The good of this thesis is to apply a numerical model for studying waveform of an internal solitary wave (ISW) on variable seabed topography. The numerical model developed by Lynett and Liu (2002) is adopted for this work but with modification to improve its accuracy, both mathematically and in programming codes. Numerical experiments using the modified model are then performed and the results compared with laboratory experiments of Kuo (2005), in order to validate its accuracy. The mathematical model derived in the present study is based on the assumption that an internal wave is weakly nonlinear and weakly dispersive in an inviscid fluid. The governing equations based on the continuity equation and Euler equations are solved for ISW propagation over variable topography. The input conditions for the numerical experiments include physical parameters related to water depth and geometry of submarine obstacle, such as depth ratio between upper and lower layers (H1/H2), height (hs) and type (triangular ridge and trapezoidal shelf) of obstacles, in addition to the amplitude (ai) of an incident ISW. From the results of numerical experiments, wave amplitude, phase speed, and wave energy of a transmitted ISW are obtained and compared with that of laboratory experiments. (Kuo, 2005) ISW propagation over a single obstacle is affected by a dimensionless parameter called ¡§blockage parameter", £a= (a1+h1)/(h1+h2-hs). Three types of interaction may be classified (weak interaction, moderate interaction, and wave breaking) depending on the value of£a . For an ISW propagating over two consecutive obstacles, the interval between them is significant in reducing its amplitude and energy, as the interval reduces. Moreover, the effect of relative height between two obstacles may also be classified into two types: (i) within the range of weak interaction, energy dissipation is less for a high obstacle first than for it as the second; (ii) within the range of moderate interaction, the energy dissipation is higher for a high obstacle first than for it as the second. Further comparisons have shown that the modified numerical model is in better agreement with the results of laboratory experiments (Kuo, 2005) than the original model of Lynett and Liu (2002). The results obtained from the present numerical experiments for ISW evolution on variable topography is encouraging which could benefit other who may be interested in internal wave propagation for practical applications in oceanography.

The marine currents around the Pacific Northwest are researched by lots of scholars. The methods of the on-site observation, such as the shipping measurements and data buoys, were applied by researcher in the past. However, it is difficult to get comprehensive information on space by early methods, and it is often limited by the manpower and funding. With computer technology advances, numerical models get improving the accuracy and resolution. Therefore, development of the numerical models also becomes one of the methods to understand the ocean. There are many current models and large databases which are developed. However, few studies combine the two. Therefore, this study adopts the simulated results of POLCOMS (Proudman Oceanographic Laboratory Coastal-Ocean Modeling System) in 2002 near the northwest Pacific (9.9¢X N ~ 41.9¢X N, 104.9¢X E ~ 139.9¢X E) to analyze some situations. The result can be compared with the measured data, and test the model. In order to evaluate the accuracy of the results of the model, the simulated tracks can be calculated by the result of the model and the initial location of the measured data. However, the resolutions of time and space are only one day and 7.5 degree. Hence, the methods of linear interpolation and bilinear interpolation are applied to interpolate the model result in the time dimension and space dimension. By using the latitude and longitude of the initial points, the azimuth, and the geographic distance, the simulated tracks can be calculated. Therefore, the results of POLCOMS can be confirmed by global drifter data from NOAA/AOML. According to the results of evaluating, the simulation trends of the seasons are similar to measured data. It can prove that this model has a certain degree of accuracy. However, simulation and the measured data can not be completely similar when abnormal weather phenomenon occurs. It is because the model was driven by the average wind field. There are suggestions to make the model complete by adding the weather information during the periods of the typhoons. Besides, the model can simulate the temperature and salinity of the ocean. Increasing the comparison of them will make the model integrated in the future, and obtain more correct information of the flow fields around the Pacific Northwest.

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Polyhydroxyalkanoates (PHAs) are biodegradable plastic synthesized by microorganisms from renewable carbon resources and they are promising substitutes for conventional fossil-fuel-based plastics due to their similar physical properties. Pure cultures of particular microorganisms are commonly used for industrial PHA production but high production costs due to requirements of sterile conditions and refined substrates hinder the mass production of PHAs. Thus, model development for PHA production by microbes is essential to investigate the PHA formation and microbial metabolisms for enhanced productivity and PHA contents. In the present study, a comprehensive numerical model has been developed and calibrated for the non-growth associated PHA production process by Cupriavidus necator. The model parameters were calibrated with 8 selected experimental studies and the simulation results show good agreement with experimental data. Two methods were used to conduct sensitivity analysis: the simple method and the overall relative sensitivity analysis method. Maximum specific residual biomass growth rate was the most sensitive parameter. The calibrated model was used to investigate fed-batch feeding strategies that optimize PHA accumulation by limited nutrient feeding in the PHA production phase. The simulation results showed limited phosphorous feeding accumulated more PHA than limited nitrogen feeding. The optimal feeding strategy was determined to be limited phosphorous feeding at 5% of initial phosphorous during the PHB production phase, yielding simulated 226.0 g/L PHB at the end of the 168-hour operation. / Thesis / Master of Applied Science (MASc)

