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Dissertations / Theses on the topic 'Microswimmers'

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Published: 4 June 2021
Last updated: 4 May 2024

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1

Putz, Victor B. "Collective behaviour of model microswimmers." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:2018148e-336d-4be2-8c8c-c40278bb2d90.

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At small length scales, low velocities, and high viscosity, the effects of inertia on motion through fluid become insignificant and viscous forces dominate. Microswimmer propulsion, of necessity, is achieved through different means than that achieved by macroscopic organisms. We describe in detail the hydrodynamics of microswimmers consisting of colloidal particles and their interactions. In particular we focus on two-bead swimmers and the effects of asymmetry on collective motion, calculating analytical formulae for time-averaged pair interactions and verifying them with microscopic time-resolved numerical simulation, finding good agreement. We then examine the long-term effects of a swimmer's passing on a passive tracer particle, finding that the force-free nature of these microswimmers leads to loop-shaped tracer trajectories. Even in the presence of Brownian motion, the loop-shaped structures of these trajectories can be recovered by averaging over a large enough sample size. Finally, we explore the phenomenon of synchronisation between microswimmers through hydrodynamic interactions, using the method of constraint forces on a force-based swimmer. We find that the hydrodynamic interactions between swimmers can alter the relative phase between them such that phase-locking can occur over the long term, altering their collective motion.
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2

Oyama, Norihiro. "Direct Numerical Calculation on the Collective Motion of Model Microswimmers." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225640.

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3

Xu, Tiantian. "Propulsion Characteristics and Visual Servo Control of Scaled-up Helical Microswimmers." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2014. http://tel.archives-ouvertes.fr/tel-00977906.

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L'utilisation de micronageurs hélicoidaux capables de se mouvoir dans des liquides à faible nombre de Reynolds trouve son intérêt dans beaucoup d'applications: de tâches in-vitro dans des laboratoires sur puce (transport et tri de micro-objets; assemblage de micro-composants...), à des applications in-vivo en médecine mini-invasive (livraison interne et ciblée de médicaments, curiethérapie, thermothérapie...); grace à leur dimensions microscopiques et agilité permettant l'accès à des endroits normalement très restreints. Plusieurs types de nageurs hélicoidaux actionnés magnétiquement possédant divers paramètres géométriques, formes de tête et positions de la partie magnétique ont été proposés dans de précédents travaux. Cependant, l'influence de tous ces paramètres n'a pas clairement été étudiée. À notre connaissance, les micronageurs hélicoidaux dans l'état de l'art sont principalement contrôlés en boucle ouverte, en raison de la complexité de la commande du champ magnétique actionnant la propulsion, et du nombre limité de retours ayant des critères satisfaisants. Cette thèse vise à: comparer les performances de déplacement de nageurs hélicoidaux avec des conceptions différentes afin d'améliorer leur design et de les caractériser, et réaliser un asservissement visual de nageur hélicoidal. Pour se faire, des nageurs hélicoidaux de tailles millimétriques ont été conçus et sont mis en conditions à faible nombre de Reynolds. La conception de ces "millinageurs" servira de base à la conception de micronageurs. Une commande boucle fermée par retour visuel de l'orientation d'un micronageur hélicoidal dans un espace 3D, et un suivi de trajectoires sur plan horizontal ont été effectués. Cette méthode de commande sera par la suite appliquée à des micronageurs hélicoidaux.
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4

Rode, Sebastian [Verfasser], Gerhard Gutachter] Gompper, and Ulrich Benjamin [Gutachter] [Kaupp. "Flagellated and Ciliated Microswimmers / Sebastian Rode ; Gutachter: Gerhard Gompper, Benjamin Kaupp." Köln : Universitäts- und Stadtbibliothek Köln, 2017. http://d-nb.info/1161096825/34.

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5

Rode, Sebastian Verfasser], Gerhard [Gutachter] Gompper, and Ulrich Benjamin [Gutachter] [Kaupp. "Flagellated and Ciliated Microswimmers / Sebastian Rode ; Gutachter: Gerhard Gompper, Benjamin Kaupp." Köln : Universitäts- und Stadtbibliothek Köln, 2017. http://d-nb.info/1161096825/34.

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6

Chawan, Aschvin Bhagirath. "Novel methods for microfluidic mixing and control." Thesis, Virginia Tech, 2014. http://hdl.handle.net/10919/54016.

