Thesis (MScEng)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: When a sailing ship passes a moored ship the moored ship experiences forces and moments. These forces and moments cause the moored ship to move. The resulting ship motions due to the passing ship can sometimes be more severe than the ship motions due to ocean waves and can cause serious accidents at moorings such as the failing of mooring lines or even the total break away of the ship from the berth. Since bulk carriers and tankers were traditionally the largest seafaring ships, passing ship studies have focused mainly on these vessels, but recently container ships have grown to a comparable size. In this study an existing numerical model “Passcat” is validated with physical model measurements for a Post Panamax container ship passing a Panamax bulk carrier. Other existing mathematical formulae are also evaluated by comparison with these model tests. In the physical model tests the passing speed (V), passing distance (G), depth draft ratio (d/D) and the presence of walls and channels were varied. It was found that the passing ship forces are proportional to the passing speed to the power of 2.32. This is slightly higher than the generally accepted quadratic relationship for passing ship induced forces. Similar relationships were found for the other variables. The numerical model results were compared to the physical model measurements by determining agreement ratios. A perfect agreement between the numerical and physical models would result in an agreement ratio of 1. Agreement ratio boundaries, wherein agreement would be regarded as good, were drawn between 0.7 and 1.3. The numerical model, Passcat, was found to under predict the passing ship forces. It was found that Passcat is valid for a wide range of sensitivities and remains within the agreement ratio limits as long as passing speed is limited to 10 knots (kt), depth draft ratio to more than 1.164, passing distance to less than four times the moored ship beam (Bm) for surge and sway estimation and passing distance to less than three times the moored ship beam for yaw estimations. These limits are true for no structures in the water. For structures in the water only the passing speed limits are different. When quay walls are present, the surge and sway forces will only provide acceptable answers at passing speeds below 9kt. When 9Bm or 12Bm channels are present, the sway force will only provide acceptable answers at passing speeds below 7kt. When a 6Bm channel is present, the yaw moments will only provide acceptable answers at passing speeds below 6kt. From the mathematical model evaluation study it was found that empirical or semi empirical methods can not provide answers with good agreement to the physical model when walls or channels are present. For the open water case, it is only the Flory method that can provide answers with good agreement to the physical model for surge, sway and yaw forces. The Flory method can provide answers with acceptable agreement within narrow boundaries of passing distance (1 to 2 times the beam of the moored ship), passing speed (4 kt to 14 kt) and depth draft ratio (less than 1.7). The numerical model, Passcat can be used with little effort to provide answers with better agreement to the physical model for a larger range of variables. / AFRIKAANSE OPSOMMING: Wanneer ’n skip verby ‘n vasgemeerde skip vaar, ondervind die vasgemeerde skip kragte en momente. Hierdie kragte induseer beweging van die vasgemeerde skip. Die beweging kan soms groter wees as die effek van wind of golwe. Indien die bewegings groot genoeg is kan dit van die vasmeer lyne van die skip laat breek, of al die lyne laat breek sodat die skip vry in die hawe ronddryf. Aangesien erts skepe en tenk skepe vir jare die grootste skepe in the wêreld was, het die meeste van die skip interaksie studies op daardie skepe gefokus. Die grootte van behouering skepe het egter in die onlangse tye gegroei om dimensies soortgelyk aan die van erts en tenk skepe te hê. In hierdie studie word ’n bestaande numeriese model “Passcat” gestaaf met fisiese model metings op ’n Post Panamax behoueringskip wat verby ‘n Panamax erts skip vaar. Bestaande wiskundige formules is ook getoets deur dit met dieselfde fisiese model metings te vergelyk. In die fisiese model studie is die spoed van die skip (V), tussenafstand (G), diepte diepgang verhouding (d/D) en die teenwoordigheid van kaai mure en kanale in die water getoets. Daar is gevind dat die kragte op die vasgemeerde skip direk eweredig is aan die spoed van die skip tot die mag 2.32. Dit is effens meer as die algemeen aanvaarde kwadratiese verhouding tussen vloeistof sleurkrag en vloeisnelheid asook tussen skip interaksie kragte en vaar snelheid. Soortgelyke verhoudings is vir al die veranderlikes bereken. Numeriese model resultate is vergelyk met die fisiese model om die verhouding van ooreenstemming te bepaal. ’n Perfekte ooreenstemming word voorgestel deur ’n verhouding van ooreenstemming van 1. Grense waarbinne die verhouding van ooreenstemming as goed beskou word is getrek tussen 0.7 en 1.3. Daar is gevind dat die numeriese model, Passcat, kragte oor die algemeen onderskat. Passcat is geldig vir 'n breë reeks van veranderlikes en sal geldig bly solank die skip spoed tot 10 knope, diepte diepgang verhouding tot meer as 1.164, tussenafstand tot minder as vier skipwydtes (Bm) vir 'surge' en 'sway' kragte en tot minder as drie skipwydtes vir 'yaw' momente beperk word. Hierdie grense is opgestel vir geen strukture in die water. Vir strukture in die water word slegs die skip spoed aangepas. Wanneer daar mure in die water is sal 'surge' en 'sway' slegs geskikte antwoorde gee as die skip spoed tot 9 knope beperk word. Vir 9Bm of 12Bm kanale sal geskikte antwoorde vir 'sway' kragte slegs voorkom met 'n skip spoed minder as 7 knope. Vir 6Bm kanale sal geskikte antwoorde vir 'yaw' momente slegs voorkom met 'n skip spoed van minder as 6 knope. Van die wiskundige model evaluasie studie is gevind dat empiriese of semi empiriese metodes nie resultate met goeie ooreenstemming tot the fisiese model metings kan gee, wanneer daar kaai of kanaal mure in die water is nie. Vir die oopwater geval is dit slegs die Flory metode wat antwoorde kan voorsien wat goed ooreenstem met die fisiese model vir 'surge', 'sway', en 'yaw' kragte. Die Flory metode voorsien hierdie resultate binne noue grense vir tussenafstand (1 tot 2 wydtes van die vasgemeerde skip), verbyvaar spoed (4 knope tot 14 knope) en diepte diepgang verhouding (minder as 1.7). Die numeriese model, Passcat, kan met min moeite antwoorde bereken wat beter ooreenstemming vir 'n groter reeks veranderlikes gee.

