Control of instabilities in non-Newtonian free surface fluid flows

Free surface flows in inclined channels can develop periodic instabilities that are propagated downstream as shock waves with well-defined wavelengths and amplitudes. Such disturbances are called roll waves and are common in channels, torrential lava, landslides, and avalanches. The prediction and detection of such waves over certain types of structures and environments are useful for the prevention of natural risks. In this work, a mathematical model is established using a theoretical approach based on Cauchy's equations with the Herschel-Bulkley rheological model inserted into the viscous part of the stress tensor. This arrangement can adequately represent the behavior of muddy fluids, such as water-clay mixture. Then, taking into account the shallow water and the Rankine-Hugoniot's (shock wave) conditions, the equation of the roll wave and its properties, profile, and propagation velocity are determined. A linear stability analysis is performed with an emphasis on determining the condition that allows the generation of such instabilities, which depends on the minimum Froude number. A sensitivity analysis on the numerical parameters is performed, and numerical results including the influence of the Froude number, the index flow and dimensionless yield stress on the amplitude, the wavelength of roll waves and the propagation velocity of roll waves are shown. We show that our numerical results were in agreement with Coussot's experimental results (1994).

Implementação de aparato experimental para medição de instabilidades tipo Roll Waves em fluidos não- newtonianos

Pós-graduação em Engenharia Mecânica - FEIS

Experimental setup for measuring roll waves on laminar open channel flows

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Impact of biannual rossby waves on the Indian Ocean Dipole

Topex/Poseidon sea surface height anomalies during 1993-2002 are decomposed using 2-D finite impulse response filters which showed biannual Rossby waves (BRWs) in the equatorial Indian Ocean (peak at 1.5 degrees S) and in the southern tropical Indian Ocean (peak at 10.5 degrees S) during Indian Ocean Dipole (IOD) years. Anomalous downwelling BRWs in the equatorial Indian Ocean triggered by the wind stress curl-induced Ekman pumping near the eastern boundary started propagating westward from the eastern boundary in July/August 1993 and 1996, i.e., more than one year prior to the formation of the IOD events of 1994 and 1997 respectively. These strong downwelling signals reach the western equatorial Indian Ocean during the peak dipole time.

Global interannual trends and amplitude modulations of the sea surface height anomaly from the TOPEX/Jason-1 altimeters

This study uses the global Ocean Topography Experiment (TOPEX)/Jason-1 altimeters` time series to estimate the 13-yr trend in sea surface height anomaly. These trends are estimated at each grid point by two methods: one fits a straight line to the time series and the other is based on the difference between the average height between the two halves of the time series. In both cases the trend shows large regional variability, mostly where the intense western boundary currents turn. The authors hypothesize that the regional variability of the sea surface height trends leads to changes in the local geostrophic transport. This in turn affects the instability-related processes that generate mesoscale eddies and enhances the Rossby wave signals. This hypothesis is verified by estimates of the trend of the amplitude of the filtered sea surface height anomaly that contains the spectral bands associated with Rossby waves and mesoscale eddies. The authors found predominantly positive tendency in the amplitude of Rossby waves and eddies, which suggests that, on average, these events are becoming more energetic. In some regions, the variation in amplitude over 13 yr is comparable to the standard deviation of the data and is statistically significant according to both methods employed in this study. It is plausible that in this case, the energy is transferred from the mean currents to the waves and eddies through barotropic and baroclinic instability processes that are more pronounced in the western boundary current extension regions. If these heat storage patterns and trends are confirmed on longer time series, then it will be justified to argue that the warming trend of the last century provides the energy that amplifies both Rossby waves and mesoscale eddies.

Strategies for detecting DNA hybridisation using surface plasmon fluorescence spectroscopy

Die Anregung und Emission von Fluorophoren nahe planaren Metalloberflächen und schiefen Gittern wurde mittels Oberflächenplasmonen Fluoreszenz Spektroskopie (SPFS) untersucht. Die Fluorophore konnten durch das evaneszente Plasmonenfeld angeregt und die einzelnen Abregungskanäle identifiziert werden.Die Sensorarchitektur für den Nachweis der Hybridisierung bestand aus auf einer Streptavidin-Matrix immobilisierten unmarkierten Sondensträngen. Cy5 markierte Zielsequenzen wurden aus der Lösung hybridisiert und die Adsorptionskinetiken konnten oberflächensensitiv detektiert werden.Ein neues Detektionsschema für unmarkierte Zielstränge wurde mittels fluoreszenzmarkirten Sondensträngen realisiert. Die Hybridisierung führte zu der Bildung von steifen helikalen Bereichen in der Probe und separierte den Farbstoff von der Metalloberfläche. Reduzierte Fluorezenzlöschung zeigte daher das Hybridisierungsereignis an.Die Verwendung eines potentiellen Förster-Paares zur Detektion von DNA Hybridisierung wurde untersucht. Donor und Akzeptor wurden an Ziel- und Sondenstrang immobilisiert und das Hybridisierungsereignis konnte anhand der Auslöschung der Donor-Fluorezenz nachgewiesen werden.Schließlich wurde der Einsatz von einzelstrangbindenden Proteinen (SSB) zur Steigerung der Sensitivität bezüglich Basenfehlpaarungen betrachtet. Verdrängungsreaktionen zwischen Proteinen und markierten Zielsträngen wurden anhand von SPS und Fluorezenzkinetiken studiert.