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Microfluidics is a constantly evolving area of research. The implementation of new technologies and fabrication processes offers novel methodologies to solve existing problems. There are currently a large number of established techniques to address issues associated with microscale mixing and valving. We present mixing and valving techniques that utilize simplified and inexpensive techniques. The first technique addresses issues associated with microscale mixing. Exercising control over animal locomotion is well known in the macro world but in the micro-scale world, control requires more sophistication. We present a method to artificially magnetize microorganisms and use external permanent magnets to control their motion in a microfluidic device. This effectively tethers the microorganisms to a location in the channel and controls where mixing occurs. We use the bulk and ciliary motion of the microswimmers to generate shear flows, thus enhancing cross-stream mixing by supplementing diffusion. The device is similar to an active mixer but requires no external power sources or artificial actuators. The second technique examines a methodology involving the integration of electroactive polymers into microfluidic devices. Under the influence of high applied voltages, electroactive polymers with fixed boundary conditions undergo out-of-plane deformation. We use this finding to create a valve capable blocking flow in microchannels. Electrolytic fluid solutions are used as electrodes to carry the voltage signal to the polymer surface. Currently we have demonstrated this methodology as a proof of concept, but aim to optimize our system to develop a robust microvalve technology.
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7

Geiseler, Alexander [Verfasser], and Peter [Akademischer Betreuer] Hänggi. "Artificial Microswimmers in Spatio-Temporally Modulated Activating Media / Alexander Geiseler ; Betreuer: Peter Hänggi." Augsburg : Universität Augsburg, 2018. http://d-nb.info/1156544718/34.

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8

Ives, Thomas Robert. "Microswimming in complex fluids." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31225.

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Many microorganisms have the ability to propel themselves through their fluid environments by periodically actuating their body. The biological fluid environments surrounding these microswimmers are typically complex fluids containing many high-molecular weight protein molecules, which give the fluid non-Newtonian rheological properties. In this thesis, we investigate the effect that one such rheological property, viscoelasticity, has on microswimming. We consider a classical model of a microswimmer, the so-called Taylor's waving sheet and generalise it to arbitrary shapes. We employ the Oldroyd-B model to study its swimming analytically and numerically. We attempt to develop a mechanistic understanding of the swimmer's behaviour in viscoelastic fluids. It has recently been suggested that continuum models of complex biological fluids might not be appropriate for studying the swimming of flagellated microorganisms as the size of biological macromolecules is comparable to the typical width of a microorganism's flagellum. A part of this thesis is devoted to exploring this scenario. We propose an alternative method for modelling complex fluids using a two-fluid depletion region model and we have developed a numerical solver to find the swimming speed and rate of work for the generalised Taylor's waving sheet model swimmer using this alternate depletion region model. This thesis is organised as follows. In the first chapter, we outline a physical mechanism for the slowing down of Taylor's sheet in an Oldroyd-B fluid as the Deborah number increases. We demonstrate how a microswimmer can be designed to avoid this. In the second chapter, we investigate swimming in an Oldroyd-B fluid near a solid boundary and show that, at large amplitudes and low polymer concentrations, the swimming speed of Taylor's sheet increases with De. In the third chapter, we show how the Oldroyd-B model can be adapted using depletion regions. In the final chapter, we investigate optimal swimming in a Newtonian fluid. We show that while the organism's energetics are important, the kinematics of planar-wave microswimmers do not optimise the hydrodynamic 'efficiency' typically used for mathematical optimisation in the literature.
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9

Jahanshahi, Soudeh [Verfasser], Hartmut [Gutachter] Löwen, and Alexei [Gutachter] Ivlev. "Microswimmers and microflyers in various complex environments / Soudeh Jahanshahi ; Gutachter: Hartmut Löwen, Alexei Ivlev." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2019. http://d-nb.info/1201881935/34.

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10

Wagner, Martin [Verfasser], Gerhard [Gutachter] Gompper, Ulrich K. [Gutachter] Deiters, and Marisol [Gutachter] Ripoll. "Colloidal Microswimmers driven by Thermophoresis / Martin Wagner ; Gutachter: Gerhard Gompper, Ulrich K. Deiters, Marisol Ripoll." Köln : Universitäts- und Stadtbibliothek Köln, 2017. http://d-nb.info/114862368X/34.

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11

Eisenstecken, Thomas Verfasser], Roland G. [Akademischer Betreuer] Winkler, and Carsten [Akademischer Betreuer] [Honerkamp. "Microswimmers - from active brownian polymers to swarming bacteria / Thomas Eisenstecken ; Roland G. Winkler, Carsten Honerkamp." Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://d-nb.info/1169214495/34.

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12

Eisenstecken, Thomas [Verfasser], Roland G. Akademischer Betreuer] Winkler, and Carsten [Akademischer Betreuer] [Honerkamp. "Microswimmers - from active brownian polymers to swarming bacteria / Thomas Eisenstecken ; Roland G. Winkler, Carsten Honerkamp." Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://d-nb.info/1169214495/34.

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13

Kössel, Fabian Rouven [Verfasser]. "Emerging patterns from the collective dynamics of microswimmers in an external field / Fabian Rouven Kössel." Mainz : Universitätsbibliothek Mainz, 2020. http://d-nb.info/1206374446/34.

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14

Schauer, Oliver [Verfasser], and Sourjik [Akademischer Betreuer] Victor. "Antigen 43-mediated biotin display and fabrication of bacteria-driven microswimmers / Oliver Schauer ; Betreuer: Sourjik Victor." Marburg : Philipps-Universität Marburg, 2019. http://d-nb.info/1187443638/34.