Notre motivation est de comprendre la locomotion humaine pour un meilleur contrôle des systèmes virtuels (robots et mannequins). La locomotion humaine a été étudiée depuis longtemps dans des domaines différents. Nous considérons la locomotion comme le déplacement d’un repère attaché au corps humain (direction et orientation) au lieu de la trajectoire articulaire du corps complet. Notre approche est basée sur le fondement calculatoire de la locomotion humaine. Le but est de trouver un modèle qui explique la forme de la locomotion humaine dans l’espace. Pour ce faire, nous étudions tout d’abord le comportement des trajectoires au sol pendant la locomotion intentionnelle. Quand un humain marche, il met un pied devant l’autre et par conséquence, l’orientation du corps suit la direction tangente de la trajectoire. C’est ce qu’on appelle l’hypothèse de comportement nonholonome. Cependant, dans le cas d’un pas de côté, l’orientation du corps n’est plus semblable à la direction de trajectoire, et l’hypothèse n’est plus valable. Le comportement de la locomotion devient holonome. Le but de la thèse est de distinguer ces deux comportements et de les exploiter en neuroscience, robotique et animation graphique. La première partie de la thèse présente une étude qui permet de déterminer des configurations de comportement holonome par un protocole expérimental et par une fonction qui segmente les comportements nonholonomes et holonomes d’une trajectoire. Dans la deuxième partie, nous établissons un modèle unifiant comportements nonholonomes et holonomes. Ce modèle combine trois vitesses générant la locomotion humaine : tangentielle, angulaire et latérale. Par une approche de commande optimale inverse nous proposons une fonction multi-objectifs qui optimise des trajectoires calculées pour les rendre proches des trajectoires humaines naturelles. La dernière partie est l’application qui utilise les deux comportements pour synthétiser des locomotions humaines dans un environnement d’animation graphique. Chaque locomotion est caractérisée par trois vitesses et est donc considérée comme un point dans l’espace de commande 3D (de trois vitesses). Nous avons collecté une librairie qui contient des locomotions de vitesses différentes – des points dans l’espace 3D. Ces points sont structurés en un nuage de tétraèdres. Quand une vitesse désirée est donnée, elle est projetée dans l’espace 3D et on trouve le tétraèdre qui la contient. La nouvelle animation est interpolée par quatre locomotions correspondant aux quatre sommets du tétraèdre. On expose plusieurs scénarios d’animations sur un personnage virtuel. / Our motivation is to understand human locomotion to better control locomotion of virtual systems (robots and mannequins). Human locomotion has been studied so far in different disciplines. We consider locomotion as the level of a body frame (in direction and orientation) instead of the complexity of many kinematic joints systems as other approaches. Our approach concentrates on the computational foundation of human locomotion. The ultimate goal is to find a model that explains the shape of human locomotion in space. To do that, we first base on the behavior of trajectories on the ground during intentional locomotion. When human walk, they put one foot in front of the other and consequently, the direction of motion is deduced by the body orientation. That’s what we called the nonholonomic behavior hypothesis. However, in the case of a sideward step, the body orientation is not coupled to the tangential direction of the trajectory, and the hypothesis is no longer validated. The behavior of locomotion becomes holonomic. The aim of this thesis is to distinguish these two behaviors and to exploit them in neuroscience, robotics and computer animation. The first part of the thesis is to determine the configurations of the holonomic behavior by an experimental protocol and an original analytical tool segmenting the nonholonomic and holonomic behaviors of any trajectory. In the second part, we present a model unifying nonholonomic and holonomic behaviors. This model combines three velocities generating human locomotion: forward, angular and lateral. The experimental data in the first part are used in an inverse optimal control approach to find a multi-objective function which produces calculated trajectories as those of natural human locomotion. The last part is the application that uses the two behaviors to synthesize human locomotion in computer animation. Each locomotion is characterized by three velocities and is therefore considered as a point in 3D control space (of three speeds). We collected a library that contains locomotions at different velocities - points in 3D space. These points are structured in a tetrahedra cloud. When a desired speed is given, it is projected into the 3D space and we find the corresponding tetrahedron that contains it. The new animation is interpolated by four locomotions corresponding to four vertices of the selected tetrahedron. We exhibit several animation scenarios on a virtual character.

