Biophysics of Helices: Devices, Bacteria and Viruses
Creators: name: Katsamba, Panayiota
Publisher: name: Apollo - University of Cambridge Repository
Year: 2018
Subjects: 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

description: 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.
description: This work was funded by the EPSRC (3 years) and the last year was funded by Prof Eric Lauga's grant from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement 682754 to Prof Eric Lauga).