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15

Hoell, Christian [Verfasser], Hartmut [Gutachter] Löwen, and Andreas [Gutachter] Menzel. "Microswimmers: dynamical density functional theory and discrete particle models / Christian Hoell ; Gutachter: Hartmut Löwen, Andreas Menzel." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2019. http://d-nb.info/1199101982/34.

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16

MONTINO, ALESSANDRO. "Some topics in continuum and statistical mechanics: microswimmers, crawlers in viscous environments, microstructures in magnetic materials." Doctoral thesis, Gran Sasso Science Institute, 2017. http://hdl.handle.net/20.500.12571/9861.

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17

Codutti, Agnese [Verfasser], Stefan [Akademischer Betreuer] Klumpp, and Damien [Akademischer Betreuer] Faivre. "Behavior of magnetic microswimmers : simulations for natural swimmers and synthetic propellers / Agnese Codutti ; Stefan Klumpp, Damien Faivre." Potsdam : Universität Potsdam, 2018. http://d-nb.info/1219514659/34.

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18

Palacci, Jérémie. "Manipulation of Colloids by Osmotic Forces." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00597477.

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19

Zöttl, Andreas [Verfasser], Holger [Akademischer Betreuer] Stark, Dieter [Akademischer Betreuer] Breitschwerdt, and Gerhard [Akademischer Betreuer] Gompper. "Hydrodynamics of microswimmers in confinement and in Poiseuille flow / Andreas Zöttl. Gutachter: Dieter Breitschwerdt ; Holger Stark ; Gerhard Gompper. Betreuer: Holger Stark." Berlin : Technische Universität Berlin, 2014. http://d-nb.info/1067385878/34.

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20

Wischnewski, Christian Jochen [Verfasser], Jan [Akademischer Betreuer] Kierfeld, and Heinz [Gutachter] Rehage. "Deformation of ferrofluid-filled elastic capsules and swelling elastic disks as microswimmers / Christian Jochen Wischnewski ; Gutachter: Heinz Rehage ; Betreuer: Jan Kierfeld." Dortmund : Universitätsbibliothek Dortmund, 2019. http://d-nb.info/1199106461/34.

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21

Wischnewski, Christian [Verfasser], Jan [Akademischer Betreuer] Kierfeld, and Heinz [Gutachter] Rehage. "Deformation of ferrofluid-filled elastic capsules and swelling elastic disks as microswimmers / Christian Jochen Wischnewski ; Gutachter: Heinz Rehage ; Betreuer: Jan Kierfeld." Dortmund : Universitätsbibliothek Dortmund, 2019. http://d-nb.info/1199106461/34.

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22

Theers, Mario Verfasser], Roland G. [Akademischer Betreuer] Winkler, Carsten [Akademischer Betreuer] [Honerkamp, and Hartmut [Akademischer Betreuer] Löwen. "Mesoscale hydrodynamic simulations : from a single colloid to the collective dynamics of microswimmers / Mario Theers ; Roland G. Winkler, Carsten Honerkamp, Hartmut Löwen." Aachen : Universitätsbibliothek der RWTH Aachen, 2017. http://d-nb.info/1157122523/34.

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23

Theers, Mario [Verfasser], Roland G. Akademischer Betreuer] Winkler, Carsten [Akademischer Betreuer] [Honerkamp, and Hartmut [Akademischer Betreuer] Löwen. "Mesoscale hydrodynamic simulations : from a single colloid to the collective dynamics of microswimmers / Mario Theers ; Roland G. Winkler, Carsten Honerkamp, Hartmut Löwen." Aachen : Universitätsbibliothek der RWTH Aachen, 2017. http://d-nb.info/1157122523/34.

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24

Samatas, Sotiris. "Emergence and collective phenomena in chiral microswimmer suspensions." Electronic Thesis or Diss., Bordeaux, 2023. http://www.theses.fr/2023BORD0453.

