網頁圖形界面在分子模擬上的應用

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姓名

林宏達(Hung-Da Lin) 查詢紙本館藏

畢業系所

化學學系

論文名稱

網頁圖形界面在分子模擬上的應用
(A web-based graphical user Interface for molecular simulation)

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至系統瀏覽論文 ( 永不開放)

摘要(中)

Pine-MD (Protein INformation Extraction from Molecular Dynamics Simulation) 是一套由本實驗室自行發展，運作於Linux指令模式下，用來進行分析分子動態模擬結果的程式，其中包含一些基本的性質分析，也包含有別於其他分析軟體的性質分析。然而，由於程式運作於Linux指令模式下，新進的人員學習不易，另外，有經驗的使用者也會出現忘記指令、打錯指令等情形，而近年來由於網際網路發展與普及，在科學領域上有許多基於網頁瀏覽器的運用，在這裡希望能藉助網際網路圖形化、互動性等優點，解決前述提到的問題。
本實驗室透過建置維基網站，以及自行研發的網頁介面軟體 Pine-MD Graphical User Interface (Pine-MD GUI) 嘗試解決上述問題並整合資源。藉由實驗室維基網站的建立，將Pine-MD的指令與格式作有系統的整合，藉由維基共筆的特性，將有助於程式的更新與發展。而Pine-MD GUI是一套用來輔助Pine-MD的網頁介面軟體，使用者可以直接透過點選的方式輸入Pine-MD指令取代原本手動編輯的不便，而不論是實驗室的維基網站或是Pine-MD GUI，都希望能透過網頁的方式更有效率的進行科學的研究。
利用Pine-MD GUI網站架構，我們分析細菌膜在Na+, Mg2+ 及Ca2+ 陽離子存在下，膜微觀性質的變化，發現在Ca2+ 對細菌膜的影響有別於Na+及 Mg2+ 離子: Ca2+ 使得細菌膜結構更為緊實且主要分佈於磷脂質的磷酸基團附近。

摘要(英)

Pine-MD (Protein INformation Extraction from Molecular Dynamics Simulation) is an in-house program designed to analyze the results of molecular dynamics simulations. It capcitity includes the analysis of molecular geometry, molecular conformation, inter-molecular structure, configuration, structure comparsion and classification, membrane properties, time-correlation property and statistics. This program uses text-based commands working under Linux environment, which is not user-friendly. Taking the fast development of web-based techniques, we setup a Lab Wiki and designed a program called Pine-MD GUI interacfacing with Pine-MD to integrate research resource and to assist the analysis of MD simulations.
With the aid of Lab Wiki, lab researchers can access the detailed and updated commands and methods of Pine-MD through the internet everywhere. Moreover, the program developers can easily update the commands and methods of their newly develpoed programs through Lab Wiki.
Pine-MD GUI is a newly developed program interfacing with Pine-MD working through Intenet browser. Pine-MD GUI has the following features making it user friendly: Its graphical interface reduced the text-command inputs by users; it guides users step-by-step for analysis which decreased the learning time of new users; in particular, its pop-up menu allows users to do atom section directly and friendly without any mistake. It improves the molecular simulation research effectively.
Using Pine-MD GUI, we analyze the miscroscopic properties of model bacterial membranes under Na+, Mg2+ and Ca2+ environments obtained from all-atom MD simulations. Results show that member under Ca2+ ion environments is packed more order that those of other two ions. Interestingly, Ca2+ ions prefer to locate around the phosphate groups different from those of other two ions.

關鍵字(中)

★ 分子模擬
★ 圖形介面

關鍵字(英)

★ graphic user interface
★ molecular dynamics

論文目次

摘要 II
ABSTRACT III
總目錄 IV
圖目錄 VII
表目錄 IX
第一章導論 1
1-1 分子動態模擬 1
1-1-1分子動態模擬的特性 1
1-1-2分子動態模擬的應用 2
1-1-3分子動態模擬的缺點 3
1-2 分子動態模擬分析軟體-Pine-MD 3
1-3 網頁技術在分子動態模擬方面的運用 4
1-4 研究動機 7
第二章 PINE-MD 8
2-1 Pine-MD 8
2-1-1 Pine-MD 指令文件範例 8
2-1-2 指令文件 (Command File) 11
程式設定 (Program Setup) 11
讀取分子座標或結構檔案 (Read PDB/PSF Files) 13
原子選擇 (Atom Selection) 14
讀取軌跡檔 (Read Trajectory Files) 18
性質計算 (Property Calculation) 20
分子結構 (Molecular Geometry) 20
性質: 兩原子間的距離 20
性質: 三個原子形成的角度 20
性質: 四個原子形成的線性雙面角 21
分子構形 (Molecular Conformation) 22
性質: 計算蛋白質的二級結構 22
性質: 計算氫鍵 25
分子間結構 (Inter-Molecular Structure) 26
性質: Radial Distribution Function (RDF) 26
性質: 計算迴轉半徑 (Radius of Gyration, Rg) 27
組態 (Configuration) 27
性質: 兩原子形成的向量和z-軸 (0, 0, 1) 形成的夾角 27
性質: 計算選擇原子的質量中心 28
結構比較及分類 (Structure Comparsion and Classification) 28
性質: 比較兩結構的Root Mean Squared Deviation (RMSD) 28
性質: Principle Component Analysis (PCA) 29
膜性質 (Membrane Property) 32
性質: 生物膜的面積 32
性質: 生物膜中個別磷脂質的平均頭基面積 32
性質: 生物膜的厚度 33
性質: 系統中的粒子隨z-軸方向的分佈 33
性質: 磷脂質長碳鏈的秩序參數 34
性質: 探討分子形成cluster的情形 34
性質: 探討生物膜中磷脂質形成domain的情形 35
時間相關性質 (Time-Correlation Property) 35
性質: 擴散係數 35
統計 (Statistics) 36
2D Potential of Mean Force (2D-PMF) 36
2D-WHAM (Weighted Histogram Analysis Method) 37
輸出計算結果 (Write Out Results) 42
第三章 PINE-MD GRAPHICAL USER INTERFACE 43
3-1 利用網頁介面設計Pine-MD GUI 44
3-1-1 首頁 44
3-1-2 Pine-MD GUI網站主要頁面 45
3-1-3 顯示結果 61
3-1-4 暫存檔案與跳頁選單 61
3-2 網頁編輯程式語言 62
3-2-1 XML 63
3-2-2 Javascript 64
3-2-3 PHP 66
3-2-4 AJAX 67
第四章利用PINE-MD GUI分析細菌膜的模擬 71
4-2-1 細菌膜的簡介 71
4-2-2 離子對細菌膜的影響 72
4-2-4 模擬系統及模擬方法 73
4-2-4 結果與討論 74
4-2-5 討論 79
第五章總結 81
參考文獻 82
附錄 84

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指導教授

蔡惠旭(Tsai Hui-Hsu Gavin)

審核日期

2011-1-23

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