高密度二維群游細菌系統之動力學

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：13

、訪客IP：3.145.54.61

姓名

廖致超(Chih-Chao Liao) 查詢紙本館藏

畢業系所

物理學系

論文名稱

高密度二維群游細菌系統之動力學
(Dynamic of High-Density 2D Bacterial Swarming System)

相關論文

★ 多細菌鞭毛馬達的同步轉動量測	★ Investigating Stators Assembly of Flagellar Motors in Escherichia Coli by PALM
★ 被動粒子在不同的流體型態	★ Lab on the Agar Plates
★ Probing the Physical Environments of Bacterial Swarm Colony	★ Spiral-coil Formation in Semi-flexible Self-propelled Chain System
★ Real-Time Measurement of Vibrio alginolyticus Polar Flagellar Growth	★ Foraging behavior of Caenorhabditis elegans
★ Jamming State of Active Nematics	★ 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
★ 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

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

[檢視]

[下載]

本電子論文使用權限為同意立即開放。
已達開放權限電子全文僅授權使用者為學術研究之目的，進行個人非營利性質之檢索、閱讀、列印。
請遵守中華民國著作權法之相關規定，切勿任意重製、散佈、改作、轉貼、播送，以免觸法。

摘要(中)

群游行為是一種細菌藉由轉動鞭毛馬達產生推進力，進而在物體表面上移動的運動行為。在近二十年內，科學家們對群游細菌的研究已經展示出了群游細菌多樣化且迷人的集體行為。在菌落中較厚的區域，細菌形成類紊流、邊界波浪、邊界湧流等運動結構。但是由於無法追蹤單一細菌，只能針對集體性質做探討。然而在菌落中有一單層結構，可以清楚見到細菌間的體積排斥力使細菌形成群集，並排列成有序結構。這樣的單層結構菌落是一個良好的實驗系統，可以提供我們來檢驗主動系統的行為。
雖然科學家們對群游細菌性質及集體行為的研究已經進行數年了，但很多細菌運動的細節還是不清楚的，尤其實在高密度細菌的狀態下。例如細菌是如何擴張菌落？多鞭毛細菌如何控制它的鞭毛形成鞭毛束並產生推進力？
這篇論文主要探討的是：1. 藉由觀察群游溶藻弧菌在單層菌落中的運動行為，研究二維自我推進粒子的性質與集體運動。2. 利用共軛焦顯微術研究細菌如何擴張菌落。
藉由追蹤每一個單一細菌在單層菌落的運動，我們展示了群游溶藻弧菌在不同密度下的集體行為。我們發現，在密度介於0.2~0.6的區間，巨型數量震盪現象(Giant number fluctuation)會發生在我們的系統中。而在更高的密度時，我們觀測到細菌可以形成區域有序結構，且結構的有序性會隨著細菌長度和密度增加而被增強。我們也發現群游溶藻弧菌的一些特殊性質。其一：在壅塞環境下，多數細菌都已無法移動時，有少數的細菌可以在菌落中進行長距離的位移。我們認為這個現象是源自於細菌間產生推進力能力的差異。另一個特殊性質為：我們發現，群游溶藻弧菌具有反轉速度方向的能力。這個現象的機制與已知的大腸桿菌速度反轉的機制不同，在本論文中，我們量測出在三個不同密度下，速度反轉的頻率都約為0.7次每秒，但細菌反轉其速度方向的機制還不清楚。
另外我們發現，在菌落擴張時，細菌的運動會使得菌落前沿的表面有明顯的形狀變化。實驗結果表示，在菌落擴張期，菌落的表面張力是會隨著細菌的集體運動而改變的。

摘要(英)