Nas duas últimas décadas, houve um enorme aumento no número de estruturas proteicas resolvidas, e entre elas há uma variedade imensa de proteínas com mais de uma conformação observada. Essa quantidade incontestável de dados experimentais corroboram a hipótese de que cada proteína exista num espaço conformacional próprio, onde ela possa adotar inúmeras conformações, umas mais distintas ou estáveis que outras. Essas conformações estão distribuídas nesse espaço de acordo com sua energia potencial, que pode ser definida como uma superfície cheia de rugosidades, poços e barreiras energéticas. Duas conformações distantes nesse espaço são muito diferentes entre si, enquanto que duas conformações próximas são mais semelhantes. Da mesma forma, se distinguem os movimentos necessários para passar de uma conformação à outra. Para uma proteína passar de um estado a outro, geralmente identificados com grandes mudanças conformacionais, é necessário um movimento coletivo. Por ser de grande amplitude, esse tipo de movimento ocorre com baixa frequência, e dificilmente é observado em simulações clássicas de dinâmica molecular. Assim, existem métodos dedicados à obtenção destes movimentos, como a análise de modos normais, os modelos de redes elásticas e a análise de componentes principais. Neste trabalho, adaptamos o método de transformada de Fourier para recuperar modos harmônicos que compõem uma trajetória simulada suficientemente longa para analisar três proteínas distintas quanto a seus movimentos biológicos de importância funcional. Uma é a DEA, cuja simetria hexagonal observamos influenciar nos modos coletivos e na transição entre estados. Outra é a MosR, que simulamos em seus dois estados diferentes, oxidado ou reduzido, para encontrar como a oxidação é capaz de impedir os movimentos coletivos que levam à conformação ligada ao DNA. Nestas duas proteínas, observamos que nenhum modo por si só é responsável pela transição entre as conformações experimentais, mas que eles dependem de outros modos ou outras mudanças conformacionais ocorrendo de forma combinada. A terceira proteína analisada é um regulador transcricional, assim como a MosR, a ElrR, cuja estrutura é conhecida somente na forma apo. Neste trabalho, construímos modelos da ElrR ligada ao DNA pela combinação linear de modos harmônicos para modelar um possível ligante na nova conformação do sítio alostérico. As amplitudes usadas nessa combinação foram obtidas pelo método de mínimos quadrados, visando minimizar o desvio em relação somente às coordenadas que as hélices de reconhecimento devem apresentar para se ligar ao sítio de DNA. Este prognóstico foi feito pela análise metódica das estruturas de 27 reguladores transcricionais, homodiméricos com o motivo HTH, em complexo com DNA. Essa análise também nos permitiu descrever a estereoquímica do encaixe das hélices de reconhecimento nos sulcos maiores do DNA com novos parâmetros geométricos, intimamente relacionados com a simetria do complexo, com a sequência de resíduos das hélices de reconhecimento e com a sequência de bases do sítio de DNA, de forma a auxiliar na modelagem de novos complexos. / There was an enormous increase in the deposited protein structures in the past two decades, among them there is a great variety of proteins with more than one observed conformation. This undenieble amount of experimental data ratify the hypothesis that each protein posseses its own conformational space, where it can adopt countless conformations, some more distinct or stable than others. These conformations are distributed in the space according to its potential energy, which maybe defined as a rough landscape fulled with energetic wells and barriers. Two conformations lying apart from each other in this landscape do not carry much resemblances, while neighbouring conformations are very similar. The motions required to get one conformation to another are just as distinguishable. There must be a collective motion inbetween two states of a protein, commonly characterized by large conformation changes. This type of motion is related to large amplitudes and low frequencies, thus it is hardly seen in classical molecular dynamics simulations. Therefore, there are dedicated methods to obtain these motions, as normal modes analysis, elastic network models and essential dynamics. In this work we adapted the method of Fourier transform filtering to retrieve harmonic modes that compose a simulated trajectory and thus analise the biological motions with functional importance of three distinct proteins. One is DEA, which hexagonal symmetry was observed to affect its collective motions and the transition between biological states. Another protein is MosR, which we simulated in two different states, oxidized or reduced, to learn how the formation of a disulphide bridge is able to preclude the collective motions that lead to a DNA-binding conformation. With these two proteins we observed that no mode by itself is responsible for the transition between experimental conformations, and they actually depend on other conformational changes occurring in a combined manner. The third protein that we analised, ElrR, is a transcriptional regulator, like MosR, which structure is known only on its apo form. Hence in this work we built models of ElrR bound to DNA by the linear combination of harmonic modes aiming to model a ligand that would fit in the allosteric site upon the conformational changes driven by the collective motions. The amplitudes we used in this method were calculated by the least square method to minimize the deviation to the positions of the recognition helices when bound to the DNA. This prognostic of the target position of the recognition helices was made upon the methodical analysis of 27 structures of homodimeric transcriptional regulators, that present the Helix-Turn-Helix motif, complexed with DNA. This approach allowed us to describe the stereochemical fitting of the recognition helices into the DNA major grooves with new geometrical parameters intimatelly related to the symmetry of the complex, the residue sequence of the recognition helices and the base sequence of the DNA site, providing thus support to model new complexes.

