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研究生： 陳柏亨
Po-Heng Chen
論文名稱： 主動粒子的擴張行為
Active Rods Expansion
指導教授： 羅健榮
Chien-Jung Lo
口試委員:
學位類別： 碩士
Master
系所名稱： 理學院 - 物理學系
Department of Physics
論文出版年： 2023
畢業學年度： 111
語文別： 英文
論文頁數： 81
中文關鍵詞： 主動粒子 、群游 、主動擴張
外文關鍵詞： active particle, swarm, active expansion
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    • 本篇透過觀察溶藻弧菌 (Vibrio alginolyticus) 的變異株 YM19 (Laf+, Pof-) 在瓊脂表面上不同的運動，來研究微米大小主動粒子的動力學行為。我們基於焦耳擴張 (被動擴張)，將細菌行為歸納為二階段模型。第一階段為細菌進入「空腔」時，會先在通道口聚集並緩慢朝中心擴張，同時會有少部分的細菌沿著腔體內側邊緣快速移動。第二階段包含三種不同的擴散模式以及與咖啡環效應相反的現象使得在最後獲得不同的沉澱圖案。

    此外，我們還通過製造具有高低落差的瓊脂表面材料，觀察了細菌在不同地形上的移動行為。這些地形包括「懸崖」(用以表示瓊脂表面高到低的變化) 和「微型瓊脂柱體」。我們觀察到細菌會避免跌落懸崖，而是沿著懸崖邊緣平行移動。然而，由於細菌的聚集和推擠，有時會發生細菌跌落懸崖的事件。在這種情況下，細菌會沿著懸崖壁移動。當細菌遇到微型瓊脂柱體時，我們觀察到它們會沿著柱體的邊緣平行移動，形成所謂的「河道」。隨著細菌的增加和聚集，河道會不斷擴張。同時，我們還觀察到細菌會從河道內向各個方向進行聚集和堆積。隨著河道邊緣的擴張，細菌會前往下一個柱體並重複相同的移動模式，直到整個系統被填滿。

    透過以上兩個研究，我們的結果顯示微米大小的主動粒子（細菌）在瓊脂表面上展現出複雜且有趣的動力學行為。我們觀察到細菌在擴張過程中呈現出不同的模式，並形成特殊的圖案。此外，細菌在遇到地形障礙時，避免跌落懸崖並沿著邊緣移動，以及在微型瓊脂柱體上形成河道並進行聚集和擴張，移動的行為仿佛伴隨著策略。這些研究結果豐富了我們對微米尺度主動粒子行為的理解。

    Through the observation of the movement of Vibrio alginolyticus variant strain YM19 (Laf+, Pof-) on agar surfaces, we investigated the dynamics of micrometer-sized active rods. Based on Joule expansion (passive expansion), we categorized the bacterial behavior into a two-stage model. In the first stage, when the bacteria enter the "cavity," they gather at the channel opening and slowly expand towards the center, while a small fraction of bacteria rapidly moves along the inner edge of the cavity. The second stage involves three different diffusion modes and a phenomenon contrary to the coffee ring effect, resulting in distinct precipitation patterns.

    Furthermore, we examined bacterial movement on different terrain by creating agar surfaces with varying heights, including "cliffs" (representing changes in agar surface height from high to low) and "micro-pillars." We observed that bacteria avoid falling off cliffs and instead move parallel to the cliff edges. However, due to bacterial aggregation and pushing, occasional incidents of bacterial falling off cliffs occur. In such cases, bacteria move along the cliff walls. When bacteria encounter micro-pillars, we observed that they move parallel to the edges, forming "channels." As bacteria increase and aggregate, these channels expand continuously. Additionally, we noticed bacterial gathering and accumulation in various directions within the channels. As the channel edges expand, bacteria move to the next pillar and repeat the same movement pattern until the entire system is filled.