Bacterial swarming motility is a rapid and collective translocation of a bacterial population on the semi-solid surface by rotating their flagellar motors to generate thrusting force. In the last decades, people have demonstrated that there are many fascinating collective behaviors and pattern formations in the swarming colony of bacterial cells. In multiple layer region of swarming colony, turbulence state, edge waving, and edge streaming were observed in the swarm of Vibrio alginolyticus. People can only studied the collective behavior of bacterial cells due to the technical difficulty of individual cell tracking of high density region. However, the capability of single cell tracking can provide further insight to the collective behavior of the complex bacterial swarm. It is clear to see that cell alignment due to the excluded volume effect in the single layer region. Therefore, the swarming bacterial cells in single layer region is an ideal experimental system to study both bacterial properties and dynamics in active system.
People have studied the properties and collective behaviors of swarming bacterial cells for many years, but there are still many questions left unsolved especially in high cell density system. For example, how does the bacterial cells expand the colony, how does bacterial cells with peritrichous flagella form flagella bundle and generate propulsion. In this work, we studied the mechanism behind colony expansion with the use of confocal microscope, and demonstrate both the properties and collective behaviors of self-propelled particles in two dimensional systems by observing the swarming motion of Vibrio alginolyticus in single layer region.
By tracking the motion of each bacterial cell in single layer region of the swarm. We demonstrated the collective behaviors of swarming Vibrio alginolyticus with different cell density. Giant number fluctuation was observed in the system when the cell density is in the range of 0.2 to 0.6. At high cell density, bacterial cells were able to form a local order nematic structure, and the order is enhanced when both the average cell length and cell density increased. Two interesting properties of swarming Vibrio alginolyticus were observed in the system. First, some of the swarming bacterial cells were able to reverse their velocity direction with a frequency 0.7 hertz in three different densities. The mechanism of these velocity reversal events are different from the known mechanism of velocity reversal event in E. coli swarm. Second, some bacterial cells are able to travel long distance in high cell density system. Here, long range displacement events are considered as a result of wide distribution in force generation of cells. But the mechanism behind the velocity reverse events are not clear.
We also show that during the expansion, the motion of bacterial cells could change the local surface curvature of the colony, and make the surface tension a variable during the expansion.

關鍵字(中)

★ 溶藻弧菌

關鍵字(英)

★ Vibrio alginolyticus

論文目次

摘要 v
Abstract vi
Contents viii
List of Abbreviations x
List of Figures xi
Chapter 1 1
Background 1
1.1 Self-Propelled Particles 1
1.1.1 Self-propelled Rod 3
1.1.2 Models 4
1.1.2.1 Vicsek Model 5
1.1.2.2 Volume Exclusion 6
1.2 Simulations 8
1.2.1 Properties of Self-Propelled Particles 11
1.3 Experimental Works 13
1.3.1 Janus Particles 13
1.3.2 Swarming Motion in Single Layer 15
1.4 Bacterial Swarming Motion 20
1.5 Molecular Motors 32
1.6 Flagella Filaments 33
1.6.1 Polar Filaments 35
1.6.2 Lateral Filaments 35
1.7 Bacterial Motility 37
1.7.1 Vibrio alginolyticus 38
1.7.2 Vibrio alginolyticus Structure 38
1.7.3 Vibrio alginolyticus Energetic 39
1.8 Aim of this Work 39
Chapter 2 41
Experimental Techniques 41
2.1 Apparatus 41
2.1.1 Inverted Microscope 41
2.1.2 Charge Coupled Device 42
2.1.3 Phase Contrast Attachment 43
2.1.4 Confocal Microscope 44
2.2 Swarming Observation 45
2.2.1 Artificial single layer 46
2.3 Analysis Method 46
2.3.1 Image Processing 46
2.3.2 Single Particle Tracking 47
2.3.3 Density Measurement 49
2.3.4 Length and Body angle 49
2.3.5 Number Fluctuation 50
2.3.6 Order Parameter 51
2.3.7 Velocity Reverse 52
2.3.8 Particle Image Velocimetry 52
2.3.9 Surface profile 53
Chapter 3 55
Collective Motion of Swarming Cell 55
3.1 Swarming Properties 55
3.1.1 Rotational Brownian Motion 56
3.1.2 Cell Length 57
3.1.3 Density 59
3.1.4 Swarming Velocity 62
3.2 Giant Number Fluctuation 64
3.3 Order Parameter 67
3.3.1 Nematic Order Parameter 68
3.3.2 Tetratic Order Parameter 71
3.4 Vibrio as a Special Case of Self-Propelled Rod 73
3.4.1 Straight Swarming Time at Different Cell Density 73
3.4.2 Long Range Displacement at High Cell Density 74
Chapter 4 76
Colony Expansion 76
4.1 Error Estimation 76
4.2 Surface Profile and Active Colony 80
4.3 Surface Profile and Dead Colony 85
Chapter 5 88
Conclusion and Future Work 88
5.1 Collective Motion of Swarming Cell 88
5.2 Colony Expansion 89
5.3 Future Work 90
Reference 91

