch reefs, coral knobs (sensu James, 1983), coral thrombolite reefs (sensu Leinfelder et al., 1994) or “Klein- and Mitteldickichte” (sensu Laternser, 2001). Their growth fabric corresponds to the superstratal (dense) pillarstone (sensu Insalaco, 1998). As the top of the ßorigenuna-Bank displays an erosional unconformity (so-called Hauptdiskontinuität), the top of the reefs are erosionally capped. Their maximum height amounts to at least the maximum thickness of the ßorigenuna-Bank which does not exceed 4 metres. The diversity of coral fauna of the reefs is relatively low; a total of 13 species is recorded. The coral community is over- whelmingly dominated by the thin-branched ramose Thamnasteria dendroidea (Lamouroux) that forms aggregations of colonies (77?. dendroidea thickets). Leafy to platy Fungiastrea arachnoides (Parkinson) and Thamnasteria concinna (Goldfuss) occur subordinately, other species are only of minor importance. In a few cases, the reef-core consisting of Th. dendroidea thickets is laterally encrusted by platy F. arachnoides and Th. concinna colonies, and microbial carbonates. This zonation reflects probably a succession of different reef builders as a result of changing environmental conditions (allogenic succession). Moreover, some reefs are overlain by a biostrome made of large Solenopora jurassica nodules passing laterally in a nerinean bed. Mikrobial carbonates promoted reef growth and favoured the preservation of reef organismn in their growth position or in situ. They exhibit a platy, dendroid, or reticulate growth form or occur as downward-facing hemispheroids. According to their microstructure, they consist of a peloidal, clotted, or unstructured fabric (predominately layered and poorly structured thrombolite as well as clotted leiolite) (sensu Schmid, 1996). Abundant endo- and epibiontic organisms (bivalves, gastropods, echinoids, asteroids, ophiuroids, crabs etc) are linked to the reefs. With regard to their guild structure, the reefs represent occurrences at which only a few coral species serve as builder. Moreover, microbial carbonates contribute to both building and binding of the reefs. Additional binder as well as baffler are present, but not abundant. According to the species diversity, the dweller guild comprises by far the highest number of invertebrate taxa. The destroyer guild chiefly encompasses bivalves. The composition of the reef community was influenced by the habitat structure of the Th. dendroidea thickets. Owing to the increase in encrusting organisms and other inhabitants of the thickets, the locational factors changed, since light intensity and hydrodynamic energy level and combined parameters as oxygen supply declined in the crowded habitat. Therefore a characteristic succession of organisms is developed that depends on and responds to changing environmental conditions („community replacement sequence“). The succession allows the differentiation of different stages. It started after the cessation of the polyps with boring organisms and photoautotrophic micro-encrusters (calcareous algae, Lithocodium aggregatum). Following the death of these pioneer organisms, encrusting and adherent organisms (serpulids, „Terebella“ species, bryozoans, foraminifers, thecideidinids, sklerospongid and pharetronid sponges, terebratulids), small mobile organisms (limpets), and microbial induced carbonates developed. The final stage in the community replacement sequence gave rise to small cryptic habitats and organisms that belong to these caves (cryptobionts, coelobites). The habitat conditions especially favoured small non-rigid demosponges (“soft sponges”) that tolerate reduced water circulation. Reef rubble is negligible, so that the reefs are bordered by fossiliferous micritic limestone passing laterally in micritic limestone. Approximately 10% of the study area (outcropping florigemma-Bank) corresponds to reefal deposits whereas the remaining 90% encompass lagoonal inter-reefal deposits. The reef development is a good example for the interaction between reef growth, facies development and sea-level changes. It was initiated by a sea-level rise (transgression) and corresponding decrease in the hydrodynamic energy level. Colonization