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Various numerical modelling software packages are available for predicting moored ship motions and forces. The focus of this study was to validate the numerical models QUAYSIM and WAVESCAT and how these models together form a procedure for predicting moored ship motions and forces under the impact of high and low frequency waves. The validation procedure applied in the study involved numerical modelling of a given physical model situation in which moored ship motions and forces were measured under both high and low frequency wave conditions. A physical model with built-in bathymetry was provided by the Council for Scientific and Industrial Research (CSIR) Hydraulics Laboratory in Stellenbosch. The model consisted of a moored container vessel at a jetty, with various mooring lines and fenders. A JONSWAP spectrum, which combines high and low frequency wave components, was used to simulate wave conditions for the modelling of ship motions. The wave periods and wave heights were measured at observation stations located at specific points in the basin. Other measurements such as those of the forces in the fenders and mooring lines were also determined. A multi-step approach was used to numerically predict the ship motions and forces. Firstly, the coastal processes occurring within the basin, which was set up to simulate the physical model wave behaviour, were measured to calibrate the SWAN Delft3D-WAVE model. The wave heights and periods for the respective observation stations were obtained and compared to the physical model measurements. The Delft3D-FLOW SURFBEAT model was used to calculate the low frequency waves in the coastal area. Low frequency waves are the main cause of larger ship motions and forces, therefore it is important to investigate them as part of the ship motion prediction procedure. After the waves had been computed, wave forces acting on the vessel needed to be determined for both high and low frequency waves. These wave forces were modelled with the combinations SURFBEAT/LF-STRIP (low frequency waves) and SWAN/WAVESCAT (high frequency waves). LF-STRIP provided the link between low frequency wave models and ship motion models, converting the low frequency waves into long wave forces acting on the vessel. WAVESCAT converted the high frequency waves to short wave forces. The calculated long wave forces and short wave forces served as the input required to run the ship motion model QUAYSIM to determine the movements of the moored ship as well as the restraining forces in the lines and fenders. The ship motions and forces were compared to the physical model, with the intention of possibly validating the QUAYSIM/WAVESCAT approach for predicting moored ship motions. The study provides an overview of both the setup and results of the physical and numerical model. A description of each of the numerical models SWAN, SURFBEAT, LF-STRIP, WAVESCAT and QUAYSIM is provided, along with a comparison between the physical and numerical models for each procedure. The validation procedure provided useful documentation of the quality of these numerical modelling approaches, already in use in some design projects. The numerical models WAVESCAT and QUAYSIM models of ship motion have shown to provide a good correlation between the physical model and the numerical approach. However, improvements are still required. Good comparisons were obtained for the long wave motions (horizontal movements - surge, sway and yaw). The surge and sway motions were slightly overestimated by QUAYSIM. The magnitude of the yaw was comparable but the not well represented in spectral plots. / AFRIKAANSE OPSOMMING: Daar is verskeie numeriese modellering-sagtewareprogramme beskikbaar waarmee skipbewegings en -kragte voorspel kan word. Die fokus van hierdie studie was om die numeriese modelle QUAYSIM en WAVESCAT te valideer. Saam vorm hierdie twee modelle ’n prosedure om vasgemeerde skipbewegings en -kragte veroorsaak deur lang- en kortgolfaksie te bepaal. Die validasieprosedure wat in hierdie studie gebruik is, behels ’n numeriese modelering van ’n fisiese situasie waar ’n vasgemeerde skip se bewegings en kragte onder kort- en langgolfkondisies gemeet is. ’n Fisiese model met ingeboude batimetrie is voorsien deur die Council for Scientific and Industrial Research (CSIR) se hidroliese laboratorium in Stellenbosch. Die model bestaan uit ’n vasgemeerde houerskip by ’n pier met verskeie ankerlyne en bootbuffers. ’n JONSWAPspektrum, wat kort- en langgolfkomponente kombineer, is gebruik om golfomstandighede vir die modellering van skipbewegings te simuleer. Golfperiodes en golfhoogtes is by spesifieke waarnemingstasies in die gesimuleerde hawe-area gemeet. Verdere opmetings, soos dié van die kragte in die bootbuffers en ankerlyne, is ook gedoen. ’n Stap-vir-stap benadering is gevolg om die skipbewegings numeries te voorspel. Eerstens is die kusprosesse wat in die gesimuleerde hawe plaasvind, gekalibreer met die numeriese paket SWAN Delft3D-WAVE. Die golfhoogtes en golfperiodes vir elke waarnemingstasie is bereken en vergelyk met die fisiese model se opmetings. Die SURFBEAT-module van Delft3D-FLOW is gebruik om die lae-frekwensie golwe in die kusarea te bereken. Lae-frekwensie golwe is die hoofoorsaak van skipbewegings en daarom is dit belangrik om dit te ondersoek gedurende die voorspellingsprosedure van skipbewegings. Na die golwe bereken is, moes die kragte wat beide kort en lang golwe op die skip uitoefen ook bereken word. Hierdie golfkragte is gemodelleer deur middel van die kombinasies SURFBEAT/LFSTRIP (langgolwe) en SWAN/WAVESCAT (kortgolwe). LF-STRIP het die skakel tussen golfmodelle en skipbewegingsmodelle verskaf en die lae-frekwensie golwe omgeskakel in langgolfkragte wat op die skip uitgeoefen is. WAVESCAT het die hoë-frekwensiegolwe omgeskakel in kortgolfkragte wat op die skip uitgeoefen is. Die berekende langgolf- en kortgolfkragte is ingevoer op die skipbewegingsmodel QUAYSIM om die skipbewegings en inperkingskragte in die bootbuffers en ankerlyne te bepaal sodat dit vergelyk kon word met die fisiese model, met die doel om moontlik die QUAYSIM/WAVESCAT-prosedure om gemeerde skipbewegings te voorspel te valideer. Die studie verskaf ’n oorsig van die opstel en resultate van die fisiese en numeriese modelle. Elk van die numeriese modelle SWAN, SURFBEAT, LF-STRIP, WAVESCAT en QUAYSIM word beskryf en vergelykings word getref tussen die numeriese en fisiese modelle vir elke prosedure. Die validasieprosedure verskaf nuttige dokumentasie van die kwaliteit van hierdie numeriese modeleringsprosedures wat reeds in sekere ontwerpprojekte gebruik word. Die numeriese WAVESCAT en QUAYSIM modelle van skipbewegings het ’n goeie korrelasie tussen die fisiese model en die numeriese benadering gelewer. Verbeteringe is wel steeds nodig. Goeie vergelykings is verkry vir langgolfbewegings (horisontale bewegings – stuwing (“surge”), swaai (“sway”) en gier (“yaw”)). Die stu- en swaaibewegings was effens oorskat met QUAYSIM. Die grootte van die gier was wel vergelykbaar maar is nie grafies goed uitgebeeld nie.

