去氧核醣核酸(DNA)在高濃度的情況下會形成液晶相，而DNA液滴在乾燥的過程中形成的液晶會呈現一個特殊的排列，而這排列可以藉由偏光顯微鏡(POM)來觀察。而不同的材料與製程參數會很大程度的影響排列結果，因此，了解這背後的運作機制可以幫助我們應用在製作特殊排列的表面。
在這份論文中，我們分別討論DNA薄膜中分子排列的實驗結果與理論架構。首先藉由控制不同的參數來觀察DNA排列週期與角度的變化，並利用液晶的排列理論來建構DNA週期排列的模型。而我們的結果導出刷膜厚度及DNA液晶濃度與DNA排列模型有關。而這模型的建構可以幫助我們應用在排列與DNA有交互作用的分子上。

Deoxyribonucleic acid (DNA), which is a widely used biopolymer, may exhibit liquid crystal phase when the concentration is high enough. The molecular alignment behaviors can be observed by examining the evaporation process of a droplet of DNA solution. The alignment of molecules results in optical anisotropy, which can be analyzed by polarized optical microscope (POM). There are several material parameters as well as preparation conditions that affect the alignment of DNA biomolecules. Therefore, it is of great importance to understand the mechanisms behind the molecular alignment in order to fully manipulate the templated patterns for applications.
In this study, we carried out both theoretical and experimental studies to investigate the formation of zigzag patterns formed in a film of dense DNA solution. The geometrical features of zigzag patterns are analyzed by POM. Several parameters are varied to examine the corresponding changes in the zigzag patterns and the experimental results are fitted by a theoretical model based on free energy of liquid crystals. Our results show that zigzag structure is related to the thickness of the film and the concentration of DNA liquid crystal. This controllable zigzag pattern can be applied to align other materials which interact with DNA molecule on the film.

ACKNOWLEDGMENT i
CHINESE ABSTRACT ii
ABSTRACT iii
CONTENTS iv
LIST OF FIGURES vii
LIST OF TABLES xiv
Chapter 1 Introduction 1
1.1 Introduction of liquid crystal 1
1.2 Introduction of deoxyribonucleic acid (DNA) 4
1.2.1 Introduction of DNA biopolymer 5
1.2.2 DNA in liquid crystal phase 6
1.3 Structure formation via liquid crystal alignment 8
1.3.1 Periodic liquid crystal alignment structure 8
1.3.2 Biopolymer liquid crystal alignment structure without electromagnetic field 9
1.4 Structure formation by DNA-based materials 11
1.4.1 Structure formation by evaporation of DNA droplet 11
1.4.2 Structure formation by shearing DNA film 12
1.4.3 Application of shearing DNA film 14
1.5 Motivation 14
Chapter 2 Methods 16
2.1 Theoretical formulation of molecular alignment in zigzag pattern 16
2.1.1 Liquid crystal elastic energy and equilibrium theory 16
2.1.2 DNA pattern forming mechanism 17
2.2 Experimental setup 19
2.2.1 Sonicator 19
2.2.2 DNA gel electrophoresis 19
2.2.3 Vacuum evaporation system 20
2.2.4 UV/Vis spectroscopy 22
2.2.5 Setup for shearing film 22
2.2.6 Polarized optical microscopy (POM) 23
2.3 Preparation of DNA LC film 23
2.3.1 Preparation of DNA solutions 23
2.3.2 Fabrication of DNA films 24
2.4 Image analysis 24
2.4.1 CCD calibration 24
2.4.2 DNA film image 26
2.4.3 Zigzag angle and period analysis 27
Chapter 3 Result and discussion 28
3.1 Analysis of images under POM 28
3.1.1 Image of DNA film under POM 29
3.1.2 Molecular alignment analysis 32
3.1.3 Effect of ethanol on DNA zigzag pattern film 33
3.2 Analysis of patterns for different parameters 38
3.2.1 Effect of DNA chain length 38
3.2.2 Varying the distance h 39
3.2.3 Varying the concentration 40
3.2.4 Varying shearing-speed 42
3.2.5 Mechanism of each parameter influence 43
3.3 Modeling molecular alignment by the elastic theory 44
3.3.1 Free energy and surface interaction 44
3.3.2 Modeling the zigzag structure 47
3.4 Analysis of experiment with model 49
3.4.1 Period of zigzag pattern v.s. distance h_0 49
3.4.2 Period of zigzag v.s. concentration and distance 51
3.5 Future application 53
Chapter 4 Conclusion 54
REFERENCE 55

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