No description available.

The objective of this study is to evaluate the regional differences between the worldwide based NGA-W1 ground motion models and available Turkish strong ground motion dataset and make the required adjustments in the NGA-W1 models. A strong motion dataset using parameters consistent with the NGA ground motion models is developed by including strong motion data from Turkey. Average horizontal component ground motion is computed for response spectral values at all available periods using the GMRotI50 definition consistent with the NGA-W1 models. A random-effects regression with a constant term only is used to evaluate the systematic differences in the average level of shaking. Plots of residuals are used to evaluate the differences in the magnitude, distance, and site amplification scaling between the Turkish dataset and the NGA-W1 models. Model residuals indicated that the ground motions are overestimated by all 5 NGA-W1 models significantly, especially for small-to-moderate magnitude earthquakes. Model residuals relative to distance measures plots suggest that NGA-W1 models slightly underestimates the ground motions for rupture distances within 100-200 km range. Models including the aftershocks over-predict the ground motions at stiff soil/engineering rock sites. The misfit between the actual data and model predictions are corrected with adjustments functions for each scaling term. Turkey-Adjusted NGA-W1 models proposed in this study are compatible with the Turkish strong ground motion characteristics and preserve the well-constrained features of the global models. Therefore these models are suitable candidates for ground motion characterization and PSHA studies conducted in Turkey.

Infinitely divisible distributions and processes have been the object of extensive research not only from the theoretical point of view but also for practical use, for example, in queueing theory or mathematical finance. In this thesis, we will study some of their subclasses with a view towards financial modeling. As generalizations of stable distributions, we study the tempered stable distributions and introduce the new classes of layered stable distributions as well as the mixed stable distributions, along with the corresponding Levy processes. As a further generalization of infinitely divisible processes, fractional tempered stable motions are defined. These theoretical studies will be complemented by some more practical ones, such as the simulation of sample paths, parameter estimations, financial portfolio hedging, and solving stochastic differential equations.

The Central and Eastern United States (CEUS) is a region that is characterized by low frequency-high consequence seismic events such as the New Madrid sequence of 18111812. The infrequent nature of earthquakes in the region has led to a perception that the seismic risk in the area is low, and the current building stock reflects this perception. The majority of steel-framed buildings in the CEUS were designed without regard to seismic loads. Such frames possess limited seismic resistance, and may pose an unacceptable risk if a large earthquake were to occur in the region. A key ingredient of building performance and seismic risk assessment is the fragility, a term that describes the probability of failure to meet a performance objective as a function of demand on the system. The effects of uncertainties on building seismic performance can be displayed by a seismic fragility relationship. This fragility can be used in a conditional scenario-based seismic risk assessment or can be integrated with seismic hazard to obtain an estimate of annual or lifetime risk. The seismic fragility analyses in this study focus on steel frames that are typical of building construction in regions of infrequent seismicity; such frames have received little attention to date in building seismic risk assessment. Current steel building stock in Shelby Co., TN has been represented by five code-compliant model frames with different lateral force-resisting systems, i.e., braced-frames, partially-restrained moment frames and a rigid moment frame. The performance of model frames under certain hazard levels was assessed using fragility curves. Different rehabilitation methods were discussed and applied. Results indicate that PR frames behave better than expected and rehabilitated frames perform quite well even under severe earthquakes.