Surface-plasmon optical and electrochemical characterization of biofunctional surface architectures

The development and characterization of biomolecule sensor formats based on the optical technique Surface Plasmon Resonance (SPR) Spectroscopy and electrochemical methods were investigated. The study can be divided into two parts of different scope. In the first part new novel detection schemes for labeled targets were developed on the basis of the investigations in Surface-plamon Field Enhanced Spectroscopy (SPFS). The first one is SPR fluorescence imaging formats, Surface-plamon Field Enhanced Fluorescence Microscopy (SPFM). Patterned self assembled monolayers (SAMs) were prepared and used to direct the spatial distribution of biomolecules immobilized on surfaces. Here the patterned monolayers would serve as molecular templates to secure different biomolecules to known locations on a surface. The binding processed of labeled target biomolecules from solution to sensor surface were visually and kinetically recorded by the fluorescence microscope, in which fluorescence was excited by the evanescent field of propagating plasmon surface polaritons. The second format which also originates from SPFS technique, Surface-plamon Field Enhanced Fluorescence Spectrometry (SPFSm), concerns the coupling of a fluorometry to normal SPR setup. A spectrograph mounted in place of photomultiplier or microscope can provide the information of fluorescence spectrum as well as fluorescence intensity. This study also firstly demonstrated the analytical combination of surface plasmon enhanced fluorescence detection with analyte tagged by semiconducting nano- crystals (QDs). Electrochemically addressable fabrication of DNA biosensor arrays in aqueous environment was also developed. An electrochemical method was introduced for the directed in-situ assembly of various specific oligonucleotide catcher probes onto different sensing elements of a multi-electrode array in the aqueous environment of a flow cell. Surface plasmon microscopy (SPM) is utilized for the on-line recording of the various functionalization steps. Hybridization reactions between targets from solution to the different surface-bound complementary probes are monitored by surface-plasmon field-enhanced fluorescence microscopy (SPFM) using targets that are either labeled with organic dyes or with semiconducting quantum dots for color-multiplexing. This study provides a new approach for the fabrication of (small) DNA arrays and the recording and quantitative evaluation of parallel hybridization reactions. In the second part of this work, the ideas of combining the SP optical and electrochemical characterization were extended to tethered bilayer lipid membrane (tBLM) format. Tethered bilayer lipid membranes provide a versatile model platform for the study of many membrane related processes. The thiolipids were firstly self-assembled on ultraflat gold substrates. Fusion of the monolayers with small unilamellar vesicles (SUVs) formed the distal layer and the membranes thus obtained have the sealing properties comparable to those of natural membranes. The fusion could be monitored optically by SPR as an increase in reflectivity (thickness) upon formation of the outer leaflet of the bilayer. With EIS, a drop in capacitance and a steady increase in resistance could be observed leading to a tightly sealing membrane with low leakage currents. The assembly of tBLMs and the subsequent incorporation of membrane proteins were investigated with respect to their potential use as a biosensing system. In the case of valinomycin the potassium transport mediated by the ion carrier could be shown by a decrease in resistance upon increasing potassium concentration. Potential mediation of membrane pores could be shown for the ion channel forming peptide alamethicin (Alm). It was shown that at high positive dc bias (cis negative) Alm channels stay at relatively low conductance levels and show higher permeability to potassium than to tetramethylammonium. The addition of inhibitor amiloride can partially block the Alm channels and results in increase of membrane resistance. tBLMs are robust and versatile model membrane architectures that can mimic certain properties of biological membranes. tBLMs with incorporated lipopolysaccharide (LPS) and lipid A mimicking bacteria membranes were used to probe the interactions of antibodies against LPS and to investigate the binding and incorporation of the small antimicrobial peptide V4. The influence of membrane composition and charge on the behavior of V4 was also probed. This study displays the possibility of using tBLM platform to record and valuate the efficiency or potency of numerous synthesized antimicrobial peptides as potential drug candidates.