參考文獻

1. Zhang, H.P., et al., Collective motion and density fluctuations in bacterial colonies. Proceedings of the National Academy of Sciences, 2010. 107(31): p. 13626.
2. Großmann, R., F. Peruani, and M. Bär, Mesoscale pattern formation of self-propelled rods with velocity reversal. Physical Review E, 2016. 94(5): p. 050602.
3. Farrell, F.D.C., et al., Pattern Formation in Self-Propelled Particles with Density-Dependent Motility. Physical Review Letters, 2012. 108(24): p. 248101.
4. Fily, Y. and M.C. Marchetti, Athermal Phase Separation of Self-Propelled Particles with No Alignment. Physical Review Letters, 2012. 108(23): p. 235702.
5. Abaurrea Velasco, C., et al., Collective behavior of self-propelled rods with quorum sensing. Physical Review E, 2018. 98(2): p. 022605.
6. Vutukuri, H.R., et al., Dynamic self-organization of side-propelling colloidal rods: experiments and simulations. Soft Matter, 2016. 12(48): p. 9657-9665.
7. Theurkauff, I., et al., Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling. Physical Review Letters, 2012. 108(26): p. 268303.
8. Nishiguchi, D., et al., Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria. Physical Review E, 2017. 95(2): p. 020601.
9. Wensink, H.H., et al., Meso-scale turbulence in living fluids. Proceedings of the National Academy of Sciences, 2012. 109(36): p. 14308-14313.
10. Vicsek, T., et al., Novel Type of Phase Transition in a System of Self-Driven Particles. Physical Review Letters, 1995. 75(6): p. 1226-1229.
11. Abkenar, M., et al., Collective behavior of penetrable self-propelled rods in two dimensions. Physical Review E, 2013. 88(6): p. 062314.
12. Torres-Carbajal, A., S. Herrera Velarde, and R. Castaneda-Priego, Brownian motion of a nano-colloidal particle: The role of the solvent. Physical Chemistry Chemical Physics, 2015. 17: p. 19557.
13. McCandlish, S.R., A. Baskaran, and M.F. Hagan, Spontaneous segregation of self-propelled particles with different motilities. Soft Matter, 2012. 8(8): p. 2527-2534.
14. Shi, X.-q. and H. Chaté, Self-Propelled Rods: Linking Alignment-Dominated and Repulsion-Dominated Active Matter. 2018: p. 2-6.
15. Wang, Y.-K., C.-J. Lo, and W.-C. Lo, Formation of spiral coils among self-propelled chains. Physical Review E, 2018. 98(6): p. 062613.
16. Kayser, R.F. and H.J. Raveché, Bifurcation in Onsager′s model of the isotropic-nematic transition. Physical Review A, 1978. 17(6): p. 2067-2072.
17. Duman, Ö., et al., Collective dynamics of self-propelled semiflexible filaments. Soft Matter, 2018. 14(22): p. 4483-4494.
18. Narayan, V., N. Menon, and S. Ramaswamy, Nonequilibrium steady states in a vibrated-rod monolayer: tetratic, nematic, and smectic correlations. Journal of Statistical Mechanics: Theory and Experiment, 2006. 2006(01): p. P01005-P01005.
19. Müller, T., et al., Ordering of granular rod monolayers driven far from thermodynamic equilibrium. Physical Review E, 2015. 91.
20. Zhang, J., B.A. Grzybowski, and S. Granick, Janus Particle Synthesis, Assembly, and Application. Langmuir, 2017. 33(28): p. 6964-6977.
21. Jiang, H.-R., N. Yoshinaga, and M. Sano, Active Motion of a Janus Particle by Self-Thermophoresis in a Defocused Laser Beam. Physical Review Letters, 2010. 105(26): p. 268302.
22. Be′er, A., et al., Periodic reversals in Paenibacillus dendritiformis swarming. Journal of bacteriology, 2013. 195(12): p. 2709-2717.
23. Böttcher, T., H.L. Elliott, and J. Clardy, Dynamics of Snake-like Swarming Behavior of Vibrio alginolyticus. Biophysical journal, 2016. 110(4): p. 981-992.
24. Lin, S.N., W.C. Lo, and C.J. Lo, Dynamics of self-organized rotating spiral-coils in bacterial swarms. Soft Matter, 2014. 10(5): p. 760-6.
25. Turner, L., et al., Visualization of Flagella during Bacterial Swarming. Journal of Bacteriology, 2010. 192(13): p. 3259-3267.
