長鏈被動粒子浸於主動群泳菌落的結構動力學

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徐嘉駿(Jia-Jiun Shiu) 查詢紙本館藏

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物理學系

論文名稱

長鏈被動粒子浸於主動群泳菌落的結構動力學
(Configuration dynamics of long passive filaments immersed in swarming bacteria bath)

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★ Stochastic thermodynamics of colloidal heat engines	★ Impact of Individual Variants in Cell Lengths on the Dynamics of Bacterial Swarming

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至系統瀏覽論文 (2025-7-1以後開放)

摘要(中)

群泳被認為是主動運動，意即微生物於表面上進行集體快速噴射或漩渦運動。
先前研究已經聚焦於群泳微生物所展現的非平衡物理之基本物理原則 [1, 2]。
然而，由於使用球形粒子作為追蹤物的極限，發生在高維空間尺度的群泳動力學仍然所知甚少。
在本論文中，我們研究長鏈被動追蹤物(DH5 extalpha，極低活動度的長鏈細菌)在群泳菌群(emph{Vibrio alginolyticus})中的動力學，其中，群泳菌群作為非平衡力的來源。此方法類似於近年使用奈米碳管探索多維細胞骨架的運動模式 [3]。
首先，我們由追蹤物的中心點和端點的均方根位移去分析並比較不同長度追蹤物之間的不同。
其次，我們透過分解追蹤物的形狀為簡振模的強度並轉化為二維的構形(模態對)相空間，從中觀察其形狀變化。
藉由計算相空間的機率通量，我們從通量流場發現通量環在短時間或單一軌跡出現，代表著其細緻平衡的破壞，然而在經過長時間平均後，通量環便無法觀測到。我們結合其他統計結果並提出此現象發生的原因。

摘要(英)

Swarming refers to a collective rapid jet flow or swirling motion of microorganisms on a surface, which is considered active motion.
Previous studies have focused on the underlying physical principles of the non-equilibrium dynamics generated by swarming microorganisms [1, 2].
However, the swarming dynamics occurring on multiple spatiotemporal scales are still poorly understood due to the limited capability of the employed spherical tracers.
Here, we investigate the dynamics of a long passive filament (DH5 extalpha, a long bacteria with engineered immotile flagella) in a bacterial swarming bath (emph{Vibrio alginolyticus}), which serves as the source of non-equilibrium forces.
This method is similar to a recent demonstration that uncovered the multiscale cytoskeletal dynamics of a cell using carbon nanotube [3].
We first obtain the mean-squared displacement of end-points and middle points of cells to compare the difference results in three length scales of tracers.
Secondly, we analyze the filament shapes at each moment as follows.
Each configuration is decomposed into several normal mode amplitudes.
Then, in the configurational (mode-pair) phase space, we generate the probability flux between mode-pairs to obtain the current field.
We find flux loops that indicate broken detailed balance for single and short-time trajectories, while no obvious loops for long-time averaged ones.

關鍵字(中)

★ 群泳
★ 細緻平衡的破壞

關鍵字(英)

★ Swarming
★ Broken detailed balance

論文目次

摘要 i
Abstract iii
Acknowledgements v
1 Introduction 1
2 Background and Theories 3
2.1 Swarming mobility . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Free-end flexible filaments in active matter . . . . . . . . . . . . 6
2.3 Normal modes of free-end flexible filaments in a dense medium . 7
2.4 Mode-pair phase space and broken detailed balance . . . . . . . 11
3 Experiment method 15
3.1 Swarm plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.1.1 Vibrio alginolyticus, YM19 . . . . . . . . . . . . . . . . . 15
3.1.2 Escherichia coli, DH5α . . . . . . . . . . . . . . . . . . . 16
3.1.3 Preparing the swarm plate . . . . . . . . . . . . . . . . . 16
3.2 Observation and analysis . . . . . . . . . . . . . . . . . . . . . . 18
3.2.1 Principle for phase-contrast microscopy . . . . . . . . . . 18
3.2.2 Experiment setup and alignments . . . . . . . . . . . . . 19
3.2.3 Image process and objects tracking . . . . . . . . . . . . 22
3.2.4 Decomposition of filament configuration . . . . . . . . . 23
4 Results 25
4.1 Filaments in YM19 bath . . . . . . . . . . . . . . . . . . . . . . 25
4.2 Diffusion of filaments in an active bath . . . . . . . . . . . . . . 26
4.3 Configuration of filaments . . . . . . . . . . . . . . . . . . . . . 31
4.4 Probability flux analysis of passive filaments . . . . . . . . . . . 35
5 Conclusion and Outlook 39
5.1 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.2 Outlook: The flexible filaments in B. subtilis bath . . . . . . . . 40
Bibliography 43

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指導教授

田溶根(Yonggun Jun)

審核日期

2024-6-20

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