Mangroves trap sediment and are the first coastal defence line for many coastal areas. Unfortunately, mangrove coasts worldwide are eroding due to deforestation, exposing local communities to flood hazards. In Demak, Indonesia, a Building with Nature approach was chosen to counteract erosion. Permeable dams were built on the foreshore to attenuate waves and restore the sediment balance. The dams have increased the bed level locally and mangroves expand after construction. A new project called MuMaCo (Mussels as Mangrove facilitators for Coastal defence) is launched to integrate mussel aquaculture into the mangrove rehabilitation project in Demak. Mussels increase the roughness and diameter of the bamboo poles, which could increase their wave attenuation capacity. Moreover, mussel culture gives the local communities an economic incentive to sustain the structures. This thesis describes and quantifies how mussels' growth influences the forces acting on bamboo poles. Small-scale experiments are performed in the wave flume of the Delft University of Technology on a scale of 1:3 and 1:6. Physical models were used for experiments with steady flow and waves. The steady flow experiments cover a range of Reynolds (Re) numbers between 10^3 and 10^4 to seek the drag crisis. Single mussel covered cylinders for both scales are compared to smooth cylinders and cylinders with an equivalent diameter. For the wave experiments, cnoidal waves with Keulegan-Carpenter ($KC$) numbers ranging from 3 to 113 that correspond with measured waves in Demak are chosen. Moreover, only mussel covered cylinders are compared to a smooth cylinder for a scale of 1:6. During the experiments, the flow velocity, force, and surface elevation are measured, and the drag and inertia coefficients are obtained with the help of the Morison equation. The drag coefficient shows a clear relationship with the Reynolds numbers for steady flow. Although the drag coefficients display the same qualitative behavior as in other studies in the literature, the drag coefficients of the smooth cylinder are more than 40 % larger than in the literature. This is probably due to large variations in the offset of the velocity meters (EMS) during the experiments. The large mussels show higher drag coefficients than the smooth cylinder. For the wave experiments, the drag coefficients show good correspondence to other studies in the literature, but the inertia coefficients are a factor two larger than expected for smooth cylinders. Treating the peak and trough of the cnoidal wave as individual sinusoidal waves shows similar results and suggest that cnoidal waves can be represented by KC numbers, as it is done for linear waves. The best fit to the literature values was found by solving the Morison equation with the measured force with the depth-integrated velocity squared and acceleration from the Fenton theory. This suggests that the results of the wave experiments have been uncertain due to inaccuracies in the EMS recordings. This thesis presents a method to schematize mussels for laboratory experiments and provides a qualitative comparison of the forces acting on poles with and without mussels

The coastline of Demak, Indonesia has been eroded during the last 15 years. To restore the natural coastal protection which existed out of mangroves forest, permeable dams, consisting of bamboo poles with a brushwood filling, have been built to attenuate the waves and facilitate sedimentation behind the dams and thus creating a habitat for mangroves. However these designs required a lot of maintenance, so a new type of design is proposed without a filling of brushwood, containing only vertical bamboo poles. Next to this the possibility to include aquaculture in the design is proposed. Therefore this study assesses the wave transformation by the new designs in Demak, Indonesia with the numerical wave model SWASH. In order to do that first the hydrodynamic conditions are analyzed to obtain the design conditions for the structures, and then SWASH is validated against laboratory experiments to find the right drag coefficient values. The design wave conditions are based on the local water depth, offshore wave heights and periods and local bathymetry. The offshore waves are based on a dataset from WaveWatch III, which compares well with measurements of a local storm event. The dataset of WaveWatch III is filtered and extrapolated to determine the wave conditions for return periods(R) of 1 and 5 years. This resulted in offshore waves with Hm0 = 2.08 and 2.39m, and Tp = 6.9 and 7.5 s respectively. The water level is mainly influenced by the tidal elevation and the surge levels. The surge levels are obtained from a risk assessment of the coast of North Java (Willemsen et al., 2019), which vary between 0.63 to 0.68mfor R = 1 and 5 years respectively. The tidal levels are determined using the water depth measurements of two transects from Van Domburg et al. (2018) and analysed with Matlab tool Utide by Codiga (2011), resulting in a spring tidal range of 85 cm and a neap tidal range of 50 cm.
