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I investigate use of the simulated annealing heuristic to seek phylogenetic trees judged optimal according to the principle of parsimony. I begin by looking into the central data structure in phylogenetic research, the tree. I discuss why it is usually necessary to employ a heuristic, rather than an exact method, when seeking parsimonious trees. I summarise different heuristic approaches. I explain how to use the program LVB, written to use simulated annealing in the search for parsimonious trees. I use LVB, with different combinations of values for parameters controlling the annealing search, to re-analyse two DNA sequence data matrices, one of 50 objects and one of 365 objects. Equations to estimate suitable control parameters, on the basis of desired run time and quality of result, are fitted to data obtained by these analyses. Future directions of research are discussed.

As a result of ¡§the X-ray Phase Problem¡¨, traditional direct methods can¡¦t solve the structures of the large molecules. For exploring alternate methods, Wu-Pei Su applied simulated annealing to solve the structure of the large molecules and obtained success. Adopting his concept, we wrote a program for solving the structure of the molecules by C Program Language. And for decreasing the running time of the program, we introduced the concept of genetic algorithm into simulated annealing method.

On account of ¡§the X-ray Phase Problem¡¨, it¡¦s impossible to get the electronic density by inverse Fourier transformation(IFT). And the crystal structure of molecule can¡¦t be solved by IFT. There are many methods to overcome the problem, such as Direct Method, Heavy Atom, and Simulated Annealing. But for macro-molecules, we still face a great challenge due to tremendous computing load. We propose a method by using wavelets to resolve the electronic density. We hope the multiresolution nature of wavelets can reduce the computing load for simulated annealing method.

The £\-helix structure of protein is very similar to the cylindrical structure. Especially, the Sperm-Whale Myoglobin molecules has 70% £\-helix structure. Therefore, we use simulated annealing method to solve ¡§X-ray phase problem¡¨, and apply Metropolis algorithm to avoid local minimum. We hope that the new method can build £\-helix structure of Sperm-Whale Myoglobin molecule. Therefore, we use multi cylinders as the Myoglobin¡¦s tertiary structure and solve the cylinder¡¦s structure with the simulated annealing method.

Thesis (Ph. D.)--York University, 2001. / Typescript. Includes bibliographical references (leaves 107-115). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pNQ67907.

Zugl.: Kassel, Univ., Diss., 2007

published_or_final_version / Electrical and Electronic Engineering / Master / Master of Philosophy

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Thesis (Ph. D.)--Indiana University, 2004. / Includes bibliographical references (leaves 232-249). Also available online (PDF file) by a subscription to the set or by purchasing the individual file.