Universität zu Köln

Zhou, Kai ORCID: 0000-0001-6837-9430 (2024). Non-equilibrium dynamics of bacterial colonies. PhD thesis, Universität zu Köln.

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Abstract

Colonies of bacteria endowed with a pili-based self-propulsion machinery are ideal models for investigating the structure and dynamics of active many-particle systems. We study Neisseria gonorrhoeae colonies with a molecular-dynamics-based approach. A generic, adaptable simulation method for particle systems with fluctuating bond-like interactions is devised. In a first study, the simulations are employed to investigate growth of bacterial colonies and the dependence of the colony structure on cell-cell interactions. In colonies, pilus retraction enhances local ordering. For colonies consisting of different types of cells, the simulations show a segregation depending on the pili-mediated interactions among different cells. These results agree with experimental observations. Next, we quantify the power-spectral density of colony-shape fluctuations in silico. Simulations predict a strong violation of the equilibrium fluctuation-response relation. Furthermore, we show that active force generation enables colonies to spread on surfaces and to invade narrow channels. The methodology can serve as a foundation for future studies of active many-particle systems at boundaries with complex shape. Bacterial colonies can attach and wet on surfaces like liquid droplets. Little is known about what factors affect the wetting of bacterial colonies. In a second study, we combine experimental data with our particle-based simulations and analytical calculations to show that azithromycin treatment enhances the wettability of Neisseria gonorrhoeae colonies. We show that the steady-state contact angle is not only determined by parameters that determine an equilibrium state, but also depends on dynamical quantities like the friction constant. Thus, surface-wetting of Neisseria gonorrhoeae colonies is a genuine non-equilibrium process. The thickness of the diffuse interface of the colonies is non-negligible compared to the colony radius, which gives rise to a finite Tolman length and a contact angle that depends on the size of the colony. The spreading dynamics is changed with azithromycin treatment, different spreading power laws are shown. In a third study, we investigate the dynamics of colonies consisting of two types of bacteria. In certain growth conditions, one finds experimentally that bacteria inside of the colony change the dynamics of their pili and become less adhesive. In simulations, we show that the configuration of such mixed colonies can become unstable, leading to a rapid folding and reorganization of the colony structure, which one can interpret as a non-equilibrium capillary instability. In a fourth study, we investigate bacterial colonies directionally migrate on geometrically asymmetric surfaces. The binding of bacterial pili to the asymmetric surfaces generates unbalanced forces, which drive the colony to migrate forward. Overall, we have demonstrated the versatility and predictive power of particle-based simulations of bacteria, which enable the discovery of novel non-equilibrium phenomena in bacterial collectives.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Zhou, Kai ka.zhou86@gmail.com orcid.org/0000-0001-6837-9430 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-726261
Date:	2024
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > Forschungszentrum Jülich
Subjects:	Natural sciences and mathematics Physics
Uncontrolled Keywords:	Keywords Language Non-equilibrium dynamics English Living matter English Bacterial colonies English
Date of oral exam:	25 March 2024
Referee:	Name Academic Title Sabass, Benedikt Prof. Dr. Bollenbach, Tobias Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/72626