Four different configurations from the experiments of Jansen (2019) are used to validate SWASH: single row, longitudinal(the spacing in flow direction is longer than the lateral spacing), open uniform and dense uniform configuration. These configurations are modelled in the numerical wave model SWASH by use of the vegetation module. The most influential factors are: the drag coefficient, the way to describe mass conservation and the number of stems(cylinders) per m2. For the drag coefficient the bulk drag coefficient of Gijon Mancheno et al. (2021) is used, which contains factors for sheltering, blockage and the KC state of the flow. For the densely packed configurations the bulk drag coefficient proved to have a better agreement than the drag coefficient of a single cylinder. The sensitivity to the number of stems per m2 is small when implementing the longitudinal configuration as an average amount of stems perm2 or by specifying the individual rows of the configuration and so locally increasing the number of stems. Three methods of describing the mass conservation in SWASH are evaluated: by means of a cross sectional approach that is expressed by the blockage factor in the bulk drag coefficient Gijon Mancheno et al. (2021), by a volumetric approach due to activating the porosity in SWASH which means that the blockage factor cannot be included in the drag coefficient and by a combination of these two. For the longitudinal configuration the best agreement is found the cross sectional approach and for the single row configuration the best agreement is found by the volumetric approach.
Once SWASH is validated, the designs of several structures are investigated. Firstly, a design consisting out of two rows of bamboo poles is considered where the spacing between the rows is varied to find an optimum distance. The transmission rate Et /Ei decreased from 75% to 55% with a spacing sx = 0.42 m to 5.8 m, larger spacings did not result in less transmission. If one wants to be conservative at least three rows are needed to have a lower transmission rate of 50 %. When mussels are considered, the structures have to be placed in deeper water as mussels can only grow between MLWS and 40 cm above the bed. To provide enough space for mussel growth, the poles have to be placed more sparsely. The effect of a larger water depth in combination with a limited pole length and sparse structures is larger than the extra drag and frontal area provided by mussels, especially since they did not cover the whole pole length, and resulted in high transmission rates. It is thus recommended to, or place a high number of rows of mussel poles or place a few rows without mussels followed by poles for mussels. This decision however also depends on benefits that mussel poles may bring and the cost of the materials, therefore a cost/benefit analysis is required.
This thesis found an efficient design that can be used in reducing wave attenuation along muddy coasts without the need of a brushwood filling. Hereby it provides an economically and user friendly alternative with respect to the current design, as it requires less material and maintenance.

Demak is a regency within the province of Central Java, Indonesia, with a mud-mangrove coast bordering the Java Sea. The region is facing a rapid retreat of the coastline, threatening the livelihood of a large part of the population. The main cause of the erosion is the deforestation of the green belt of mangroves. This has disturbed the delicate sediment balance in the area drastically. This MSc thesis was carried out within BioManCO. This is a project of Delft University of Technology and Universitas Diponegoro and aims to develop a bio-morphodynamic model for mangrove-mud coasts. This will eventually be used to identify the conditions under which autonomous reforestation of a sustainable mangrove green belt will take place, restoring the natural coastal protection. Semi-permeable dams are already being implemented to restore the sediment balance in the area. In this approach, however, the existence of a fluid mud layer is neglected. The observation of relatively steep slopes of the interface between mud and water indicates potential mud transport within the mud layer. Such a transport would contribute to the shoreward flux of sediment and thus to the restoration of the coastal profile. If a hybrid dam is implemented, it will block the flow of sediment and might therefore defy its own purpose; attenuating flow and waves in order to capture sediment and restore the eroded coastal profile. The objective of this thesis is to assess wave damping as a driving mechanism for set-up of the fluid mud layer at the coast of Demak and to identify under what conditions such a set-up can exist. Significant attenuation of waves can be achieved by viscous dissipation of wave energy in the mud layer. The set-up of the fluid mud interface is hypothesised to be balancing the wave force resulting from the reduction of wave energy in shoreward direction. To gain insight in the damping of waves and, more generally, in the dynamics of the coastal system of Demak, a field campaign has been carried out. Based on these measurements a SWAN-Mud model has been set up and has been coupled to an idealised model that calculates the equilibrium slope based on modelled wave-damping. The field observations show that the interface level is indeed sloping upwards towards the coast. This slope, however, does not seem to change significantly during the field campaign, indicating that the occurring waves are not able to move the layer. A strong daily variation in wave height and period, dependent on the prevailing wind system, is observed. SWAN-Mud is able to reproduce these measurements convincingly, even with the simple schematisation used in this thesis. The damping of the waves is influenced by the water depth and the wave period, and to a lesser extent by the wave height. It is also strongly dependent on the thickness and viscosity of the mud layer. The use of a fluid mud module to model the dissipation of waves at the coast of Demak is proven to be necessary. The developed conceptual model assumes a balance between the wave force in the mud layer and a pressure gradient due to a set-up of the fluid mud interface. This model shows that waves are able to force positive slopes in shoreward direction. However, for the range of mud parameters, water depths and wave characteristics as measured in Demak, these calculated slopes are too mild in comparison with the observed slopes. The adopted approach neglects the yield stress in the fluid mud layer. This internal strength might be able to balance and thus maintain the observed slopes after first being forced by the waves. Over time, this could lead to a build-up of sediment against the coast which could potentially be colonised and fixated by mangrove species. This build-up has a possible implication for the management of the coastal area of Demak. The hybrid dams might indeed be blocking a restoration mechanism of the mud coast which defies the original purpose of building these dams.

