Automatic Structure Generation using Genetic Programming and Fractal Geometry

Three dimensional model design is a well-known and studied field, with numerous real-world applications. However, the manual construction of these models can often be time-consuming to the average user, despite the advantages o ffered through computational advances. This thesis presents an approach to the design of 3D structures using evolutionary computation and L-systems, which involves the automated production of such designs using a strict set of fitness functions. These functions focus on the geometric properties of the models produced, as well as their quantifiable aesthetic value - a topic which has not been widely investigated with respect to 3D models. New extensions to existing aesthetic measures are discussed and implemented in the presented system in order to produce designs which are visually pleasing. The system itself facilitates the construction of models requiring minimal user initialization and no user-based feedback throughout the evolutionary cycle. The genetic programming evolved models are shown to satisfy multiple criteria, conveying a relationship between their assigned aesthetic value and their perceived aesthetic value. Exploration into the applicability and e ffectiveness of a multi-objective approach to the problem is also presented, with a focus on both performance and visual results. Although subjective, these results o er insight into future applications and study in the fi eld of computational aesthetics and automated structure design.

DFT Studies of the Organocatalytic Aldol Reaction and a Frustrated Lewis Pair

The computational study, and in particular the density functional theory (DFT) study of the organocatalytic α-chlorination-aldol reaction and the chiral backbone Frustrated Lewis Pair (FLP) system served as a valuable tool for experimental purposes. This thesis describes methods to consider different transition states of the proline- catalyzed α-chlorination aldol reaction to determine the reasonable transition state in the reaction between the enamine and α-chloro aldehydes. Moreover, the novel intramolecular Frustrated Lewis pair based on a chiral backbone for the asymmetric hydrogenation of imines and enamines was designed and the ability of hydrogen splitting by this new FLP system was examined by computational modeling and calculating the hydrogen activation energy barrier.

The effect of calculators on the numerical problem-solving skills and attitudes of primary students towards mathematics /

The purpose of this study was to determine the effect that calculators have on the attitudes and numerical problem-solving skills of primary students. The sample used for this research was one of convenience. The sample consisted of two grade 3 classes within the York Region District School Board. The students in the experimental group used calculators for this problem-solving unit. The students in the control group completed the same numerical problem-solving unit without the use of calculators. The pretest-posttest control group design was used for this study. All students involved in this study completed a computational pretest and an attitude pretest. At the end of the study, the students completed a computational posttest. Five students from the experimental group and five students from the control group received their posttests in the form of a taped interview. At the end of the unit, all students completed the attitude scale that they had received before the numerical problem-solving unit once again. Data for qualitative analysis included anecdotal observations, journal entries, and transcribed interviews. The constant comparative method was used to analyze the qualitative data. A t test was also performed on the data to determine whether there were changes in test and attitude scores between the control and experimental group. Overall, the findings of this study support the hypothesis that calculators improve the attitudes of primary students toward mathematics. Also, there is some evidence to suggest that calculators improve the computational skills of grade 3 students.

Investigation of molecular polarizabilities and derivatives in halomethanes

The research undertaken was to obtain absolute Raman intensities for the symmetric stretching vibrations of the methyl halides, CH3X with (X=F, CI, Br), by experiment and theory. The intensities were experimentally measured using the Ar+ ion gas laser as excitation source, a Spex 14018 double monochromator and a RCA C-31034 photomultiplier tube as detector. These intensities arise from changes in the derivative of the polarizability (8 a'), with respect to vibration along a normal coordinate (8qi). It was intended that these derivatives obtained with respect to normal coordinates would be converted to derivatives with respect to internal coordinates, for a quantitative comparison with theory. Theoretical numerical polarizability derivatives for the stretching vibrations are obtained using the following procedure. A vibration was simulated in the molecule by increasi.ng and decreasing the respective bond by the amount ±o.oosA for the C-H bonds and ±o.oIA for the C-X (X=F, CI, Br) bond. The derivative was obtained by taking the difference in the polarizability for the equilibrium geometry and the geometry when a particular bond is changed. This difference, when divided by the amount of change in each bond and the number of bonds present results in the derivative of the polarizability with respect to internal coordinate i.e., !1u/!1r. These derivatives were obtained by two methods: I} ab initio molecular orbital calculation and 2} theory of atoms in molecules (AIM) analysis. Due to errors in the experimental setup only a qualitative analysis of the results was undertaken relative to the theory. Theoretically it is predicted that the symmetric carbonhalogen stretch vibrations are more intense than the respective carbon-hydrogen stretch, but only for the methyl chloride and bromide. The carbon fluorine stretch is less intense than the carbon-hydrogen stretch, a fact which is attributed to the small size and high electronegativity of the fluorine atom. The experimental observations are seen to agree qualitatively with the theory results. It is hoped that when the experiment is repeated, a quantitative comparison can be made. The analysis by the theory of atoms in molecules, along with providing polarizabilities and polarizability derivatives, gives additional information outlined below. The theory provides a pictorial description of the main factors contributing to the molecular polarizability and polarizability derivative. These contributions are from the charge transfer and atomic dipole terms i.e., transfer of charge from one atom to another and the reorganization of atomic electronic charge distribution due to presence of an electric field. The linear relationship between polarizability and molecular volume was also observed.

