Order and Fluctuations in Collective Dynamics of Swimming Bacteria: Experimental Exploration of Active Matter Physics (Springer Theses)

Supervisor’s Foreword\nList of PublicationsIn reverse chronological order of publication:Daiki Nishiguchi, Igor S. Aranson, Alexey Snezhko, and Andrey Sokolov, “Engineering bacterial vortex lattice via direct laser lithography”, Nature Communications, 9, 4486 (2018). DOI: https://doi.org/10.1038/s41467-018-06842-6Daiki Nishiguchi, Junichiro Iwasawa, Hong-Ren Jiang, and Masaki Sano, “Flagellar dynamics of chains of active Janus particles fueled by an AC electric field”, New Journal of Physics, 20, 015002 (2018). arXiv: 1709.07756. DOI: https://doi.org/10.1088/1367-2630/aa9b48Daiki Nishiguchi, Ken H. Nagai, Hugues Chaté, and Masaki Sano, “Long-range nematic order and anomalous fluctuations in suspensions of swimming filamentous bacteria”, Physical Review E Rapid Communications, 95, 020601(R) (2017). arXiv: 1604.0427. DOI: https://doi.org/10.1103/PhysRevE.95.020601Daiki Nishiguchi and Masaki Sano, “Mesoscopic turbulence and local order in Janus particles self-propelling under an ac electric field”, Physical Review E, 92, 052309 (2015). arXiv: 1506.06591. DOI: https://doi.org/10.1103/PhysRevE.92.052309Papers 1 and 3 include the main contents of this thesis described in Chaps. 5 and 6, respectively. Papers 2 and 4 are introduced in Chap. 4.Supplementary movies related to this dissertation are available on the web sites of the journals. Especially, the papers 1 and 2 are published in open access journals and are freely available.The original dissertation, before modification and updates for publication in Springer Theses, is available on UTokyo Repository (DOI: https://www.doi.org/10.15083/00075579).\nAcknowledgements\nContents\n1 General Introduction\n	1.1 Active Matter Physics\n	1.2 Exploration of Universality in Collective Motion\n	1.3 Organization of the Thesis\n	References\n2 Standard Models on Collective Motion\n	2.1 Overview of Standard Models\n	2.2 The Original Vicsek Model\n		2.2.1 Definition\n		2.2.2 Physical Properties\n	2.3 Toner-Tu Theory\n		2.3.1 Idea and Definition\n		2.3.2 Predictions from Toner-Tu Theory\n		2.3.3 Remarks for Analysis with a Finite System Size\n		2.3.4 Toner-Tu-Ramaswamy Phase\n	2.4 Vicsek-Style Models with Different Symmetry\n		2.4.1 Definitions on Active Nematics and Self-propelled Rods\n		2.4.2 Properties of the Models\n	2.5 Vicsek Universality Class\n	2.6 Experimental Efforts to Find the TTR Phases\n		2.6.1 Experimental Difficulties\n		2.6.2 Experimental Systems\n		2.6.3 Summary of Experimental Approaches\n	References\n3 Collective Motion of Filamentous Bacteria\n	3.1 Introduction\n	3.2 Strategy: Use of Filamentous Cells in Confinement\n	3.3 Experimental Procedure and Setup\n		3.3.1 Preparation of Non-tumbling Filamentous Cells\n		3.3.2 Observation Devices\n	3.4 Analysis and Results\n		3.4.1 Overview of the System\'s Behavior\n		3.4.2 Collision Statistics\n		3.4.3 Image Processing\n		3.4.4 Existence of True Long-Range Order\n		3.4.5 Existence of Giant Number Fluctuations\n		3.4.6 Interpretation of True Long-Range Order and GNF\n		3.4.7 Correlation Functions\n		3.4.8 Boltzmann Approach\n	3.5 Discussion and Conclusion\n	3.6 Appendix\n		3.6.1 Structure Tensor Method and Coherency\n		3.6.2 Calculation of Correlation Function of Director Fluctuations Cδnperp(R)\n		3.6.3 Relations Among Nematic Order Parameters: |langlee2iθ rangle|, S, S, Q, 2\n	References\n4 Active Turbulence\n	4.1 Bacterial Turbulence\n	4.2 Basic Properties of Bacterial Turbulence\n		4.2.1 Constant Correlation Length\n		4.2.2 Power Spectrum\n	4.3 Continuum Theory\n		4.3.1 Formalism\n		4.3.2 Difficulty in Boundary Conditions\n	4.4 Bacterial Turbulence in Confinement\n		4.4.1 Spiral Formation in a Droplet\n		4.4.2 Vortex Lattices in Connected Circular Cavities\n		4.4.3 Summary and Interpretations\n	References\n5 Encounter of Bacterial Turbulence  with Periodic Structures\n	5.1 Introduction\n	5.2 Experimental Procedure and Setup\n	5.3 Results\n		5.3.1 Antiferromagnetic Vortex Lattice\n		5.3.2 Vorticity and Enstrophy\n		5.3.3 Antiferromagnetic Order Parameter\n		5.3.4 Persistence of Vortices: Life Times\n		5.3.5 Correlation Function of Velocity Field\n		5.3.6 Hexagonal Lattice\n		5.3.7 Self-organization of Swimming Bacteria Around Chiral Pillars\n		5.3.8 Lattice Size Scaling Experiment\n		5.3.9 Theoretical Description on Persistent Time\n	5.4 Conclusion\n	5.5 Appendix\n		5.5.1 Properties of Reference Area\n		5.5.2 Visualization of Vorticity\n	References\n6 General Conclusion and Outlook\n	References\nAppendix  Curriculum Vitae