Surfactant mediated adsorption of negatively charged latex particles to a cellulose surface

The adsorption of anionic, carboxyl functionalized latex particles, recharged by a cationic surfactant acting as fabric softener/conditioner, to a cellulose surface was investigated with evanescent wave video microscopy. This technique allows to monitor the deposition and release of individual particles in real-time with an excellent selectivity and sensitivity. Since the recharged particles and the conditioner compete for the free surface, the initial deposition rate and final surface coverage are found to be strongly dependent on the ratio of particle and conditioner concentrations.

The role of upper-level dynamics and surface processes for the Pakistan flood of July 2010

In July and August 2010 floods of unprecedented impact afflicted Pakistan. The floods resulted from a series of intense multi-day precipitation events in July and early August. At the same time a series of blocking anticyclones dominated the upper-level flow over western Russia and breaking waves i.e. equatorward extrusions of stratospheric high potential vorticity (PV) air formed along the downstream flank of the blocks. Previous studies suggested that these extratropical upper-level breaking waves were crucial for instigating the precipitation events in Pakistan. Here a detailed analysis is provided of the extratropical forcing of the precipitation. Piecewise PV inversion is used to quantify the extratropical upper-level forcing associated with the wave breaking and trajectories are calculated to study the pathways and source regions of the moisture that precipitated over Pakistan. Limited-area model simulations are carried out to complement the Lagrangian analysis. The precipitation events over Pakistan resulted from a combination of favourable boundary conditions with strong extratropical and monsoonal forcing factors. Above-normal sea-surface temperatures in the Indian Ocean led to an elevated lower-tropospheric moisture content. Surface monsoonal depressions ensured the transport of moist air from the ocean towards northeastern Pakistan. Along this pathway the air parcel humidity increased substantially (60–90% of precipitated moisture) via evapotranspiration from the land surface. Extratropical breaking waves influenced the surface wind field substantially by enhancing the wind component directed towards the mountains which reinforced the precipitation.

Blackfolds, plane waves and minimal surfaces

Minimal surfaces in Euclidean space provide examples of possible non-compact horizon geometries and topologies in asymptotically flat space-time. On the other hand, the existence of limiting surfaces in the space-time provides a simple mechanism for making these configurations compact. Limiting surfaces appear naturally in a given space-time by making minimal surfaces rotate but they are also inherent to plane wave or de Sitter space-times in which case minimal surfaces can be static and compact. We use the blackfold approach in order to scan for possible black hole horizon geometries and topologies in asymptotically flat, plane wave and de Sitter space-times. In the process we uncover several new configurations, such as black helicoids and catenoids, some of which have an asymptotically flat counterpart. In particular, we find that the ultraspinning regime of singly-spinning Myers-Perry black holes, described in terms of the simplest minimal surface (the plane), can be obtained as a limit of a black helicoid, suggesting that these two families of black holes are connected. We also show that minimal surfaces embedded in spheres rather than Euclidean space can be used to construct static compact horizons in asymptotically de Sitter space-times.

Quantitative component analysis of the coarse fraction of surface sediments from the Persian Gulf

