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博碩士論文 etd-0118113-003037 詳細資訊
Title page for etd-0118113-003037
論文名稱
Title
以分子動力學進行去氧核醣核酸雜化體系中之螢光傳輸暨液晶分子鬆弛運動之研究
Investigations of the FRET properties in DNA hybridization systems and the relaxation motions of liquid crystals
系所名稱
Department
畢業學年期
Year, semester
語文別
Language
學位類別
Degree
頁數
Number of pages
89
研究生
Author
指導教授
Advisor
召集委員
Convenor
口試委員
Advisory Committee
口試日期
Date of Exam
2012-12-21
繳交日期
Date of Submission
2013-01-18
關鍵字
Keywords
量子力學、去氧核醣核酸、雜化、螢光傳輸、液晶、鬆弛、分子動力學
Hybridization, DNA, Liquid crystal, FRET, Molecular dynamics, Relaxation
統計
Statistics
本論文已被瀏覽 5739 次,被下載 344
The thesis/dissertation has been browsed 5739 times, has been downloaded 344 times.
中文摘要
分子動力學用於研究化學微觀體系之物理性質及結構性質非常有效。本論文中,我們使用分子動力學研究兩個不同領域的系統,一是去氧核醣核酸雜化體系中螢光共振傳輸的研究,另一是液晶分子在去除外加電場後的鬆弛運動之研究。

在本文第一部份,利用分子動力學及量力子學研究去氧核醣核酸雜化體系中螢光共振傳輸的現象。我們使用量子力學方式來推測兩個螢光基團,香豆素500及乙錠的螢光性質,其結果與光譜實驗結果符合。在273K到313K之間的模擬結果與Mergny的雜化研究結果相比對,結果相當的符合。研究中亦針對Förster理論中之轉向因子的性質做進一步研究,結果發現當螢光基團接合於較固定的分子結構時,其轉向因子並不能以等向性假設之平均轉向因子近似之。傳輸效率亦與一級動力學假設相比較,其結果顯示螢光傳輸現象近似於一級動力學反應。

第二部份,以分子動力學研究在小體系中5CB液晶及7CPB液晶,於PI膜間的鬆弛運動。真實的液晶體系過為龐大而無法模擬,本研究藉由模擬小體系於不同條件下的鬆弛性質,推導出描述液晶鬆弛的動力方程式,此方程式符合現實液晶體系的實驗結果。此方程式亦推論出液晶層的鬆弛時間與厚度的平方呈正比,此一現象與Erickson-Leslie的結論相符合。
Abstract
The molecular dynamic (MD) simulation is useful to investigate the physical properties and structures in microscopic systems. In this thesis, we applied molecular dynamic simulations in two different areas: the DNA hybridization systems and the liquid crystal systems.

In part I, MD and quantum mechanics were used to investigate fluorescence resonance energy transfer between coumarin and ethidium in two Mergny’s DNA hybridization systems. The FRET efficiencies were compared with Mergny’s experiments from 273 K to 313 K, and showed good agreement. The simulated orientation factor and isotropically averaged orientation factor were compared, and the results demonstrated that the assumption of isotropic orientations is invalid when FRET probes are close to each other. The first order kinetic assumptions were also used to calculate the transfer efficiencies, and the results show this D-A FRET process approximates the first order kinetic reactions.

In part II, MD simulations were used to investigate relaxation motions of nematic liquid crystals 4-cyano-4'-pentylbiphenyl (5CB) and 4'-cyanophenyl 4-heptylbenzoate (7CPB) molecules sandwiched between poly-3-APM polyimide (PI) films. A dynamic equation describing the motions was derived by analyzing the simulation results for small systems. The results calculated by the derived parameters fit the experimental observations with commonly used cell gaps. The derived equation also satisfies the theoretical conclusion from the Erickson-Leslie equation that the relaxation time is proportional to the square of the thickness of the LC cell.
目次 Table of Contents
論文審定書 i
誌謝 ii
Abstract iii
摘要 iv
TEXT CONTENT v
FIGURE CONTENT vii
TABLE CONTENT ix
PART I Computer simulation to investigate the FRET application in DNA hybridization systems 1
I.1 Introduction 1
I.2 Method 5
I.2-1 Initial structure 5
I.2-2 MD Ssimulations 6
I.2-2-1 AMBER forcefield 8
I.2-2-2 CUDA 9
I.2-3 Software operations 11
I.2-3-1 DS Modeling 11
I.2-3-2 AMBER 16
I.2-4 Semi-empirical quantum mechanical calculations 23
I.2-5 Estimation of transfer efficiency 24
I.3 Results and discussions 27
I.3-1 Quantum calculation result 27
I.3-2 Simulation results 29
I.3-2-1 Results of 30mer 29
I.3-2-2 Result of 45-HP 34
I.3-3 Estimated transfer efficiencies 40
I.4 Conclusion 43
I.5 References 45
PART II Investigation of the relaxation motions of 5CB and 7CPB liquid crystal molecules sandwiched between polyimide films by molecular dynamics simulations 49
II.1 Introduction 49
II.2 Method 52
II.2-1 MD Simulation 52
II.2-1-1 Models 52
II.2-1-2 CGenFF force field 55
II.2-2 Software operations 56
II.2-2-1 Accelrys MS Modeling 56
II.2-2-2 NAMD 59
II.3 Results and discussions 67
II.3-1 Simulation details 67
II.3-2 Comparisons with the experiments 71
II.3-3 The effects of thicknesses 75
II.4 Conclusion 76
II.5 Reference 77
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