臺灣博碩士論文加值系統

為了瞭解溶液系統在微觀結構下的物理行為，例如：胺基酸水溶液，本實驗利用自行建立的Voronoi tessellation方法分析溶劑在溶質周遭的空間分佈，而Voronoi多面體可以藉由建立Delaunay simplexes得到。分析中，以非氫原子為單元並引入空間相關的指標參數。在均質溶液系統中每一個Voronoi polyhedron不完全相同，但應該擁有相同的指標參數。與標準參數或均質系統的參數相較之下，在溶質表面單元的指標參數可以給予溶質與溶劑間的作用資訊。因此，這項指數必須考量局部性的異常分佈的顯著差異，進一步以統計熵(statistical entropy)嘗試解釋熱力學行為。比較二十種不同胺基酸的支鏈對表面作用的表現，並得到不同支鏈對於統計熵的貢獻。

To understand the physical behavior of solvent system in microscopic structure, such as amino acids in aqueous solution, the Voronoi tessellation method was employed to analyze space distribution of solvent surrounding the solute. The Voronoi polyhedra can be constructed through Delaunay simplexes. In our analysis, each non-hydrogen atom is treated as an independent element and a space-dependent factor is introduced for every element. In an equilibrium homogenous system, each Voronoi polyhedron is not identical but should have same average factor which is treated as the standard by definition. Compared with the standard factor of the homogenous system, i.e., pure water system, the factor on the solute surface should give out the information of interaction between the solvent and the solute. Therefore, this space-dependent factor must include the locally abnormal distribution with statistical significance. We then constructed the statistical entropy based on this factor to interpret thermodynamic behavior of amino acids, peptides and even proteins. Through analyzing the solvation differences between 20 standard amino acids, we quantify contribution of the different side-chain toward solvation of the solute surfaces in terms of statistical entropy.

摘要 ii
第一章、緒論及文獻回顧 1
第一節、蛋白質結構與能量曲面 3
第二節、結構與統計熵 5
第三節、Voronoi 鑲嵌以及相關分析 7
第四節、拓樸性質與量測性質 13
第五節、Asphericity(似球率) 18
總結 21
第二章、方法與算則 22
第一節、模擬方法 22
第二節、Voronoi 分析方法 23
第三章、結果與討論 28
第一節、純水系統 29
第二節、簡單溶質 31
第三節、胺基酸水溶液 33
第四節、胺基酸單體表面水分子比較 37
第五節、參數相依性質比較 40
第六節、在序列中鑲嵌胺基酸做分子表面水分子比較 42
結論與應用 47
參考文獻 48

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