Physical modeling of motile and sedimenting plankton: from simple flows to turbulence
by José Agustín Arguedas Leiva
Date of Examination:2022-05-16
Date of issue:2022-11-22
Advisor:Dr. Michael Wilczek
Referee:Prof. Dr. Andreas Tilgner
Referee:Prof. Dr. Ramin Golestanian
Referee:Prof. Dr. Stefan Klumpp
Referee:PD Dr. Olga Shishkina
Referee:Dr. David Zwicker
Persistent Address:
http://dx.doi.org/10.53846/goediss-9557
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Abstract
English
Planktonic microorganisms play a fundamental role in oceanic ecology and chemical cycles. Different planktonic species are found at various levels of the oceanic trophic chain, ranging from photosynthetic organisms to grazing species higher in the food chain. Many planktonic species have developed migration strategies to aid their survival. This includes motility and density regulation. Physical aspects, such as transport and collision rates, have a direct impact on planktonic survival and are influenced by the planktonic migration strategies. Furthermore, collision rates between planktonic organisms also play an important role in the formation of macroscopic plankton blooms. These have a direct effect on the ecology of oceans and lakes. In this dissertation we use physical modeling to study motile and sedimenting microorganisms in a fluid flow. We aim at shedding light on the key features of microorganism dynamics in fluid flows as a function of their key parameters: shape, motility, and density offset. In chapter 1 we introduce the biological setting of plankton, and give a very brief overview of the physical modeling approaches for plankton in fluid flows. Subsequently in chapter 2 we introduce the theoretical framework of turbulence and the methodology of our numerical simulations. In chapter 3 we start by examining microswimmers in a simple two-dimensional toy-model. We use methods from dynamical systems theory to uncover the role played by shape and motility in determining the microorganism dynamics in this simple setting. We explicitly identify the Hamiltonian dynamics followed by spherical microswimmers. Additionally, we find that elongated microswimmers more easily escape simple vortex structures than other shapes. In chapter 4 we then move on to ellipsoidal microswimmers in realistic mild turbulent flows. We analyze transport and rotation rates of motile ellipsoids. We find that elongated microswimmers have an advantage in transport, which is in part due to shape-dependent rotation rates. We also investigated the collision rates of motile spheres, and we were able to extract a master curve interpolating between the passive and motile limits for different sized spheres. We quantified the effect of motility and found that even very small motility greatly enhances collision rates. In chapter 5 we study of sedimentation of elongated microorganisms in mild turbulence. We measure the collision rates of elongated microorganisms in terms of size, energy dissipation rate, and aspect ratio. We then find a master curve interpolating between a passive particle and a sedimentation dominated limit. We characterize the role played by shape, which increases collision rates of elongated microorganisms in comparison with equal-volume spheres. This shape-induced enhancement helps to explain the timescales for formation of blooms of elongated planktonic species. In summary, in this dissertation we study the effect of shape, motility, and density regulation on physical models of planktonic microorganisms. Our findings help to shed light on the interplay between these planktonic parameters, the role of oceanic turbulence, and biologically relevant physical measures, such as transport, collision rates, and planktonic bloom formation times.
Keywords: turbulence; active swimmers; motile particles; sedimenting particles; numerical simulation