In the Persian Gulf and the Gulf of Oman marl forms the primary sediment cover, particularly on the Iranian side. A detailed quantitative description of the sediment components > 63 µ has been attempted in order to establish the regional distribution of the most important constituents as well as the criteria governing marl sedimentation in general. During the course of the analysis, the sand fraction from about 160 bottom-surface samples was split into 5 phi° fractions and 500 to 800 grains were counted in each individual fraction. The grains were cataloged in up to 40 grain type catagories. The gravel fraction was counted separately and the values calculated as weight percent. Basic for understanding the mode of formation of the marl sediment is the "rule" of independent availability of component groups. It states that the sedimentation of different component groups takes place independently, and that variation in the quantity of one component is independent of the presence or absence of other components. This means, for example, that different grain size spectrums are not necessarily developed through transport sorting. In the Persian Gulf they are more likely the result of differences in the amount of clay-rich fine sediment brought in to the restricted mouth areas of the Iranian rivers. These local increases in clayey sediment dilute the autochthonous, for the most part carbonate, coarse fraction. This also explains the frequent facies changes from carbonate to clayey marl. The main constituent groups of the coarse fraction are faecal pellets and lumps, the non carbonate mineral components, the Pleistocene relict sediment, the benthonic biogene components and the plankton. Faecal pellets and lumps are formed through grain size transformation of fine sediment. Higher percentages of these components can be correlated to large amounts of fine sediment and organic C. No discernable change takes place in carbonate minerals as a result of digestion and faecal pellet formation. The non-carbonate sand components originate from several unrelated sources and can be distinguished by their different grain size spectrum; as well as by other characteristics. The Iranian rivers supply the greatest amounts (well sorted fine sand). Their quantitative variations can be used to trace fine sediment transport directions. Similar mineral maxima in the sediment of the Gulf of Oman mark the path of the Persian Gulf outflow water. Far out from the coast, the basin bottoms in places contain abundant relict minerals (poorly sorted medium sand) and localized areas of reworked salt dome material (medium sand to gravel). Wind transport produces only a minimal "background value" of mineral components (very fine sand). Biogenic and non-biogenic relict sediments can be placed in separate component groups with the help of several petrographic criteria. Part of the relict sediment (well sorted fine sand) is allochthonous and was derived from the terrigenous sediment of river mouths. The main part (coarse, poorly sorted sediment), however, was derived from the late Pleistocene and forms a quasi-autochthonous cover over wide areas which receive little recent sedimentation. Bioturbation results in a mixing of the relict sediment with the overlying younger sediment. Resulting vertical sediment displacement of more than 2.5 m has been observed. This vertical mixing of relict sediment is also partially responsible for the present day grain size anomalies (coarse sediment in deep water) found in the Persian Gulf. The mainly aragonitic components forming the relict sediment show a finely subdivided facies pattern reflecting the paleogeography of carbonate tidal flats dating from the post Pleistocene transgression. Standstill periods are reflected at 110 -125m (shelf break), 64-61 m and 53-41 m (e.g. coare grained quartz and oolite concentrations), and at 25-30m. Comparing these depths to similar occurrences on other shelf regions (e. g. Timor Sea) leads to the conclusion that at this time minimal tectonic activity was taking place in the Persian Gulf. The Pleistocene climate, as evidenced by the absence of Iranian river sediment, was probably drier than the present day Persian Gulf climate. Foremost among the benthonic biogene components are the foraminifera and mollusks. When a ratio is set up between the two, it can be seen that each group is very sensitive to bottom type, i.e., the production of benthonic mollusca increases when a stable (hard) bottom is present whereas the foraminifera favour a soft bottom. In this way, regardless of the grain size, areas with high and low rates of recent sedimentation can be sharply defined. The almost complete absence of mollusks in water deeper than 200 to 300 m gives a rough sedimentologic water depth indicator. The sum of the benthonic foraminifera and mollusca was used as a relative constant reference value for the investigation of many other sediment components. The ratio between arenaceous foraminifera and those with carbonate shells shows a direct relationship to the amount of coarse grained material in the sediment as the frequence of arenaceous foraminifera depends heavily on the availability of sand grains. The nearness of "open" coasts (Iranian river mouths) is directly reflected in the high percentage of plant remains, and indirectly by the increased numbers of ostracods and vertebrates. Plant fragments do not reach their ultimate point of deposition in a free swimming state, but are transported along with the remainder of the terrigenous fine sediment. The echinoderms (mainly echinoids in the West Basin and ophiuroids in the Central Basin) attain their maximum development at the greatest depth reached by the action of the largest waves. This depth varies, depending on the exposure of the slope to the waves, between 12 to 14 and 30 to 35 m. Corals and bryozoans have proved to be good indicators of stable unchanging bottom conditions. Although bryozoans and alcyonarian spiculae are independent of water depth, scleractinians thrive only above 25 to 30 m. The beginning of recent reef growth (restricted by low winter temperatures) was seen only in one single area - on a shoal under 16 m of water. The coarse plankton fraction was studied primarily through the use of a plankton-benthos ratio. The increase in planktonic foraminifera with increasing water depth is here heavily masked by the "Adjacent sea effect" of the Persian Gulf: for the most part the foraminifera have drifted in from the Gulf of Oman. In contrast, the planktonic mollusks are able to colonize the entire Persian Gulf water body. Their amount in the plankton-benthos ratio always increases with water depth and thereby gives a reliable picture of local water depth variations. This holds true to a depth of around 400 m (corresponding to 80-90 % plankton). This water depth effect can be removed by graphical analysis, allowing the percentage of planktonic mollusks per total sample to be used as a reference base for relative sedimentation rate (sedimentation index). These values vary between 1 and > 1000 and thereby agree well with all the other lines of evidence. The "pteropod ooze" facies is then markedly dependent on the sedimentation rate and can theoretically develop at any depth greater than 65 m (proven at 80 m). It should certainly no longer be thought of as "deep sea" sediment. Based on the component distribution diagrams, grain size and carbonate content, the sediments of the Persian Gulf and the Gulf of Oman can be grouped into 5 provisional facies divisions (Chapt.19). Particularly noteworthy among these are first, the fine grained clayey marl facies occupying the 9 narrow outflow areas of rivers, and second, the coarse grained, high-carbonate marl facies rich in relict sediment which covers wide sediment-poor areas of the basin bottoms. Sediment transport is for the most part restricted to grain sizes < 150 µ and in shallow water is largely coast-parallel due to wave action at times supplemented by tidal currents. Below the wave base gravity transport prevails. The only current capable of moving sediment is the Persian Gulf outflow water in the Gulf of Oman.