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Nous étudions les phénomènes collectifs dans les suspensions en bulk de micronageurs sphériques à trajectoires chirales en utilisant des simulations numériques à grande échelle. Le modèle est générique. Il correspond à la solution d'ordre le plus bas d'un modèle général d'autopropulsion à nombres de Reynolds faibles, constitué d'un dipôle source rotatif non axisymétrique. Nous montrons que les nageurs purement circulaires et hélicoïdaux peuvent spontanément synchroniser leur rotation. L'état synchronisé correspond à un alignement des vitesses avec un ordre d'orientation élevé dans les directions polaire et azimutale. Pour illustrer la robustesse de l'état synchronisé, nous considérons un mélange racémique de nageurs hélicoïdaux où la synchronisation intra-espèce est observée tandis que le système reste comme un fluide spatialement uniforme. Nos résultats démontrent la synchronisation hydrodynamique en tant que phénomène collectif naturel pour les micronageurs à trajectoires chirales. Une fois la synchronisation atteinte, nous montrons que le système peut manifester des comportements collectifs post-synchronisation complexes impliquant séparation de phase et propagation d'ondes d'ordre polaire local. Nos observations fournissent une base convaincante pour les recherches futures sur les flux collectifs émergents et la diffusivité augmentée induite a cause de l'activité dans les suspensions de micronageurs chiraux
We study collective phenomena in bulk suspensions of spherical microswimmers with chiral trajectories using large scale numerics. The model is generic. It corresponds to the lowest order solution of a general model for self-propulsion at low Reynolds numbers, consisting of a nonaxisymmetric rotating source dipole. We show that both purely circular and helical swimmers can spontaneously synchronize their rotation. The synchronized state corresponds to velocity alignment with high orientational order in both the polar and azimuthal directions. To exemplify the robustness of the syncronised state, we consider a racemic mixture of helical swimmers where intraspecies synchronization is observed while the system remains as a spatially uniform fluid. Our results demonstrate hydrodynamic synchronization as a natural collective phenomenon for microswimmers with chiral trajectories. Once synchronisation is attained, we show that the system can manifest complex post-synchronisation collective behaviour involving phase separation and the propagation of waves with local polar order. Our observations provide a compelling basis for future research on emerging collective flows and activity-driven enhanced diffusivity in chiral microswimmer suspensions
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25

Ly, Aboubakry. "Effet Seebeck à l’échelle nanométrique de nanostructures chaudes." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0010/document.

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L'objectif de ce travail est d'étudier l'effet thermoélectrique à l'échelle nanométrique des nanostructures chauffées. Dans un premier temps, nous étudions les mécanismes d'autopropulsion thermo-électrophorétique de particules Janus chauffées par laser. Ce mécanisme d'autopropulsion est principalement induit par l'effet Seebeck ou l'effet thermoélectrique. Cet effet provient de la séparation des charges survenues lorsqu'un gradient de température est présent dans la solution d'électrolyte: Une forte absorption du laser par la partie métallisée de la particule génère un gradient de température qui en retour agit sur les espèces ioniques (positive et négative) et les conduits vers les zones chaudes ou les zones froides. Ce mouvement d'ions entraine la création d'un champ électrique dipolaire qui, à proximité de la particule, dépend fortement des propriétés de surface. Ce changement de comportement de ce champ électrique sur une surface isolant ou conductrice n'affecte pas la vitesse de la particule. Dans un second temps, nous étudions les effets d'interactions hydrodynamiques et de la condensation des contre-ions sur la thermophorèse des polymères d'ADN. Comme résultat principal, la mobilité thermophorétique montre, en fonction de la longueur de la chaîne, un comportement non-monotone et se compose de deux contributions induites par les forces conductrices dominantes que sont l'effet Seebeck et le gradient de permittivité. À la fin, nous comparons notre résultat théorique avec une récente expérience sur l'ADN
The aim of this work is to study the nanoscale Seebeck effect at hot nanostructures. At first, we study the thermo-electrophoresis self-propulsion mechanism for a heated metal capped Janus colloid. The self-propulsion mechanism is mainly induced by the electrolyte Seebeck effect or thermoelectric effect. This effect takes its origin from the separation of charges occurring while a temperature gradient is present in a electrolyte solution: A strong absorption of laser light by the metal side of the particle creates a temperature gradient which in turn acts on ion-species (positive and negative) and drives them to the hot or the cold region. This motion of ion results in a dipolar electric field which, close to the particle, depends strongly on the surface properties. The change of behavior of the electric field at the insulating or conducting surface does not affect the velocity of the particle. At second, we study the effect of hydrodynamic interactions and counterion condensation in thermophoresis for DNA polymer. As the main result, the thermophoretic mobility shows, in function of the chain length, a non-monotonuous behavior and consists of two contributions induced by the dominant driving forces which are the thermally induced permittivity-gradient and the electrolyte Seebeck effect. At the end, we compare our theoretical result with recent experiment on single-stranded DNA
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26

Angeletti, Andrea. "Collective dynamics of active particles." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amslaurea.unibo.it/16772/.

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Il nostro scopo è lo studio e il confronto della dinamica di particelle passive e attive in un fluido. Vengono inoltre introdotti i modelli matematici che permettono di simulare il loro comportamento. Sono studiate le propietà e la soluzione numerica dell'equazione di Langevin nella sua approsimazione in regime 'overdamped'. Mostriamo come lo spostamento quadratico medio delle particelle passive sia diffusivo, i.e. lineare nel tempo, e proporzionale al coefficiente di diffusione lineare, mentre quello di particelle attive quadratico per un tempo minore dell'inverso del coefficiente di diffusione rotazionale e diffusivo per un tempo maggiore. Con la presenza di una parete repulsiva e osservando la distribuzione di probabilità della posizione delle particelle, notiamo come quelle attive tendano ad accumularsi su di essa. Infine osserviamo che sotto l'azione di un potenziale repulsivo particelle attive tendono a formare agglomerati.
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27

Krüger, Carsten Verfasser], Stephan [Akademischer Betreuer] [Gutachter] [Herminghaus, Jörg [Gutachter] Enderlein, Christian [Gutachter] Bahr, Christoph F. [Gutachter] Schmidt, Sarah [Gutachter] Köster, and Annette [Gutachter] Zippelius. "Liquid Crystal Microswimmers - from single entities to collective dynamics / Carsten Krüger ; Gutachter: Stephan Herminghaus, Jörg Enderlein, Christian Bahr, Christoph F. Schmidt, Sarah Köster, Annette Zippelius ; Betreuer: Stephan Herminghaus." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2016. http://d-nb.info/1119447577/34.