and reef growth took place on a coarse-grained Substrate composed of oncoids, larger foraminifers and bioclasts. Reef growth took place in a calm marine lagoonal setting. Increasing abundance of spherical coral morphs towards the Northeast (section Kessiehausen, northwestem Süntel Mts) reflects higher turbidity and a facies transition to coral occurrences of the ßorigenuna-Bank Member in the adjacent Deister Mts. The reef growth was neither influenced by stonns nor by input of siliciclastic deposits, and took place in short time - probably in only a thousand years under most probably mesotrophic conditions. The mass appearance of solenoporids and nerineids in the upper part of the ßorigenuna-Bank Member point to enhanced nutrient level as a result of regression. In addition, this scenario of fluctuations in nutrient availability seems to be responsible for the cessation of reef corals. The sea level fall reached its climax in the subaerial exposure and palaeokarst development of the florigemma-Bank. The reef building corals are typical pioneer species. The blade-like, flattened F. amchnoides colonies are characterized by their light porous calcium carbonate skeleton, which is a distinct advantage in soft bottom environment. Thus, they settled on soft bottom exposing the large parts of its surface to the incoming light. On the other hand, in response to their light requirements they were also able to settle shaded canopy structures or reef caves. Th. dendroidea is an opportunistic coral species in very shallow, well illuminated marine environment. Their thin and densely spaced branches led to a very high surface/volume ratio of the colonies that were capable to exploit incoming light due to their small thamasterioid calices characterized by “highly integrated polyps”. In addition, sideward coalescence of branches during colony growth led to a wave-resistant framework and favoured the authochthonous preservation of the reefs. Asexual reproduction by fragmented colonies promoted reef development as Th. dendroidea thickets laterally extend over the sea floor or new reefs have developed from broken fragments of parent colonies. Similar build ups with Th. dendroidea as a dominant or frequent reef building coral species are known from the Paris Basin and elsewhere from the Lower Saxony Basin (Kleiner Deister Mts). These buildups developed in well-illuminated shallow water and encompass coral reefs or coral thrombolite reefs. Intra- and inter-reef deposits vary between well-winnowed reef debris limestone and mudstones representing considerably calmer conditions. Solenoporid, nerineids and diceratides belong to the characteristic fossils of these occurrences. However, diceratides are missing in theflorigemma-Bank Member. Th. dendroidea differs in its colonization of low- to high-energy environment from recent ramose scleractinian corals (e.g., Acropora and Porites sp.). The latter are restricted to agitated water habitats creating coral thickets and carpets. According to the morphologic plasticity of Th. dendroidea, thick-branched colonies developed in a milieu of high water energy, whereas fragile, wide- and thin-branched colonies prevail in low-energy settings. Due to its relatively rapid growth, Th. dendroidea was able to keep pace with increased Sedimentation rates. 68 benthonic foraminiferan species/taxa have been recognized in thin sections. Agglutinated foraminifers (textulariids) predominate when compared with rotaliids and milioliids. Numerous species are restricted to a certain facies type or occur in higher population densities, in particular Everticyclammina sp., a larger agglutinated foraminifer that occurs in rock building amounts. Among the 25 reef dwelling foraminiferal species, a few were so far only known from Late Jurassic sponge reefs. Another striking feature is the frequency of adherent foraminiferal species. Fauna and flora, in particular dasycladaleans and agglutinated foraminifers, document palaeobiogeographic relationships to the Tethys and point to (sub)tropical conditions. Moreover, in Germany this foraminiferan assemblage is yet uncompared. In Southern Germany similar tethyan type assemblages are not present in strata as young as Middle Tithonian.