Mangrove forests, which serve as a natural sea defence, have been degraded by human action during the last decades. To protect and recover these areas, different types of permeable structures consisting of bamboo have been proposed and applied. However, these structures are currently based on engineering judgement, as design rules are not available. The goal of this research is to make a step forward in the design optimization of permeable structures and gain a better understanding of the processes causing the wave dissipation inside the structure. In this study, scale experiments are conducted in the wave flume at Delft University of Technology. An array of aluminum cylinders is used as a schematization of the structure, with an element diameter of 4 cm and a minimum spacing of 2 cm. The tested wave height is 0.13 m,with a water depth of 0.6 m for the first set of experiments. These experiments evaluated wave transformation through a selected number of configurations. The water depth was 0.55 m for the second set, where the velocities and forces were also measured inside the structure. As the applied wave periods are short (T = 1 − 2 s), the tested wave conditions are in the range of small KC-numbers (4 < KC < 13). The first part of this research focuses on effect of different configurations and arrangements on the amount of energy dissipation, by measuring the incoming and reflected wave heights in front of and behind the structure. For the short waves, the horizontal arrangements dissipate more energy, as energy is dissipated by both the vertical and horizontal drag forces. However, the effect diminishes with increasing wave period. Considering the total dissipation and the amount of dissipation per element, the placement of the elements in rows perpendicular to the direction of wave propagation is found to be the most effective. To study the effect of the element diameter on the dissipation, the results are compared with previous research by Haage (2018) on a model with a diameter and spacing of 2 cm. As with the change in diameter also the structure porosity changed, a direct comparison was not possible and a comparison based on a simplified drag coefficient is done. No direct effect of the diameter is observed, as the obtained drag coefficients show the same trend and magnitude when plotted against an adapted Keulegan-Carpenter number (KC∗), which is based on the element spacing instead of diameter. Small KC∗-numbers result in large drag coefficients,which decrease when KC∗ increases. The second part of this research focuses on the processes inside the structure that cause the energy dissipation. A force and velocity sensor are applied at three locations inside the structure in separate experiments, to determine the relation of the force and velocity inside the structure with the undisturbed values. Two methods are applied for the analysis, based on two different principles. Method 1 is based on the assumption of a constant pair of force coefficients and an increase in velocity inside the structure, method 2 is based on the assumption of a constant velocity and an increase in force coefficients inside the structure.By comparing both methods, it is found that an increase in velocity is the most important factor for the increase in drag force, which is the driving factor for the energy dissipation. It is also found that the amplification factor for the velocity is dependent on both the structure porosity and frontal porosity.

This thesis investigates the origins of large sedimentation volumes in the Port of Santos, São Paulo - Brazil. The port is located in the Santos - São Vicente estuarine system, delimited by scarps and subject to intense rainfall. The terminals are placed inside the estuary and their access is provided by a 24 km long channel with mean depths of 15 m DHN, subject to annual maintenance dredging with volumes in the order of 4 Mm³ [CODESP, 2016a].
A literature-based sediment mass balance is formulated for the system. Sediment sources and sinks are assessed based on data of the period 2005 to 2012 and expert judgment. The largest sediment input is given by winter storms (65%) followed by river sediment loads (25%). Up-estuary import of fine sediment is found as a third source, computed from the deficit between sources and sinks (trapping in the mudflats and maintenance dredging).
An explorative process based model is set to evaluate the hypothetical sediment balance and expand the understanding of the system behavior. A period of six months is simulated to capture the expected seasonal variability in salinity gradients. Conditions for fluid mud formation are found in the entire channel. A rerun with salinity switched off promotes an expressive reduction (70%) in the cumulative fine sediment import. Up-estuary sediment transport is found as a result of salinity-induced residual currents, which increase in strength with deeper channels [van Maren et al., 2015].
