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研究生： 陳諾
No Chen
論文名稱： Deformation Dynamics of Active 2D Tetragonal Pseudo-Crystal
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： 2021
畢業學年度： 109
語文別： 英文
論文頁數： 61
中文關鍵詞： 主動物質 、桿狀粒子 、四方結構 、形變 、偽晶格 、非平衡 、融化 、相變 、錯位
外文關鍵詞： Active Matter, Rod-like Particle, Tetratic Order, Deformation, Pseudo-Crystal, Non-equilibrium, Melting, Phase Transition, Dislocation
相關次數： 點閱：18  下載：0 
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    • 主動推進粒子表現出各種非平衡湧現行為。主動推進粒子的形狀對於決定 全局湧現行為至關重要。與球形粒子不同，棒狀粒子通過簡單的體積排斥力和 局部交互作用湧現出有序地排列。因此，透過模擬主動布朗桿狀粒子(ABR)可 以形成仿生的紊流、群游和阻塞狀態。目前二維 ABR 的研究主要集中在集體運 動上，對動力學知之甚少。通過對細菌群落動力學的實驗觀察，我們發現局部 的動力平衡對阻塞狀態至關重要。受這一發現的啟發，我們設計了一種四方假 晶 (TPC)，該晶格具有三個垂直交叉的活性棒。然後我們使用 LAMMPS 進行布 朗動力學模擬來研究活性偽晶格的動力學。
    我們發現四元有序和晶體穩定性對密度和主動推進力敏感。在較低的系統 密度或更大的主動推進力下，TPC 會熔化成紊流狀態。另一方面，即使在高活 動力下，TPC 也可以在高密度下保持有序的晶格狀態。有趣的是，系統中存在 介於(紊流)無序狀態和(阻塞)有序狀態的中間態。通過研究此一少缺陷的長壽 命 TPC 中間態的位錯，我們揭示了 ABR 之間的剪應力誘導了熔化過程。此 外，我們發現 ABR 的密度和主動推進力的作用對我們的二維 ABR 系統中的變 形和熔化動力學有不同的影響。我們的研究為主動推進物質的研究提供了新的 方向。

    Active matter exhibits various non-equilibrium emergence behaviors. The shape of active matter individual particles is critical for the local interaction that determines the global emergence behaviors. Unlike spherical particles, rod- shaped particles show strong particle-particle alignment by simple volume exclu- sion. Therefore, active Brownian rods (ABR) can form biomimetic, turbulence, swarming, and jamming states. The current research of two-dimensional ABR focus on collective motion, and little is known about the dynamics. From the experimental observation of jamming dynamics in bacterial swarming, we found that the active force balance is critical for jamming. Inspired by this finding, we designed a tetragonal pseudo-crystal (TPC) that unit cells with three active rods crisscrossed orthogonally. We then used LAMMPS to perform Brownian dynamic simulation to study the dynamics of the active pseudo-crystal.
    We found that the tetratic order and crystal stability are sensitive to the packing ratio and the active force. At a lower packing ratio or more vital active force, the TPC can melt into a turbulence state. On the other hand, the TPC can maintain the tetratic order at a high packing ratio even at a highly active force. Interestingly, there are long-living ordered intermediate states that the system contains few defects. By studying the dislocations of intermediate states of TPC, we reveal that the shear slipping events between ABR induce the melting process. Also, we found that the role of packing ratio and active force of ABR have different effects on deformation and melting dynamics in our two-dimensional ABR system. This work provides a new direction of active matter research on the Pseudo-crystal.

    Abstract i Acknowledgements iii List of Figures vii List of Tables xi Listings xiii 1 Introduction 1 1.1 The Big Picture of Active Matter Systems . . . . . . . . . . . . . 1 1.2 Phases of Active Matter Systems .................. 2 1.2.1 Jamming in the bacterial swarming. . . . . . . . . . . . . 2 1.2.2 Phase diagram of passive spherical particles . . . . . . . . 3 1.2.3 Phase diagram of passive rod-like particle . . . . . . . . . 3 1.2.4 Phase diagram of active particles . . . . . . . . . . . . . . 4 1.3 Solid-Liquid Transition of Spherical System . . . . . . . . . . . . 6 1.4 Motivation .............................. 6 2 Methods 9 2.1 Active Brownian Rod Model..................... 9 2.1.1 Rod-likeparticles....................... 9 2.1.2 Volume exclusion and bending elasticity . . . . . . . . . . 10 2.1.3 Self-propulsionforce ..................... 12 2.1.4 Initial conditions and tetragonal pseudo-crystal . . . . . . 13 2.2 Computational Method ....................... 13 2.2.1 Brownian dynamics-LAMMPS .............. 14 2.2.2 LAMMPS-script ...................... 14 2.3 Analysis Methods........................... 16 2.3.1 Tetratic order......................... 16 2.3.2 TPC algorithm........................ 16 2.3.3 Finite strain approximate .................. 17 3 Results 19 3.1 Phase diagram ............................ 19 3.2 Structures............................... 21 3.3 Dynamics and evolution of the system ............... 22 3.4 Dislocation and Translational movement of TPC . . . . . . . . . 25 3.5 Deformation and Orientational movement of TPC. . . . . . . . 27 4 Conclusions 31 A Simulation Parameters 33 A.1 Parameters .............................. 33

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