Die mittelpleistozäne Flußentwicklung im nordöstlichen Harzvorland: Petrographie, Terrassenstratigraphie

The present study deals with the evolution of the middle Pleistocene river system in the north-eastern foreland of the Harz Mtns. Sediments of the middle fluvial terrace level (early Saalian time) are the main objectives. By using these sediments supplementary with some results of upper fluvial terrace level (early Elesterian time or older) the fluvial palaeogeography within the area has been reconstructed. The sediments were investigated with respect to their gravel spectra, heavy mineral record, sedimentary structures and altitude above the recent river beds. Due to the resulting specifics the sediments have been attributed to particular rivers in the area. Furthermore it is possible to distinguish between fluvial sediments and Elsterian as well as Saalian fluvioglacial deposits. Together with discernible middle or upper terrace characteristics this led to a spatio-temporal reconstruction of the palaeo river system of the Harz Mtns. It revealed that not only during upper terrace sedimentation but even while middle terraces were deposited the rivers partly diversed. These river diversions were mainly caused by hydrodynamic changes reflecting interaction of the fluvial system with Elsterian and Saalian ice shield formation in the north. The Rivers Ecker, Ilse, Rammelsbach, Holtemme, Goldbach, Bode, Selke and Eine were affected by this development as follows: Upper terrace level formation: • The Ecker River formerly ran between its recent river bed and that of the Use River in direction to the Großer Fallstein Mtn. • The Use River flowed to the NE towards the Huy Mtn. • The Goldbach River and the Holtemme River mutually ran to the NW south of the Huy Mtn. After uniting with the Use River and Ecker River it ran south of the Großer Fallstein Mtn. Middle terrace level formation: • The Ecker River flowed far more NE. • Near to the Harz Mtns. the Use River flowed more in the E. The tributary junction of the Rammelsbach River was located far more downstream. Thereafter the Use River ran to the N between Huy Mtn. and Großer Fallstein Mtn. to end up flowing in the area of the Großes Bruch. • The Holtemme River kept its course. Its recent tributary the Goldbach River flowed to the NE and joined the Bode River after leaving the Harz Mtn. Range. • The Eine River ran to the NW when passing todays city of Aschersleben. After flowing together with the Selke River in the area of the Seeländerei it became a tributary to the Bode River. • The Bode River within the recent tributary junction of the Holtemme ran far more in the W. In the area of the Espenbruch it flowed eastwards to the Saale River. The following general implications resulted out of the study: • The so called “mixed sediments” sensu Rosenberger & Altermann (1975) have now been interpreted as proximal fluvioglacial deposits. • High altitudes of middle terrace fluvial deposits in the courses of the Ecker River and Use River were formerly assigned to post middle Pleistocene uplift of the Großer Fallstein Mtn. (Feldmann, 2002). The present study suggests that the unusual high altitudes should rather be attributed to post middle terrace level erosion of the shortened Ilse- Rammelsbach river system or fluvioglacial processes below the glacier. • Within the north-eastern foreland of the Harz Mtns. middle terrace level deposits have previously been subdivided by cryoturbation horizons or short-term progradation of Saalian glaciation. This is not supported by own results for the examined area.

In situ characterization of sediment oxygen demand across the spectrum of non-resuspension to full resuspension with varying bed shear stress

Sediment oxygen demand (SOD) can be a significant oxygen sink in various types of water bodies, particularly slow-moving waters with substantial organic sediment accumulation. In most settings where SOD is a concern, the prevailing hydraulic conditions are such that the impact of sediment resuspension on SOD is not considered. However, in the case of Bubbly Creek in Chicago, Illinois, the prevailing slack water conditions are interrupted by infrequent intervals of very high flow rates associated with pumped combined sewer overflow (CSO) during intense hydrologic events. These events can cause resuspension of the highly organic, nutrient-rich bottom sediments, resulting in precipitous drawdown of dissolved oxygen (DO) in the water column. While many past studies have addressed the dependence of SOD on near-bed velocity and bed shear stress prior to the point of sediment resuspension, there has been limited research that has attempted to characterize the complex and dynamic phenomenon of resuspended-sediment oxygen demand. To address this issue, a new in situ experimental apparatus referred to as the U of I Hydrodynamic SOD Sampler was designed to achieve a broad range of velocities and associated bed shear stresses. This allowed SOD to be analyzed across the spectrum of no sediment resuspension associated with low velocity/ bed shear stress through full sediment resuspension associated with high velocity / bed shear stress. The current study split SOD into two separate components: (1) SODNR is the sediment oxygen demand associated with non-resuspension conditions and is a surface sink calculated using traditional methods to yield a value with units (g/m2/day); and (2) SODR is the oxygen demand associated with resuspension conditions, which is a volumetric sink most accurately characterized using non-traditional methods and units that reflect suspension in the water column (mg/L/day). In the case of resuspension, the suspended sediment concentration was analyzed as a function of bed shear stress, and a formulation was developed to characterize SODR as a function of suspended sediment concentration in a form similar to first-order biochemical oxygen demand (BOD) kinetics with Monod DO term. The results obtained are intended to be implemented into a numerical model containing hydrodynamic, sediment transport, and water quality components to yield oxygen demand varying in both space and time for specific flow events. Such implementation will allow evaluation of proposed Bubbly Creek water quality improvement alternatives which take into account the impact of SOD under various flow conditions. Although the findings were based on experiments specific to the conditions in Bubbly Creek, the techniques and formulations developed in this study should be applicable to similar sites.