Maximum interstory drift and the distribution of this drift along the height of the structure are the main causes of structural and nonstructural damage in frame type buildings subjected to earthquake ground motions. Estimation of maximum interstory drift ratio is a good measure of the local response of buildings. Recent earthquakes have revealed the susceptibility of the existing building stock to near-fault ground motions characterized by a large, long-duration velocity pulse. In order to find rational solutions for the destructive effects of near fault ground motions, it is necessary to determine drift demands of buildings. Practical, applicable and accurate methods that define the system behavior by means of some key parameters are needed to assess the building performances quickly instead of detailed modeling and calculations. In this study, simple equations are proposed in order for the determination of the elastic interstory drift demand produced by near fault ground motions on regular and irregular steel frame structures. The proposed equations enable the prediction of maximum elastic ground story drift ratio of shear frames and the maximum elastic ground story drift ratio and maximum elastic interstory drift ratio of steel moment resisting frames. In addition, the effects of beam to column stiffness ratio, soft story factor, stiffness distribution coefficient, beam-to-column capacity ratio, seismic force reduction factor, ratio of pulse period to fundamental period, regular story height and number of stories on elastic and inelastic interstory drift demands are investigated in detail. An equation for the ratio of maximum inelastic interstory drift ratio to maximum elastic interstory drift ratio developed for a representative case is also presented.

This thesis studies the dynamics and stability of some bicycles. The dynamics of idealized bicycles is of interest due to complexities associated with the behaviour of this seemingly simple machine. It is also useful as it can be a starting point for analysis of more complicated systems, such as motorcycles with suspensions, frame flexibility and thick tyres. Finally, accurate and reliable analyses of bicycles can provide benchmarks for checking the correctness of general multibody dynamics codes. The first part of the thesis deals with the derivation of fully nonlinear differential equations of motion for a bicycle. Lagrange’s equations are derived along with the constraint equations in an algorithmic way using computer algebra.Then equivalent equations are obtained numerically using a Newton-Euler formulation. The Newton-Euler formulation is less straightforward than the Lagrangian one and it requires the solution of a bigger system of linear equations in the unknowns. However, it is computationally faster because it has been implemented numerically, unlike Lagrange’s equations which involve long analytical expressions that need to be transferred to a numerical computing environment before being integrated. The two sets of equations are validated against each other using consistent initial conditions. The match obtained is, expectedly, very accurate. The second part of the thesis discusses the linearization of the full nonlinear equations of motion. Lagrange’s equations have been used.The equations are linearized and the corresponding eigenvalue problem studied. The eigenvalues are plotted as functions of the forward speed ν of the bicycle. Several eigenmodes, like weave, capsize, and a stable mode called caster, have been identified along with the speed intervals where they are dominant. The results obtained, for certain parameter values, are in complete numerical agreement with those obtained by other independent researchers, and further validate the equations of motion. The bicycle with these parameters is called the benchmark bicycle. The third part of the thesis makes a detailed and comprehensive study of hands-free circular motions of the benchmark bicycle. Various one-parameter families of circular motions have been identified. Three distinct families exist: (1)A handlebar-forward family, starting from capsize bifurcation off straight-line motion, and ending in an unstable static equilibrium with the frame perfectly upright, and the front wheel almost perpendicular. (2) A handlebar-reversed family, starting again from capsize bifurcation, but ending with the front wheel again steered straight, the bicycle spinning infinitely fast in small circles while lying flat in the ground plane. (3) Lastly, a family joining a similar flat spinning motion (with handlebar forward), to a handlebar-reversed limit, circling in dynamic balance at infinite speed, with the frame near upright and the front wheel almost perpendicular; the transition between handlebar forward and reversed is through moderate-speed circular pivoting with the rear wheel not rotating, and the bicycle virtually upright. In the fourth part of this thesis, some of the parameters (both geometrical and inertial) for the benchmark bicycle have been changed and the resulting different bicycles and their circular motions studied showing other families of circular motions. Finally, some of the circular motions have been examined, numerically and analytically, for stability.

No description available.