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28

Riley, Emily Elizabeth. "Tricks and tips for faster small-scale swimming : complex fluids and elasticity." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267468.

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Many cells exploit the bending or rotation of flagellar filaments in order to self-propel in viscous fluids. Often swimming occurs in complex, nonlinear fluids, e.g. mucus. Futhermore even in simple Newtonian fluids, if swimming appendages are deformable then locomotion is subject to fluid-structure interactions. The fundamental question addressed in this thesis is how exactly locomotion is impacted, in particular if it is faster or slower, with or without these effects. First we study locomotion in shear-thinning and viscoelastic fluids with rigid swimming appendages. Following the introductory Chapter, in Chapter 2 we propose empirical extensions of the classical Newtonian resistive-force theory to model the waving of slender filaments in non-Newtonian fluids, based on experimental measurements for the motion of rigid rods in non-Newtonian fluids and on the Carreau fluid model. We then use our models to address waving locomotion in shear-thinning fluids, and show that the resulting swimming speeds are systematically lowered a result which we are able to capture asymptotically and to interpret physically. In Chapter 3 we consider swimming using small-amplitude periodic waves in a viscoelastic fluid described by the Oldroyd-B constitutive relationship. Using Taylor’s swimming sheet model, we show that if all travelling waves move in the same direction, the locomotion speed of the organism is systematically decreased. However, if we allow waves to travel in two opposite directions, we show that this can lead to enhancement of the swimming speed, which is physically interpreted as due to asymmetric viscoelastic damping of waves with different frequencies. A change of the swimming direction is also possible. Secondly we consider the affect of fluid-structure interactions. In Chapter 4, we use Taylor’s swimming sheet model to describe an active swimmer immersed in an Oldroyd-B fluid. We solve for the shape of an active swimmer as a balance between the external fluid stresses, the internal driving moments, and the passive elastic resistance. We show that this dynamic balance leads to a generic transition from hindered rigid swimming to enhanced flexible locomotion. The results are physically interpreted as due to a viscoelastic suction increasing the swimming amplitude in a non-Newtonian fluid and overcoming viscoelastic damping. In Chapter 5 we consider peritrichously flagellated bacteria, such as Escherichia coli. The rotation of each motor is transmitted to a flexible rod called the hook which in turns transmits it to a helical filament, leading to swimming. The motors are randomly distributed over the body of the organism, and thus one expects the propulsive forces from the filament to almost cancel out leading to negligible swimming. We show that the transition to swimming is an elasto-hydrodynamic instability arising when the flexibility of the hook is below a critical threshold.
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29

Fattah, Zahra Ali. "Applications of bipolar electrochemistry : from materials science to biological systems." Phd thesis, Université Sciences et Technologies - Bordeaux I, 2013. http://tel.archives-ouvertes.fr/tel-00917770.

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Bipolar electrochemistry deals with the exposure of an isolated conducting substrate that has no direct connection with a power supply except via an electric field. Therefore it can be considered as a "wireless technique". The polarization of the substrate with respect to the surrounding medium generates a potential difference between its opposite ends which can support localized electrochemical oxidation reduction reactions and break the surface symmetry of the substrate. The method was applied in the present thesis to materials science and biological systems. In the frame of designing asymmetric particles, also called "Janus" particles, bipolar electrochemistry was adapted for the bulk preparation of these objects. Conductive substrates with different nature, sizes and shapes have been modified with various materials such as metals, ionic and inorganic compounds using this approach. Moreover, a control over the deposit topology could be achieved for substrates at different length scales. Bipolar electrodeposition is also a good tool for investigating the generation of different metal morphologies. Further developments in the bipolar setup allowed us to use the technology for microstructuration of conductive objects. Furthermore the concept has shown to be very useful in the field of the induced motion of particles. The asymmetric objects that have been prepared by bipolar electrodeposition were employed as microswimmers which could show both translational and rotational motion. The application of electric fields in the bipolar setup can be used for the direct generation of motion of isotropic objects through bubble generation. A levitation motion of objects combined with light emission was possible using this concept. Finally, bipolar electrochemistry was also used for studying the intrinsic conductivity of biological molecules (DNA), which is of great importance in the nanotechnology.
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30

Garcia, Michaël. "Hydrodynamique de micro-nageurs." Thesis, Grenoble, 2013. http://www.theses.fr/2013GRENY011/document.