Sea surface fugacity of carbon dioxide measurements in the Pacific ocean

As part of the JGOFS field program, extensive CO2 partial-pressure measurements were made in the atmosphere and in the surface waters of the equatorial Pacific from 1992 to 1999. For the first time, we are able to determine how processes occurring in the western portion of the equatorial Pacific impact the sea-air fluxes of CO2 in the central and eastern regions. These 8 years of data are compared with the decade of the 1980s. Over this period, surface-water pCO2 data indicate significant seasonal and interannual variations. The largest decreases in fluxes were associated with the 1991-94 and 1997-98 El Niño events. The lower sea-air CO2 fluxes during these two El Niño periods were the result of the combined effects of interconnected large-scale and locally forced physical processes: (1) development of a low-salinity surface cap as part of the formation of the warm pool in the western and central equatorial Pacific, (2) deepening of the thermocline by propagating Kelvin waves in the eastern Pacific, and (3) the weakening of the winds in the eastern half of the basin. These processes serve to reduce pCO2 values in the central and eastern equatorial Pacific towards near-equilibrium values at the height of the warm phase of ENSO. In the western equatorial Pacific there is a small but significant increase in seawater pCO2 during strong El Niño events (i.e., 1982-83 and 1997-98) and little or no change during weak El Niño events (1991-94). The net effect of these interannual variations is a lower-than-normal CO2 flux to the atmosphere from the equatorial Pacific during El Niño. The annual average fluxes indicate that during strong El Niños the release to the atmosphere is 0.2-0.4 Pg C/yr compared to 0.8-1.0 Pg C/yr during non-El Niño years.

Wave height (regular and irregular waves) reduction in 2m water depth over a 40-m-long salt marsh test section in a large scale laboratory flume

Coastal communities around the world face increasing risk from flooding as a result of rising sea level, increasing storminess, and land subsidence. Salt marshes can act as natural buffer zones, providing protection from waves during storms. However, the effectiveness of marshes in protecting the coastline during extreme events when water levels and waves are highest is poorly understood. Here, we experimentally assess wave dissipation under storm surge conditions in a 300-m-long wave flume that contains a transplanted section of natural salt marsh. We find that the presence of marsh vegetation causes considerable wave attenuation, even when water levels and waves are high. From a comparison with experiments without vegetation, we estimate that up to 60% of observed wave reduction is attributed to vegetation. We also find that although waves progressively flatten and break vegetation stems and thereby reduce dissipation, the marsh substrate remained remarkably stable and resistant to surface erosion under all conditions.The effectiveness of storm wave dissipation and the resilience of tidal marshes even at extreme conditions suggest that salt marsh ecosystems can be a valuable component of coastal protection schemes.

Variational Stereo Imaging of Oceanic Waves with Statistical Constraints

An image processing observational technique for the stereoscopic reconstruction of the wave form of oceanic sea states is developed. The technique incorporates the enforcement of any given statistical wave law modeling the quasi Gaussianity of oceanic waves observed in nature. The problem is posed in a variational optimization framework, where the desired wave form is obtained as the minimizer of a cost functional that combines image observations, smoothness priors and a weak statistical constraint. The minimizer is obtained combining gradient descent and multigrid methods on the necessary optimality equations of the cost functional. Robust photometric error criteria and a spatial intensity compensation model are also developed to improve the performance of the presented image matching strategy. The weak statistical constraint is thoroughly evaluated in combination with other elements presented to reconstruct and enforce constraints on experimental stereo data, demonstrating the improvement in the estimation of the observed ocean surface.

Offshore stereo measurements of gravity waves: classical epipolar and novel variational techniques

Stereo video techniques are effective for estimating the space-time wave dynamics over an area of the ocean. Indeed, a stereo camera view allows retrieval of both spatial and temporal data whose statistical content is richer than that of time series data retrieved from point wave probes. Classical epipolar techniques and modern variational methods are reviewed to reconstruct the sea surface from the stereo pairs sequentially in time. Current improvements of the variational methods are presented.