The nature of avidyÄ in Buddhism and VedÄ nta

This thesis deals with the nature of ignorance as it was interpreted in the Upani~adic tradition, specifically in Advaita Vedanta, and in early and Mahayana Buddhism , e specially in the Madhyamika school of Buddhism. The approach i s a historical and comparative one. It examines the early thoughts of both the upanis.a ds and Buddhism abou t avidya (ignorance), shows how the notion was treated by the more speculative and philosphically oriented schools which base d themselves on the e arly works, and sees how their views differ. The thesis will show that the Vedinta tended to treat avidya as a topic for metaphysical s peculation as t he s chool developed, drifting from its initial e xistential concerns, while the Madhyamika remained in contact with the e xistential concerns evident in the first discourses of the Buddha. The word "notion" has been chosen for use in referring t o avidya, even though it may have non-intellectual and emotional connotations, to avoid more popular a lternatives such as "concept" or "idea". In neither the Upani,ads, Advaita Vedanta, or Buddhism is ignorance merely a concept or an idea. Only in a secondary sense, in texts and speech , does it become one. Avidya has more to do with the lived situation in which man finds himself, with the subjectobject separation in which he f eels he exists, than with i i i intel lect ual constr ucts . Western thought has begun to r ealize the same with concerns such as being in modern ontology, and has chosen to speak about i t i n terms of the question of being . Avidya, however, i s not a 'question' . If q ue stions we r e to be put regarding the nature of a vidya , they would be more of t he sort "What is not avidya?", though e ven here l anguage bestows a status t o i t which avidya does not have. In considering a work of the Eastern tradition, we f ace t he danger of imposing Western concepts on it. Granted t hat avidya is customari ly r endered i n English as ignorance, the ways i n which the East and West view i gno rance di f f er. Pedagogically , the European cultures, grounded in the ancient Greek culture, view ignorance as a l ack or an emptiness. A child is i gnorant o f certain t hings and the purpose o f f ormal education , in f act if not in theory, is to fill him with enough knowledge so that he can cope wit h t he complexities and the e xpectations of s ociety. On another level, we feel t hat study and research will l ead t o the discovery o f solutions, which we now lack , for problems now defying solut i on . The East, on the o t her hand, sees avidya in a d i fferent light.Ignorance isn't a lack, but a presence. Religious and philosophical l iterature directs its efforts not towards acquiring something new, but at removing t.he ideas and opinions that individuals have formed about themselves and the world. When that is fully accomplished, say the sages , t hen Wisdom, which has been obscured by those opinions, will present itself. Nothing new has to be learned, t hough we do have t o 'learn' that much. The growing interest in t he West with Eastern religions and philosophies may, in time, influence our theoretical and practical approaches to education and learning, not only in the established educati onal institutions, but in religious , p sychological, and spiritual activities as well. However, the requirements o f this thesis do no t permit a formulation of revolutionary method or a call to action. It focuses instead on the textual arguments which attempt to convince readers that t he world in which they take themselves to exist is not, in essence, real, on the ways i n which the l imitations of language are disclosed, and on the provisional and limited schemes that are built up to help students see through their ignorance. The metaphysic s are provisional because they act only as spurs and guides. Both the Upanisadic and Buddhist traditions that will be dealt with here stress that language constantly fails to encompass the Real. So even terms s uch as 'the Real', 'Absolute', etc., serve only to lead to a transcendent experience . The sections dealing with the Upanisads and Advaita Vedanta show some of the historical evolution of the notion of avidya, how it was dealt with as maya , and the q uestions that arose as t o its locus. With Gau?apada we see the beginnings of a more abstract treatment of the topic, and , the influence of Buddhism. Though Sankhara' S interest was primarily directed towards constructing a philosophy to help others attain mok~a ( l iberation), he too introduced t echnica l t e rminology not found in the works of his predecessors. His work is impressive , but areas of it are incomplete. Numbers of his followers tried to complete the systematic presentation of his insi ghts . Their work focuses on expl anat i ons of adhyasa (superimposition ) , t he locus and object of ignorance , and the means by which Brahman takes itself to be the jiva and the world. The section on early Buddhism examines avidya in the context o f the four truths, together with dubkha (suffering), the r ole it p l ays in t he chain of dependent c ausation , a nd t he p r oblems that arise with t he doctrine of anatman. With t he doct rines of e arly Buddhism as a base, the Madhyamika elaborated questions that the Buddha had said t e nded not t o edi f ication. One of these had to do with own - being or svabhava. Thi s serves a s a centr e around which a discussion o f i gnorance unfolds, both i ndividual and coll ective ignorance. There follows a treatment of the cessation of ignorance as it is discussed within this school . The final secti on tries to present t he similarities and differences i n the natures o f ignorance i n t he two traditions and discusses the factors responsible for t hem . ACKNOWLEDGEMENTS I would like to thank Dr. Sinha for the time spent II and suggestions made on the section dealing with Sankara and the Advait.a Vedanta oommentators, and Dr. Sprung, who supervised, direoted, corrected and encouraged the thesis as a whole, but especially the section on Madhyamika, and the final comparison.

Polyglutamine monomer structure and its implications for molecular self-assembly

Polyglutamine is a naturally occurring peptide found within several proteins in neuronal cells of the brain, and its aggregation has been implicated in several neurodegenerative diseases, including Huntington's disease. The resulting aggregates have been demonstrated to possess ~-sheet structure, and aggregation has been shown to start with a single misfolded peptide. The current project sought to computationally examine the structural tendencies of three mutant poly glutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing, and were analyzed quantitatively by various geometry- and energy-based methods. According to the results, the experimentally-observed inhibition of aggregation appears to be due to localized conformational restraint placed on the peptide backbone by inserted prolines, which in tum confines the peptide to native coil structure, discouraging transition towards the ~sheet structure required for aggregation. Such knowledge could prove quite useful to the design of future treatments for Huntington's and other related diseases.