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Les suspensions d'objets microscopiques ayant la faculté de se déplacer par eux-mêmes dans le fluide qui les entoure sont des systèmes qui présentent un intérêt croissant dans la communauté scientifique. Du fait de leur dynamique intrinsèquement hors-équilibre au sens de la physique statistique, ils génèrent des effets particulièrement complexes. Parmi les micro-objets autopropulsés existants, les micro-algues vertes représentent une part importante de la biomasse de la Terre et participent activement au retraitement du CO2 par leur activité photosynthétique. Elles présentent de plus un remarquable potentiel dans les domaines de la production de bio-carburants, du retraitement des déchets, de la fabrication de cosmétiques et de compléments alimentaires. La compréhension de la dynamique de nage de ce type de microorganisme est d'un intérêt primordial d'un point de vue industriel. Cet ouvrage présente l'étude de la dynamique de la micro-algue Chlamydomonas Reinhardtii. En utilisant un système de suivi de particules en imagerie optique que nous avons développé, nous analysons ici le mécanisme fondamental de nage utilisé par cette algue jusqu'à ses implications en terme d'effets collectifs sur la dynamique de nage d'une suspension semi-diluée
The suspensions of microscopic objects with the ability to propel themselves into the surrounding fluid are systems of growing interest in the scientific community. Due to their intrinsic out-of-equilibrium dynamics in the sense of statistical physics, they generate complex effects. Among the existing self-propelled micro-objects, green micro-algae are an important part of the biomass of Earth and they actively participate to the recycling of CO2 by their photosynthetic activity. Moreover they have remarkable potential for the production of bio-fuels, waste reprocessing, cosmetics and dietary supplements production. From an industrial point of view, understanding the dynamics of this type of swimming microorganism is of primary interest. This work presents the study of the dynamics of microalgae Chlamydomonas Reinhardtii. Using a system of particle tracking with optical imaging that we have developed, we analyze the mechanism of stroke used by the algae up to its implications in terms of collective effects on the dynamics of swimming in a semi-dilute suspension
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31

Djellouli, Abderrahmane. "Nage par flambage de coque sphérique." Thesis, Université Grenoble Alpes (ComUE), 2017. http://www.theses.fr/2017GREAY043/document.

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Les micronageurs et parmi eux les microangeurs artificiels sont en général, limités à exister dans des écoulements dominés par des forces visqueses. Ces écoulements sont caractérisés par un bas nombre de Reynolds (Re). Cela impacte la stratégie de nage et plus particulièrement les séquences de forme possibles, qui doivent nécessairement être non-réciproques dans l'espace de déformation pour espérer induire un déplacement net non-nul. De plus, due aux forts effets de traînée, les vitesses de nage sont limités à des valeurs faibles.Dans cette thèse, on examine la possibilité d'utiliser un mécanisme de nage basé sur l'instabilité de flambage d'une sphère creuse. Cette instabilité est provoquée en soumettant la sphère à une onde de pression. La particularité de ce mécanisme est qu'il satisfait par construction la condition nécessaire de nage à bas Reynolds exposée précédemment. De plus, la rapidité de la déformation lors de l'instabilité pousse à prévoir l'apparition d'effets inertiels, et ce même à l'échelle microscopique.Une étude expérimentale a été conduite à l'échelle macroscopique dans le but de comprendre la dynamique de l'instabilité et son impact sur le fluide qui entoure la coque creuse. Ces expériences nous permettent de montrer qu'un déplacement net non-nul est produit pour tous les régimes d'écoulements.On met en évidence le rôle de paramètres géométriques, des propriétés du matériau composant la coque creuse et de la rhéologie du fluide sur l'efficacité de la nage.On montre l'existence d'un optimum de déplacement net pour des valeurs intermédiaires du nombre de Reynolds. Pour expliquer cela, on se sert de mesures de PIV résolues temporellement pour mettre en évidence la présence d'effets d'histoire non-triviaux qui augmentent le déplacement net.On dérive un simple modèle en se basant sur les observations expérimentales pour montrer que ce régime optimal de nage est atteignable pour des sphères microscopiques, ceci est possible grâce l'activation rapide de l'instabilité. Cette propriété permet aussi une excitation à haute fréquence en utilisant des ultrasons. Une étude d'échelle nous permet de prédire une vitesse de nage de 1 cm/s pour un micro-robot contrôlé à distance. Cet ordre de grandeur de vitesse est idéal pour des applications biologiques comme la distribution ciblée de médicaments
Microswimmers, and among them aspirant microrobots, are generally bound to cope with flows where viscous forces are dominant, characterized by a low Reynolds number (Re). This implies constraints on the possible sequences of body motion, which have to be nonreciprocal. Furthermore, the presence of a strong drag limits the range of resulting velocities.Here, we propose a swimming mechanism which uses the buckling instability triggered by pressure waves to propel a spherical hollow shell. The particularity of this mechanism is that it fulfills naturally the necessary condition of swimming at low Re. In addition, the swiftness of the instability might produce inertial effects even at the microscopic scale.With a macroscopic experimental model we show that a net displacement is produced at all Re regimes. We put in evidence the role of geometrical parameters, shell material properties and rheology of the surrounding fluid on the swimming efficiency.An optimal displacement is reached at intermediate Re. Using time-resolved PIV measurements, we explain that non-trivial history effects take place during the instability and enhance net displacement.Using a simple model, derived from the study of shell dynamics, we show that due to the fast activation induced by the instability, this regime is reachable by microscopic shells. The rapid dynamics would also allow high frequency excitation with standard traveling ultrasonic waves. Scale considerations predict a swimming velocity of order 1 cm/s for a remote controlled microrobot, a suitable value for biological applications such as drug delivery
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32