    Based on these two studies, our findings demonstrate the complex and intriguing dynamic behavior of micron-sized active particles (bacteria) on agar surfaces. We observed different modes of expansion during bacterial spreading, leading to distinct patterns. Moreover, when encountering terrain obstacles, bacteria exhibited avoidance of falling off cliffs and moving along the edges, as well as the formation of channels and expansion on micro agar pillars, suggesting strategic behavior during their movement. These insights enhance our understanding of the behavior of micron-sized active particles.

    摘要 . . . . . . . . . . . . . . . . . i Abstract . . . . . . . . . . . . . . . . . ii Acknowledgement . . . . . . . . . . . . . . . iii Table of Contents . . . . . . . . . . . . . . . . iv List of Figures . . . . . . . . . . . . . . . . . vi List of Tables. . . . . . . . . . . . . . . . . ix 1 Introduction . . . . . . . . . . . . . . . . . 1 1.1 Active matters . . . . . . . . . . . . . . 1 1.1.1 Swarm . . . . . . . . . . . . . . . . 1 1.1.2 Models of collective motion . . . . . . . . . . . . 4 1.1.3 Simulations for self-propelled rods . . . . . 6 1.2 Bacterial motility . . . . . . . 8 1.2.1 Flagellar systems . . . . . . . . . . . . . . . . . 8 1.2.2 Vibrio alginolytics . . . . . . . . . . . . . . . 10 1.2.3 Bacterial navigational movement . . . . . . . . . . 11 1.3 Coffee-ring effect .. . . . . . . . . . . . . . . . . 13 1.3.1 Marangoni effect . . . . . . . . . . . . 13 1.3.2 Reversed coffee-ring effect . . . . . . . . . . . . 14 2 Experimental Apparatus . . . . . . . . . . . . . . . . 17 2.1 Phase contrast microscopy system – Ti-U . . . . . . . 17 2.1.1 Phase contract system : phase annulus and phase plate . . . . . . . . . 18 2.1.2 Charge-coupled device (CCD) . . . . . . . . . . . . 20 2.2 Micro environments construction . . . . . . . . . . . 20 2.2.1 Micro-channel fabrication system . . . . . . . . . 21 2.2.2 Micro-pillar fabrication system . . . . . . . . . . 22 2.2.3 Sample preparation . . . . . . . . . . . . . . . . 23 3 Data Analysis Methods . . . . . . . . . . . . . . . . . 24 3.1 Particle image velocimetry . . . . . . . . . . . . . 24 3.2 Image processing . . . . . . . . . . . . . . . . . . 24 3.2.1 Edge detection . . . . . . . . . . . . . . . . . . 25 3.2.2 Density and velocity measurements . . . . . . . . . 26 3.2.3 Image processing tool – ImageJ . . . . . . . . . . 29 4 Bacterial Expansions . . . . . . . . . . . . . . . . . 30 4.1 Active droplet on agar . . . . . . . . . . . . . . . 31 4.1.1 The coffee ring phenomenon of passive particles . . 31 4.1.2 The anti-coffee ring phenomenon of YM19 . . . . . . 32 4.2 Active rods free expansion . . . . . . . . . . . . . .37 4.2.1 Experimental design . . . . . . . . . . . . . . . . 37 4.2.2 Lone Ranger . . . . . . . . . . . . . . . . . . . . 39 4.2.3 Caravan . . . . . . . . . . . . . . . . . . . . . . 41 4.2.4 Crowd . . . . . . . . . . . . . . . . . . . . . . . 45 4.3 Caravan type . . . . . . . . . . . . . . . . . . . . 47 4.4 The obstacle course racing of YM19 . . . . . . . . . .50 5 Conclusions and future works . . . . . . . . . . . . . .61 5.1 Bacterial expansion for new chamber . . . . . . . . . 61 5.2 Bacterial expansion for pillar obstacle . . . . . . . 62 5.3 Future works . . . . . . . . . . . . . . . . . . . . .63 References . . . . . . . . . . . . . . . . . . . . . . . .65

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