Conformational analysis of antibody binding site using EDMA methods /

Euclidean distance matrix analysis (EDMA) methods are used to distinguish whether or not significant difference exists between conformational samples of antibody complementarity determining region (CDR) loops, isolated LI loop and LI in three-loop assembly (LI, L3 and H3) obtained from Monte Carlo simulation. After the significant difference is detected, the specific inter-Ca distance which contributes to the difference is identified using EDMA.The estimated and improved mean forms of the conformational samples of isolated LI loop and LI loop in three-loop assembly, CDR loops of antibody binding site, are described using EDMA and distance geometry (DGEOM). To the best of our knowledge, it is the first time the EDMA methods are used to analyze conformational samples of molecules obtained from Monte Carlo simulations. Therefore, validations of the EDMA methods using both positive control and negative control tests for the conformational samples of isolated LI loop and LI in three-loop assembly must be done. The EDMA-I bootstrap null hypothesis tests showed false positive results for the comparison of six samples of the isolated LI loop and true positive results for comparison of conformational samples of isolated LI loop and LI in three-loop assembly. The bootstrap confidence interval tests revealed true negative results for comparisons of six samples of the isolated LI loop, and false negative results for the conformational comparisons between isolated LI loop and LI in three-loop assembly. Different conformational sample sizes are further explored by combining the samples of isolated LI loop to increase the sample size, or by clustering the sample using self-organizing map (SOM) to narrow the conformational distribution of the samples being comparedmolecular conformations. However, there is no improvement made for both bootstrap null hypothesis and confidence interval tests. These results show that more work is required before EDMA methods can be used reliably as a method for comparison of samples obtained by Monte Carlo simulations.

The electronic spectra and the determination of the excited state geometry of 3A" propynal /|nby Chhiu-Tsu Lin. -- 260 St. Catharines, Ont. : [s. n.],

Impurity free eluission spectra of HCCCHO and DCCCHO have been rephotographed using the electronic-energy-exchange method with benzene as a carrier gas. The near ultraviolet spectra of ReeCHO and DCCCHO were photographed in a sorption under conditions of high resolution with absorption path lengths up to 100 meters. The emission and absorption spectra of Propynal resulting from 3 n 1 t 1\ - A excitation has been reanalyzed in som.e detail. Botrl of the eH out-of-plane wagging modes were found to have negative anharmonicity. A barrier height of 56.8/0.0 cm- 1 and a nonplanar oft , , equilibrium angle of 17 3 /30 are calculated for the V 10/ lJ 11 modes. The in-plane and out-of-plane v1. brational modes in the 3A." and 1a~. ' elec ronic states of Propynal were subjected to a normal coordinate treatment in the approximat :on of tIle Urey-Bradley force field. From the relative oscillator strengths of the trans1·t1·0ns connect i ng t he v ibrat1•0n1ess lA' , state and t,he V1· bron1·C 3· if levels of the A state, the differences in equilibrium configuration were evaluated from an approximate Franck-Condon analysis based on the ground state normal coordinates. As this treatment gave 512 possible geometrical structures for the upper state, it 4 was necessary to resort to a comparison of the observed and calculated moments of inertia along with chemical intuition to isolate the structure. A test of the correctness of the calculated structure change and the vibrational assignment was raade by evaluating the intensities of the inplane and out-oi-plane fundarnental, sequence, and cross sequellce transitions y the exact Franck-Condon method.

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.