Klindt, Gary. "Hydrodynamics of flagellar swimming and synchronization." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-231897.

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What is flagellar swimming? Cilia and flagella are whip-like cell appendages that can exhibit regular bending waves. This active process emerges from the non-equilibrium dynamics of molecular motors distributed along the length of cilia and flagella. Eukaryotic cells can possess many cilia and flagella that beat in a coordinated fashion, thus transporting fluids, as in mammalian airways or the ventricular system inside the brain. Many unicellular organisms posses just one or two flagella, rendering them microswimmers that are propelled through fluids by the flagellar beat including sperm cells and the biflagellate green alga Chlamydomonas. Objectives. In this thesis in theoretical biological physics, we seek to understand the nonlinear dynamics of flagellar swimming and synchronization. We investigate the flow fields induced by beating flagella and how in turn external hydrodynamic flows change speed and shape of the flagellar beat. This flagellar load-response is a prerequisite for flagellar synchronization. We want to find the physical principals underlying stable synchronization of the two flagella of Chlamydomonas cells. Results. First, we employed realistic hydrodynamic simulations of flagellar swimming based on experimentally measured beat patterns. For this, we developed analysis tools to extract flagellar shapes from high-speed videoscopy data. Flow-signatures of flagellated swimmers are analysed and their effect on a neighboring swimmer is compared to the effect of active noise of the flagellar beat. We were able to estimate a chemomechanical energy efficiency of the flagellar beat and determine its waveform compliance by comparing findings from experiments, in which a clamped Chlamydomonas is exposed to external flow, to predictions from an effective theory that we designed. These mechanical properties have interesting consequences for the synchronization dynamics of Chlamydomonas, which are revealed by computer simulations. We propose that direct elastic coupling between the two flagella of Chlamydomonas, as suggested by recent experiments, in combination with waveform compliance is crucial to facilitate in-phase synchronization of the two flagella of Chlamydomonas.
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33

Gonzalez, Ibon Santiago. "DNA programmed assembly of active matter at the micro and nano scales." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:8cc298ba-d35c-4c58-8893-b1f2c9d6c65c.

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Small devices capable of self-propulsion have potential application in areas of nanoscience where autonomous locomotion and programmability are needed. The specific base-pairing interactions that arise from DNA hybridisation permit the programmed assembly of matter and also the creation of controllable dynamical systems. The aim of this thesis is to use the tools of DNA nanotechnology to design synthetic active matter at the micro and nano scales. In the first section, DNA was used as an active medium capable of transporting information faster than diffusion in the form of chemical waves. DNA waves were generated experimentally using a DNA autocatalytic reaction in a microfluidic channel. The propagation velocity of DNA chemical waves was slowed down by creating concentration gradients that changed the reaction kinetics in space. The second section details the synthesis of chemically-propelled particles and the use of DNA as a 'programmable glue' to mediate their interactions. Janus micromotors were fabricated by physical vapour deposition and a wet-chemical approach was demonstrated to synthesise asymmetrical catalytic Pt-Au nanoparticles that function as nanomotors. Dynamic light scattering measurements showed nanomotor activity that depends on H2O2 concentration, consistent with chemical propulsion. Gold nanoparticles/Origami hybrids were assembled in 2D lattices of different symmetries arranged by DNA linkers. The third section details the design process and synthesis of nanomotors using DNA as a structural scaffold. 3D DNA Origami rectangular prisms were functionalised site-specifically with bioconjugated catalysts, i.e. Pt nanoparticles and catalase. Enzymatic nanomotors were also conjugated to various cargoes and their motor activity was demonstrated by Fluorescence Correlation Spectroscopy. In the final section, control mechanisms for autonomous nanomotors are studied, which includes the conformational change of DNA aptamers in response to chemical signals, as well as a design for an adaptive dynamical system based on DNA/enzyme reaction networks.
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34

Oulmas, Ali. "Suivi de chemin 3D de nageurs magnétiques à faible nombre de Reynolds." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS070/document.

