<p>In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix <em>d</em>.</p><p>In this thesis I present a few methods for constructing a phylogenetic tree from <em>d</em>. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When <em>d</em> does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.</p><p>Finally I have tested the methods both on real measured data and constructed test cases.</p>

We present two watermarking schemes for 3D meshes : - watermarking with geometrical invariant for fragile watermarking towards authentication and integrity purposes - watermarking in the geometrical spectral domain towards robust watermarking / Nous présentons deux schémas de tatouage pour maillages surfaciques 3D : - tatouage fragile par invariants géométriques pour l'authentification et l'intégrité - tatouage robuste dans l'espace de la décomposition spectrale

The proper orthogonal decomposition (POD) has been widely used in fluid dynamic applications for extracting dominant flow features. The “gappy” POD is an extension to this method that allows the consideration of incomplete data sets. In this paper, the gappy POD is extended to handle unsteady flow reconstruction problems, such as those encountered when limited flow measurement data is available. In addition, a systematic approach for effective sensor placement is formulated within the gappy framework. Two applications are considered. The first aims to reconstruct the unsteady flow field using a small number of surface pressure measurements for a subsonic airfoil undergoing plunging motion. The second considers estimation of POD modal content of a cylinder wake flow for active control purposes. In both cases, using the dominant POD basis vectors and a small number of sensor signals, the gappy approach is found to yield accurate flow reconstruction results. / Singapore-MIT Alliance (SMA)

The goal of the research described here is to develop tools to assist the rapid analysis and design of manufacturing systems. The methods we describe are based on mathematical models of production systems. We combine earlier work on the decomposition method for factory performance prediction and design with the hedging point method for scheduling. We propose an approach that treats design and operation in a unified manner. The models we study take many of the most important features and phenomena in factories into account, including random failures and repairs of machines, finite buffers, random demand, production lines, assembly and disassembly, imperfect yield, and token-based control policies. / Singapore-MIT Alliance (SMA)

In this paper, a new methodology for predicting fluid free surface shape using Model Order Reduction (MOR) is presented. Proper Orthogonal Decomposition combined with a linear interpolation procedure for its coefficient is applied to a problem involving bubble dynamics near to a free surface. A model is developed to accurately and efficiently capture the variation of the free surface shape with different bubble parameters. In addition, a systematic approach is developed within the MOR framework to find the best initial locations and pressures for a set of bubbles beneath the quiescent free surface such that the resultant free surface attained is close to a desired shape. Predictions of the free surface in two-dimensions and three-dimensions are presented. / Singapore-MIT Alliance (SMA)

The utilisation of alternate sources of energy has reached critical levels due to the constantly growing demand for energy and the diminishing of fossil fuels. The production of hydrogen through the Hybrid Sulphur process is a possible alternative that may contribute towards alleviating the pressure on the world's energy resources. The two-step thermochemical cycle for decomposing water into hydrogen and oxygen offers the potential to obtain acceptable thermal efficiencies, while still using common and inexpensive chemicals. The process mainly makes use of two unit process operations: an electrolyser and a chemical decomposition reactor. This research project focuses on the concept design of the decomposition reactor operated adiabatically as a multi-stage reactor system with inter-stage heating, in order to simplify the reactor design. This approach allows for the independent evaluation of the reaction kinetics and the heat transfer mechanism. / Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2009.

Thesis (Ph. D.)--University of Chicago Graduate School of Business, December 1997. / Includes bibliographical references.

No description available.

To better study frequency related effects such as attenuation and tuning, we developed a frequency dependent seismic reflection analysis. Comprehensive tests on full waveform synthetics and observations from the Teal South ocean bottom seismic (OBS) data set confirmed that normal moveout (NMO) stretch could distort both frequency and amplitude information severely in shallow events and far offset traces. In synthetic tests, our algorithm recovered amplitude and frequency information ac-curately. This simple but robust target oriented NMO stretch correction scheme can be used on top of an existing seismic processing flow for further analyses. By combining the NMO stretch correction, spectral decomposition, and crossplots of am-plitude versus offset (AVO) attributes, we tested the frequency dependent workflow over Teal south and Ursa field data sets for improved reservoir characterization. As expected from NMO stretch characteristics, low frequencies have been less affected while mid and high frequency ranges were affected considerably. In seismic attribute analysis, the AVO crossplots from spectrally decomposed prestack data confirmed the improved accuracy and effectiveness of our workflow in mid and high frequency regions. To overcome poor spectral decomposition results due to low signal to noise ratio (S/N) in the Teal South application, we also implemented a substack scheme that stacks adjacent traces to increase S/N ratio while reducing the amount of data to process and increasing the accuracy of the spectral decomposition step. Synthetic tests verified the effectiveness of this additional step. An application to the Ursa, Gulf of Mexico, deep water data set showed significant improvement in high frequency data while correcting biased low frequency information.

