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Title: Biophysics of helices : devices, bacteria and viruses
Author: Katsamba, Panayiota
ISNI:       0000 0004 7651 7575
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2018
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A prevalent morphology in the microscopic world of artificial microswimmers, bacteria and viruses is that of a helix. The intriguingly different physics at play at the small scale level make it necessary for bacteria to employ swimming strategies different from our everyday experience, such as the rotation of a helical filament. Bio-inspired microswimmers that mimic bacterial locomotion achieve propulsion at the microscale level using magnetically actuated, rotating helical filaments. A promising application of these artificial microswimmers is in non-invasive medicine, for drug delivery to tumours or microsurgery. Two crucial features need to be addressed in the design of microswimmers. First, the ability to selectively control large ensembles and second, the adaptivity to move through complex conduit geometries, such as the constrictions and curves of the tortuous tumour microvasculature. In this dissertation, a mechanics-based selective control mechanism for magnetic microswimmers is proposed, and a model and simulation of an elastic helix passing through a constricted microchannel are developed. Thereafter, a theoretical framework is developed for the propulsion by stiff elastic filaments in viscous fluids. In order to address this fluid-structure problem, a pertubative, asymptotic, elastohydrodynamic approach is used to characterise the deformation that arises from and in turn affects the motion. This framework is applied to the helical filaments of bacteria and magnetically actuated microswimmers. The dissertation then turns to the sub-bacterial scale of bacteriophage viruses, 'phages' for short, that infect bacteria by ejecting their genetic material and replicating inside their host. The valuable insight that phages can offer in our fight against pathogenic bacteria and the possibility of phage therapy as an alternative to antibiotics, are of paramount importance to tackle antibiotics resistance. In contrast to typical phages, flagellotropic phages first attach to bacterial flagella, and have the striking ability to reach the cell body for infection, despite their lack of independent motion. The last part of the dissertation develops the first theoretical model for the nut-and-bolt mechanism (proposed by Berg and Anderson in 1973). A nut being rotated will move along a bolt. Similarly, a phage wraps itself around a flagellum possessing helical grooves, and exploits the rotation of the flagellum in order to passively travel along and towards the cell body, according to this mechanism. The predictions from the model agree with experimental observations with respect to directionality, speed and the requirements for succesful translocation.
Supervisor: Lauga, Eric Sponsor: EPSRC ; European Research Council (ERC)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
Keywords: helix ; bacteria ; virus ; phage ; bacteriophage ; microswimmer ; filament ; slender ; selective control ; magnetic actuation ; propulsion ; application-driven design ; elasticity ; elastohydrodynamics ; fluid-structure interaction ; constriction ; complex conduit ; adaptive design ; deformation ; nut-and-bolt mechanism ; flagellotropic ; flagellum ; bacterium ; translocation ; microscale ; fluid mechanics ; artificial-microswimmer ; deformation feedback to kinematics ; swimming ; device ; targeted-drug delivery ; microfluidics ; micromanipulation ; minimally-invasive medical applications ; biophysics ; mechanics ; biomechanics