Understanding the adsorption of salmon calcitonin, antimicrobial peptide AP114 and polymyxin B onto lipid nanocapsules

International audience

Heat transfer performance investigation of nanofluids flow in pipe

Different types of base fluids, such as water, engine oil, kerosene, ethanol, methanol, ethylene glycol etc. are usually used to increase the heat transfer performance in many engineering applications. But these conventional heat transfer fluids have often several limitations. One of those major limitations is that the thermal conductivity of each of these base fluids is very low and this results a lower heat transfer rate in thermal engineering systems. Such limitation also affects the performance of different equipments used in different heat transfer process industries. To overcome such an important drawback, researchers over the years have considered a new generation heat transfer fluid, simply known as nanofluid with higher thermal conductivity. This new generation heat transfer fluid is a mixture of nanometre-size particles and different base fluids. Different researchers suggest that adding spherical or cylindrical shape of uniform/non-uniform nanoparticles into a base fluid can remarkably increase the thermal conductivity of nanofluid. Such augmentation of thermal conductivity could play a more significant role in enhancing the heat transfer rate than that of the base fluid. Nanoparticles diameters used in nanofluid are usually considered to be less than or equal to 100 nm and the nanoparticles concentration usually varies from 5% to 10%. Different researchers mentioned that the smaller nanoparticles concentration with size diameter of 100 nm could enhance the heat transfer rate more significantly compared to that of base fluids. But it is not obvious what effect it will have on the heat transfer performance when nanofluids contain small size nanoparticles of less than 100 nm with different concentrations. Besides, the effect of static and moving nanoparticles on the heat transfer of nanofluid is not known too. The idea of moving nanoparticles brings the effect of Brownian motion of nanoparticles on the heat transfer. The aim of this work is, therefore, to investigate the heat transfer performance of nanofluid using a combination of smaller size of nanoparticles with different concentrations considering the Brownian motion of nanoparticles. A horizontal pipe has been considered as a physical system within which the above mentioned nanofluid performances are investigated under transition to turbulent flow conditions. Three different types of numerical models, such as single phase model, Eulerian-Eulerian multi-phase mixture model and Eulerian-Lagrangian discrete phase model have been used while investigating the performance of nanofluids. The most commonly used model is single phase model which is based on the assumption that nanofluids behave like a conventional fluid. The other two models are used when the interaction between solid and fluid particles is considered. However, two different phases, such as fluid and solid phases is also considered in the Eulerian-Eulerian multi-phase mixture model. Thus, these phases create a fluid-solid mixture. But, two phases in the Eulerian-Lagrangian discrete phase model are independent. One of them is a solid phase and the other one is a fluid phase. In addition, RANS (Reynolds Average Navier Stokes) based Standard κ-ω and SST κ-ω transitional models have been used for the simulation of transitional flow. While the RANS based Standard κ-ϵ, Realizable κ-ϵ and RNG κ-ϵ turbulent models are used for the simulation of turbulent flow. Hydrodynamic as well as temperature behaviour of transition to turbulent flows of nanofluids through the horizontal pipe is studied under a uniform heat flux boundary condition applied to the wall with temperature dependent thermo-physical properties for both water and nanofluids. Numerical results characterising the performances of velocity and temperature fields are presented in terms of velocity and temperature contours, turbulent kinetic energy contours, surface temperature, local and average Nusselt numbers, Darcy friction factor, thermal performance factor and total entropy generation. New correlations are also proposed for the calculation of average Nusselt number for both the single and multi-phase models. Result reveals that the combination of small size of nanoparticles and higher nanoparticles concentrations with the Brownian motion of nanoparticles shows higher heat transfer enhancement and thermal performance factor than those of water. Literature suggests that the use of nanofluids flow in an inclined pipe at transition to turbulent regimes has been ignored despite its significance in real-life applications. Therefore, a particular investigation has been carried out in this thesis with a view to understand the heat transfer behaviour and performance of an inclined pipe under transition flow condition. It is found that the heat transfer rate decreases with the increase of a pipe inclination angle. Also, a higher heat transfer rate is found for a horizontal pipe under forced convection than that of an inclined pipe under mixed convection.