The segmentation problem arises in the elaboration of a radiation therapy plan. After the cancer has been diagnosed and the radiation therapy sessions have been prescribed, the physician has to locate the tumor as well as the organs situated in the radiation field, called the organs at risk. The physician also has to determine the different dosage he wants to deliver in each of them and has to define a lower bound on the dosage for the tumor (which represents the minimum amount of radiation that is needed to have a sufficient control of the tumor) and an upper bound for each organ at risk (which represents the maximum amount of radiation that an organ can receive without damaging). Designing a radiation therapy plan that respects these different bounds of dosage is a complex optimization problem that is usually tackled in three steps. The segmentation problem is one of them. Mathematically, the segmentation problem amounts to decomposing a given nonnegative integer matrix A into a nonnegative integer linear combination of some binary matrices. These matrices have to respect the consecutive ones property. In clinical applications several constraints may arise that reduce the set of binary matrices which respect the consecutive ones property that we can use. We study some of them, as the interleaf distance constraint, the interleaf motion constraint, the tongue-and-groove constraint and the minimum separation constraint. We consider here different versions of the segmentation problem with different objective functions. Hence we deal with the beam-on time problem in order to minimize the total time during which the patient is irradiated. We study this problem under the interleaf distance and the interleaf motion constraints. We consider as well this last problem under the tongue-and-groove constraint in the binary case. We also take into account the cardinality and the lex-min problem. Finally, we present some results for the approximation problem. /Le problème de segmentation intervient lors de l'élaboration d'un plan de radiothérapie. Après que le médecin ait localisé la tumeur ainsi que les organes se situant à proximité de celle-ci, il doit aussi déterminer les différents dosages qui devront être délivrés. Il détermine alors une borne inférieure sur le dosage que doit recevoir la tumeur afin d'en avoir un contrôle satisfaisant, et des bornes supérieures sur les dosages des différents organes situés dans le champ. Afin de respecter au mieux ces bornes, le plan de radiothérapie doit être préparé de manière minutieuse. Nous nous intéressons à l'une des étapes à réaliser lors de la détermination de ce plan: l'étape de segmentation. Mathématiquement, cette étape consiste à décomposer une matrice entière et positive donnée en une combinaison positive entière linéaire de certaines matrices binaires. Ces matrices binaires doivent satisfaire la contrainte des uns consécutifs (cette contrainte impose que les uns de ces matrices soient regroupés en un seul bloc sur chaque ligne). Dans les applications cliniques, certaines contraintes supplémentaires peuvent restreindre l'ensemble des matrices binaires ayant les uns consécutifs (matrices 1C) que l'on peut utiliser. Nous en avons étudié certaines d'entre elles comme celle de la contrainte de chariots, la contrainte d'interdiciton de chevauchements, la contrainte tongue-and-groove et la contrainte de séparation minimum. Le premier problème auquel nous nous intéressons est de trouver une décomposition de la matrice donnée qui minimise la somme des coefficients des matrices binaires. Nous avons développé des algorithmes polynomiaux qui résolvent ce problème sous la contrainte de chariots et/ou la contrainte d'interdiction de chevauchements. De plus, nous avons pu déterminer que, si la matrice donnée est une matrice binaire, on peut trouver en temps polynomial une telle décomposition sous la contrainte tongue-and-groove. Afin de diminuer le temps de la séance de radiothérapie, il peut être désirable de minimiser le nombre de matrices 1C utilisées dans la décomposition (en ayant pris soin de préalablement minimiser la somme des coefficients ou non). Nous faisons une étude de ce problème dans différents cas particuliers (la matrice donnée n'est constituée que d'une colonne, ou d'une ligne, ou la plus grande entrée de celle-ci est bornée par une constante). Nous présentons de nouvelles bornes inférieures sur le nombre de matrices 1C ainsi que de nouvelles heuristiques. Finalement, nous terminons par étudier le cas où l'ensemble des matrices 1C ne nous permet pas de décomposer exactement la matrice donnée. Le but est alors de touver une matrice décomposable qui soit aussi proche que possible de la matrice donnée. Après avoir examiné certains cas polynomiaux nous prouvons que le cas général est difficile à approximer avec une erreur additive de O(mn) où m et n représentent les dimensions de la matrice donnée.