Jamming State of Active Nematics

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林敬元(Ching-Yuan Lin) 查詢紙本館藏

畢業系所

物理學系

論文名稱

(Jamming State of Active Nematics)

相關論文

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★ Probing Escherichia coli Energetics under Starvation by Single-Cell Measurements	★ Probing Cell Wall Synthetic Dynamics by Bacterial Flagellar Motor in Escherichia coli
★ Dynamics of sodium-driven stator units in bacterial flagellar motors	★ 高密度二維群游細菌系統之動力學
★ Deformation Dynamics of Active 2D Tetragonal Pseudo-Crystal	★ Probing Ion-Flux of Bacterial Flagellar Motors by Correlative Microscopy
★ Aliivibrio fischeri in Motion	★ 主動粒子的擴張行為

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摘要(中)

摘要
本篇論文在探討桿狀自我推進粒子的壅塞狀態，有別於熱平衡系統，主動系
統展現了更豐富的相變與結構，當粒子濃度高且區域間的力互相平衡時，主動系
統的壅塞狀態就此發生，我們使用表面群游細菌系統來探討這獨特壅塞狀態的形
成與區域的動態。
活動力是生物非常迷人的特質之一，從物理的觀點來看，主動性材料是由大
量的主動粒子個體組成，彼此之間由簡單的運動規則規範，而形成複雜的群聚運
動的出現，由於主動粒子的實驗材料取得相對困難因此模擬在這個領域中一直領
先於實驗。我現在做的是二維細菌的群游實驗，用只有側邊毛的溶藻弧菌來當作
自我推進的主動粒子，將養出的細菌菌液滴在1%的洋菜膠上面生長3~4 個小時
後菌落開始擴張，由於菌落擴張快速而留下了一些細菌較稀薄的二維單層區域，
在這個單層的區域中我們發現了許多不同的細菌群游狀態，而我們主要專注於細
菌的壅塞狀態。
藉由客製化的影像處理和粒子追蹤程式，我們能在這二維的壅塞系統中追蹤
每一隻細菌，我們的分析分成三個部分:壅塞狀態的整體行為、壅塞狀態的局部
行為、壅塞過程的整體行為。
1. 壅塞狀態的整體行為:壅塞狀態有幾個獨特的特徵，我們用速度、密度、軌跡、
長度和集群形狀等整體特徵來代表壅塞狀態的特質。
2. 壅塞狀態的局部行為:雖然壅塞狀態整體看起來像是完全卡住不動，但其實可
以觀察到相當多變的局部運動，這裡我們把局部區域分成三種:動態區、限制
區和卡死區，我們一次在一個區域選擇兩隻細菌，並計算牠們的MSD、細菌長軸角度和速度的關係，結果不僅顯示了這三種區域間本質上的不同也揭示了
重新排列能力的影響力。
3. 壅塞過程的整體行為:除了了解壅塞狀態的細節之外，我們也對它的形成十分
好奇，為了瞭解系統如何從非壅塞進入到壅塞狀態，我們設計了一個固定區
域的縮時攝影實驗，當系統的密度增加，整體的有序性上升同時平均速度下
降，區域有序結構的重整增加了壅塞的程度。

摘要(英)

AbstractThe aim of this thesis is to invest the jamming state of active nematics system. Unlike thermal equilibrium system, active system shows rich phases and emergent patterns. Among these states, active jamming is happened in the high agent density where all of the local active force are balanced. We use surface swarming bacteria system to investigate the formation process and the local dynamics of this unique jamming state. Motility is one of the charming features of living organism. From physics point of view, active-matter is composed of large number of individual active agents with simple rules of movement leading to complex collective behaviors. Due to the experimental difficulties of manufacturing identical active agents, theoretical work leads the research work in this field. In our research, we use surface swarming bacteria as the active-material to study the emerging behavior of active nematics in two-dimension system. Vibrio alginolyticus is a marine bacterium with dual flagellar motor systems. This system is composed by a ?? + driven polar flagellum and several H + lateral flagella. The lateral flagella will only express in the environment with high viscosity, for example, the surface, and become the main source of swarming motility on the viscous surface. In our experiment, we use a mutant strain YM19 which have lateral flagella only to be the experimental material of self-propelled rods on 2D surface. Inoculating 0.5μl’s bacteria suspension on the 1% thin VC agar plate, YM19 will then spread out in 3~4 hours to form a 2D colony with mono-layer area where the jamming state will be formed later.
By custom-wrote image processing and particle tracking software, we are able to trace each single bacterium in this 2D jamming state. Our analysis is divided into three parts, global motion of jamming state, local motion of jamming state and global motion of jamming process. 1. Global motion of jamming state: The jamming state have several unique and special characteristics. Here, we calculate some global features such as velocity, density, trajectory, length and cluster pattern to represent the property of jamming state. 2. Local motion of jamming state: Although the jamming state looks generally caged, various local dynamics can be observed in the active jamming system. Here, we separated the local area into three types, dynamic area, restricted area and caged area. We chose two bacteria in a region once and calculate their MSD, relationship between body angle and velocity correlation. The results not only show the essential differences between these three areas but also reveal the effect of different rearrangement ability. 3. Global motion of jamming process: Besides knowing the detail of the jamming state bacteria, we are also curious about the origin of it. The time-lapse experiment in the same region was done for understanding the transition from unjammed to jammed state. As the agent density increase, the overall order increase while the average velocity drops. The local arrangement of order structures enhances the jamming condition.

論文目次

Chapter 1 1
Introduction 1
1.1 Background and Motivation .1
1.2 Molecular motors2
1.3 Flagella Filaments 3
1.3.1 Polar Filaments.4
1.3.2 Lateral Filaments5
1.4 Vibrio alginolyticus5
1.4.1 Vibrio alginolyticus structure .6
1.4.2 Vibrio alginolyticus Energetic7
1.5 Self-propelled particles.7
1.5.1 Vicsek model: aligning self-propelled particles.8
1.5.2 Self-propelled rods.9
1.5.3 Self-propelled sphere: no aligning interaction .11
Chapter 2 12
Experimental Techniques.12
2.1 Microscope System 12
2.1.1 Inverted microscope .12
2.1.2 Charge coupled device .13
2.1.3 Phase contrast.14
2.2 Bacteria strains/ growth medium/ agar preparation15
2.3 Swarming observation 16
2.4 Image processing 16
2.5 Order parameter18
2.6 Clustering .18
2.7 Velocity, Density, Length and Angle .21
2.7.1 Particle tracking & Velocity.21
2.7.2 Length & Body angle .22
2.7.3 Density .22
Chapter 3 23
Jamming State of Swarming Bacteria 23
3.1 Experimental Aims.23
3.2 Experiment Design and Analysis .23
3.2.1 Growth and motility of Vibrio alginolyticus24
3.3 Result: Jamming State and Jamming Process 25
3.3.1 Jamming state: Global motion .26
3.3.2 Jamming state: Local motion .28
3.3.3 Jamming process: Global motion.45
3.4 Structure: Tetratic order .48
3.5 Conclusion49
Chapter 4 50
Future Work: Jamming State in Simulation .50
4.1 Aims of Simulation.50
4.2 Test Result: Jamming State in Simulation50
4.3 Structure: Tetratic order .54
4.4 Conclusion55
Chapter 5 56
Conclusions and outlooks.56
5.1 Jamming state of swarming bacteria 56
5.2 Jamming state in simulation .57
5.3 Outlooks .57
Reference 59

參考文獻

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指導教授

羅健榮

審核日期

2017-8-10

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