26. Lindbeck, J.C., et al., Aerotaxis in Halobacterium salinarium is methylation-dependent. 1995. 141(11): p. 2945-2953.
27. Krohs, U., Damped oscillations in photosensory transduction of Halobacterium salinarium induced by repellent light stimuli. Journal of bacteriology, 1995. 177(11): p. 3067-3070.
28. Cisneros, L., et al., Reversal of bacterial locomotion at an obstacle. Phys Rev E Stat Nonlin Soft Matter Phys, 2006. 73(3 Pt 1): p. 030901.
29. Harshey, R.M., Bacterial motility on a surface: many ways to a common goal. Annu Rev Microbiol, 2003. 57: p. 249-73.
30. Jeckel, H., et al., Learning the space-time phase diagram of bacterial swarm expansion. 2019. 116(5): p. 1489-1494.
31. Kearns, D.B., A field guide to bacterial swarming motility. Nature reviews. Microbiology, 2010. 8(9): p. 634-644.
32. Sharma, M. and S. Anand, Swarming: A coordinated bacterial activity. Current Science, 2002. 83: p. 707-715.
33. Wu, Y. and H.C. Berg, Water reservoir maintained by cell growth fuels the spreading of a bacterial swarm. Proceedings of the National Academy of Sciences, 2012. 109(11): p. 4128-4133.
34. Darnton, N., et al., Moving fluid with bacterial carpets. Biophysical journal, 2004. 86(3): p. 1863-1870.
35. Ryan, S.D., G. Ariel, and A. Be′er, Anomalous Fluctuations in the Orientation and Velocity of Swarming Bacteria. Biophysical journal, 2016. 111(1): p. 247-255.
36. Nirody, J.A., Y.-R. Sun, and C.-J. Lo, The biophysicist’s guide to the bacterial flagellar motor. Advances in Physics: X, 2017. 2(2): p. 324-343.
37. van Albada, S.B., S. Tănase-Nicola, and P.R. ten Wolde, The switching dynamics of the bacterial flagellar motor. Molecular Systems Biology, 2009. 5(1): p. 316.
38. Morimoto, Y.V. and T. Minamino, Structure and function of the bi-directional bacterial flagellar motor. Biomolecules, 2014. 4(1): p. 217-234.
39. Berg, H.C., The Rotary Motor of Bacterial Flagella. Annual Review of Biochemistry, 2003. 72(1): p. 19-54.
40. Li, N., S. Kojima, and M. Homma, Sodium-driven motor of the polar flagellum in marine bacteria Vibrio. Genes to Cells, 2011. 16(10): p. 985-999.
41. Furuno, M., et al., Characterization of polar-flagellar-length mutants in Vibrio alginolyticus. Microbiology, 1997. 143(5): p. 1615-1621.
42. Belas, R., M. Simon, and M. Silverman, Regulation of lateral flagella gene transcription in Vibrio parahaemolyticus. Journal of Bacteriology, 1986. 167(1): p. 210-218.
43. de Boer, W.E., C. Golten, and W.A. Scheffers, Effects of some chemical factors on flagellation and swarming ofVibrio alginolyticus. Antonie van Leeuwenhoek, 1975. 41(1): p. 385-403.
44. Kojima, M., et al., The bidirectional polar and unidirectional lateral flagellar motors of Vibrio alginolyticus are controlled by a single CheY species. Molecular Microbiology, 2007. 64(1): p. 57-67.
45. Golten, C. and W.A. Scheffers, Marine vibrios isolated from water along the dutch coast. Netherlands Journal of Sea Research, 1975. 9(3): p. 351-364.
46. Cookson, S., et al., Monitoring dynamics of single-cell gene expression over multiple cell cycles. Mol Syst Biol, 2005. 1: p. 2005.0024.
47. Volfson, D., et al., Biomechanical ordering of dense cell populations. 2008. 105(40): p. 15346-15351.
48. Adams, R. and L. Bischof, Seeded region growing. IEEE Transactions on Pattern Analysis and Machine Intelligence, 1994. 16(6): p. 641-647.
49. Narayan, V., S. Ramaswamy, and N. Menon, Long-Lived Giant Number Fluctuations in a Swarming Granular Nematic. 2007. 317(5834): p. 105-108.
50. Ginelli, F., The Physics of the Vicsek model. The European Physical Journal Special Topics, 2016. 225(11): p. 2099-2117.
51. Palacci, J., et al., Living Crystals of Light-Activated Colloidal Surfers. 2013. 339(6122): p. 936-940.
52. Brossard, C., et al., Principles and applications of particle image velocimetry. AerospaceLab, 2009(1): p. p. 1-11.

指導教授

羅健榮(Chien-Jung Lo)

審核日期

2020-6-24

推文