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The Upper Mississippi River is in interest to river managers and biologists' dues to its vast ecosystem and past anthropogenic impacts. In order to help restore the river to its once natural state, river managers and biologists need a strong understanding of the hydrodynamics of the system. A two-dimensional hydrodynamic model was developed in Pool 8 of the Upper Mississippi River and utilized for river management applications. The model was constructed using SMS 10.0 grid generation software and processed with SRH-2D software. SRH-2D used Manning's roughness coefficients to calibrate the model to observed water surface elevation data collected by the USGS. The model was validated to an observed water surface elevation profile and percent discharge through 17 transects within the model. The calibrated and validated model was used for river management and biological applications; hypothetical island, drawdown scenarios, residence time study, and habitat suitability assessment. The results showed that the two-dimensional hydrodynamic model could accurately represent a hypothetical island within the lower pool, simulate drawdown scenarios, develop stream traces for particle tracking and residence time calculation, and the creation of habitat suitability maps based on field data. The completion of these applications with the two-dimensional model shows the efficiently and accuracy of the model, and how two-dimensional numerical models are important tools in bridging the gap between engineers and scientists.

The present text, submitted to the University of Liège in fulfillment of the requirements for the degree of Docteur en Sciences de lIngénieur, aims at improving the understanding and description of air‐water interactions in transient flows. A particular emphasis is set on phenomena relevant in civil and environmental engineering, like rivers, pipes, and hydraulic structures. Theoretical results of this doctoral research may be summarized in two main propositions. First, I show that any mathematical model for free surface flows can be extended to pressurized flows. Second, the multiphase drift‐flux model is proven an adequate alternative to Navier‐ Stokes equations in civil and environmental engineering. These propositions underpin the development of original mathematical models and new computational codes (WOLF1D and WOLF IMPack). Validation and application on actual cases prove the efficiency of the new approach. Original concepts introduced in this thesis pave the way for further research on environmental flows, especially on the mathematical description of transport phenomena (pollutants, sediments) and heterogeneous interactions (vegetation, rough bed).

The energy requirements of forage harvesters can be quite high and can sometimes determine the size of tractor needed on a farm. Therefore, improving the energy efficiency of the forage harvester could allow a farm to reduce costs by using a smaller tractor that is less expensive and more efficient. The objective of this research was to increase the throwing distance of a forage harvester by modeling the flow of forage in the spout and the air flow in the blower and spout. These models can then be used to compare the efficiencies of prototype designs. The air flow in the blower and spout was modeled using the commercial computational fluid dynamics software FLUENT. The simulation results of air velocities and flow patterns were compared to experimental values and it was found that both were of the same order of magnitude with the model predicting slightly higher air velocities than those measured. The flow of forage in the spout was modeled analytically by taking into account the friction between the forage and the spout surface and the aerodynamic resistance after the forage leaves the spout. From this model, two improved prototype spouts that should theoretically result in longer throwing distances were designed. However, field testing of the two prototypes did not reveal any significant improvements over the current design. It was also found that the model under-predicted the throwing distance of one prototype by 2 % and over estimated the other by 12 %.