Fine sediment deposits in the final stretches of the channel that probably have been accounted in previous studies as from river discharges, according to this study are provided from marine sources. Model results suggest an annual import of 1.1 Mton of sediment, six times larger than the literature-based estimate. Additionally, results indicate that little quantity of riverine sediment reaches the channel. The literature mass-balance is therefore modified to incorporate these findings: river contribution is set to 15%, up-estuary transport to 30%, and winter storms to 55%.

Flushing basins have been used at several locations in Germany, Belgium, and the Netherlands in the past centuries to maintain the navigational depths of harbour channels. These locations are not in use anymore or are only partly responsible for channel maintenance. This thesis encompasses a study to optimize the geometric parameters of a flushing basin system in a tidal back barrier basin. The addition of a flushing basin behind a tidal harbour channel is meant to affect the sediment regime in the channel from a flood-dominant towards an ebb-dominant regime. With a one-dimensional model of a schematized reference situation, the role of three parameters: the sluice width, the horizontal area of the flushing basin and the ratio between the tidal amplitude and the channel depth, in the tide-residual sediment transport is investigated for the flushing basin system. Three conditions need to be met simultaneously to create ebb dominance along the total length of the channel: a sufficiently large flushing basin area, a small sluice width, compared to the channel width and a relatively deep channel compared to the tidal amplitude.

The Demak coastal area faces severe erosion problems. The main cause of the erosion of the coastline, which is at some places as high as 1.5 km of land, is the deforestation of the green belt of mangroves for the purpose of building fishponds. This has disturbed the delicate sediment balance in the area drastically. The BioManCO project aims to develop a bio-morphodynamic model for mangrove mudcoasts like the coast of Demak, which will eventually be used to identify the conditions under which restoration of the sediment balance may lead to autonomous reforestation of a sustainable mangrove green belt and thus the natural coastal protection. A measure to restore this sediment balance that is already being implemented in the area is the construction of semi-permeable dams. It is not clear yet however, why some of these dams work as intended and why some do not. In an earlier study a 2DH model has been set up to better understand and optimise the design of these structures using the large-scale morphodynamics of the area. A large obstacle that the development of this model and the BioManCO model faces however, is the scarcity of data in these areas. The flow patterns around these semi-permeable dams have been identified in the model, but cannot yet be verified.
The aim of this thesis is to visualise flow patterns around and the permeability of a selected dam in the field to be able to get a better understanding of the hydrodynamics of the area. As the coastal area of Demak is quite remote, low-tech drifters will be used for this purpose, made only of locally available, inexpensive materials. They will be released at different locations at different moments in the tidal cycle. Data acquisition will take place by visual observation and by a camera attached to a drone. An algorithm will be developed to process the data digitally. It will automatically detect the drifters in the images taken by the drone. Using several Ground Control Points, of which the GPS-coordinates are known, the images can be rectified, so that the relation between the pixels in every image and their location in the real world is known. Using this information and the pixel-coordinates of the detected drifters, the paths of the drifters can be extracted from the images in real-world coordinates. From these paths, flow velocites can be deduced. The permeability of the dam will be assessed by releasing milk into the flow in several configurations during which data will be acquired by means of a GoPro camera mounted above the semi-permeable dam.
The results show, that tide is the main driving force behind the flow patterns around the dam focused
on in this research. During falling tide, a circulation pattern can be seen, which is caused by a combination of the local bathymetry and a wind driven mass transport over the plot. The flow patterns however do not resemble the patterns found in earlier model runs of the area. The cause of this is
thought to be the combination of simplifications in the model and the permeability of the dams, which is not taken into account by the model, but is shown to be influential by the permeability tests. These
tests show that there is definitely mass transport through the dam considered, but also that this may not be universally applicable to all semi-permeable dams in the area, depended on their location. The drifter paths found by the developed algorithm resemble the visual observations convincingly. The found velocities are difficult to interpret, because of the large scatter on the found drifter paths. The scatter is believed to be a result of errors in the rectification process, which should be improved in the future if this technique is to be used more frequently. Also the design of the drifters and the flight plan of the drone should be revisited to increase the detected amount of drifters in the images. All in all, the technique does show great promise to acquire more data in this remote area, but needs further refinement before it can be used for scientific purposes.