Automatic dynamic mask extraction for PIV images containing an unsteady interface, bubbles, and a moving structure

When performing Particle Image Velocimetry (PIV) measurements in complex fluid flows with moving interfaces and a two-phase flow, it is necessary to develop a mask to remove non-physical measurements. This is the case when studying, for example, the complex bubble sweep-down phenomenon observed in oceanographic research vessels. Indeed, in such a configuration, the presence of an unsteady free surface, of a solid–liquid interface and of bubbles in the PIV frame, leads to generate numerous laser reflections and therefore spurious velocity vectors. In this note, an image masking process is developed to successively identify the boundaries of the ship and the free surface interface. As the presence of the solid hull surface induces laser reflections, the hull edge contours are simply detected in the first PIV frame and dynamically estimated for consecutive ones. As for the unsteady surface determination, a specific process is implemented like the following: i) the edge detection of the gradient magnitude in the PIV frame, ii) the extraction of the particles by filtering high-intensity large areas related to the bubbles and/or hull reflections, iii) the extraction of the rough region containing these particles and their reflections, iv) the removal of these reflections. The unsteady surface is finally obtained with a fifth-order polynomial interpolation. The resulted free surface is successfully validated from the Fourier analysis and by visualizing selected PIV images containing numerous spurious high intensity areas. This paper demonstrates how this data analysis process leads to PIV images database without reflections and an automatic detection of both the free surface and the rigid body. An application of this new mask is finally detailed, allowing a preliminary analysis of the hydrodynamic flow.

Asymptotic preserving and time diminishing schemes for rarefied gas dynamic

In this work, we introduce a new class of numerical schemes for rarefied gas dynamic problems described by collisional kinetic equations. The idea consists in reformulating the problem using a micro-macro decomposition and successively in solving the microscopic part by using asymptotic preserving Monte Carlo methods. We consider two types of decompositions, the first leading to the Euler system of gas dynamics while the second to the Navier-Stokes equations for the macroscopic part. In addition, the particle method which solves the microscopic part is designed in such a way that the global scheme becomes computationally less expensive as the solution approaches the equilibrium state as opposite to standard methods for kinetic equations which computational cost increases with the number of interactions. At the same time, the statistical error due to the particle part of the solution decreases as the system approach the equilibrium state. This causes the method to degenerate to the sole solution of the macroscopic hydrodynamic equations (Euler or Navier-Stokes) in the limit of infinite number of collisions. In a last part, we will show the behaviors of this new approach in comparisons to standard Monte Carlo techniques for solving the kinetic equation by testing it on different problems which typically arise in rarefied gas dynamic simulations.