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Les microrobots magnétiques, qui nagent en utilisant des modes de propulsion bio-inspirées, apparaissent très prometteurs pour la manipulation et la caractérisation d'objets à l'échelle microscopique dans des environnements confinés et très restreints, contrairement aux méthodes de micromanipulation classiques. La littérature propose une variété de microrobots avec des formes géométriques et des propriétés magnétiques différentes. Les commandes en mouvement proposées restent cependant simples, peu précises et insuffisamment robustes pour la réalisation de tâches réelles. De plus, il subsiste une incertitude sur le fait que tous ces micronageurs artificiels peuvent accomplir les mêmes tâches avec une performance égale. L'objectif de cette thèse consiste alors à proposer : des commandes de mouvement génériques par asservissement visuel dans l'espace pour tous les types de micronageurs avec des contraintes non holonomes afin d'améliorer les performances de ces micronageurs, un ensemble de critères de comparaison entre des robots avec une topologie ou un mode de propulsion différents pour le choix du micronageur le plus performant pour réaliser une tâche particulière. Des lois de commande de suivi de chemin dans l'espace sont synthétisées et validées expérimentalement sur des nageurs hélicoïdal et flexible sous différentes conditions. Ces robots évoluent dans un fluide à faible nombre de Reynolds, imitant respectivement le mécanisme de locomotion des bactéries et des spermatozoïdes et sont actionnés par un champ magnétique uniforme. Ces deux classes de nageurs possèdent une géométrie et un mode d'actionnement différents. Leurs performances sont ainsi comparées
Magnetic microrobots, which swim using bio-inspired propulsion modes, appear very promising for manipulation and characterization of objects at microscopic scale inside confined and very restricted environments, unlike conventional micromanipulation methods. The literature proposes a variety of microrobots with different geometric shapes and magnetic properties. However, the motion controls proposed remain simple, imprecise and insufficiently robust for performing real tasks. In addition, there is still uncertainty that all these artificial microswimmers can accomplish the same tasks with equal performance. The objective of this thesis is thus to propose : generic motion controls by visual servoing in space for all kinds of microswimmers with nonholonomic constraints in order to improve the microswimmer performances, a set of comparison criteria between robots with a different topology or propulsion mode for choosing the most efficient microswimmer in order to perform a specific task. Path following control laws in space are synthesized and experimentally validated on helical and flexible swimmers under different conditions. These robots operate in low Reynolds number fluid, imitating respectively bacteria and spermatozoa and are actuated with uniform magnetic field. These two classes of swimmers have different actuation mode and geometric shape. Their performances are thus compared according to the task to be performed, the environment in which the robots evolve and the manufacturing constraints
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35

Sartori, Paolo. "The Role of Interfaces in Microfluidic Systems: Oscillating Sessile Droplets and Confined Bacterial Suspensions." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3423250.

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This PhD thesis is focused on the role of interfaces that characterize microfluidic systems, such as the free air/liquid interface of drops or the liquid/solid interface of fluids enclosed in microchannels. This work has a twofold character: on one side, we studied the dynamics of sessile drops subject to oscillations of the substrate; on the other, we investigated the spatial concentration distribution of suspensions of motile bacteria, as a model system for active collids, tuned by geometrical confinement. Dynamics of sessile drops. The first topic is related to the field of wetting phenomena and open microfluidics, which deals with the behaviour of drops, typically in the nano-/microliter range, deposited on open surfaces. At such length scale, these systems are dominated by capillarity and may give rise to unexpected effects, not commonly observed at the larger scale we are used to. Our studies aim to the achievement of an active control on the motion and shape of drops by means of vibration of the substrates, for chemical or biological applications. In particular, the motion of liquid drops on an inclined substrate subject to vertical harmonic oscillations have been considered. Typically, small droplets on inclined surfaces remain pinned because of contact angle hysteresis. When vertical oscillations are applied the droplets unpin and slide down. Surprisingly, for sufficiently large oscillation amplitude the droplets move upward against gravity. The systematical investigation of the response of drops on varying peak acceleration and frequency of oscillations, for fluids with different surface tensions and viscosity, allowed the control of the unidimensional motion along the substrate. Then, we have studied the interfacial morphologies of water drops confined on the hydrophilic top face of rectangular posts of width 0.5 mm and various length. For small volumes, the liquid film adopts the shape of a homogeneous filament with a uniform cross section close to a circular segment. For larger volumes, the water interface forms a central bulge, which grows with the volume. In the case of posts longer than a characteristic length, the transition between the two film shapes on varying the volume is discontinuous and exhibits the bistability of the two morphologic states associated with a hysteresis phenomenon. Vertically oscillating the post, with fixed water volume corresponding to the bistability, at certain frequencies induces an irreversible transition from the filament to the bulge state. Self-propelled particles under geometrical confinement. The second topic deals with the behaviour of active fluids, i.e. self-propelled colloid suspensions which are intrinsically out of equilibrium systems (Active Matter). In particular, in the presence of geometrical structures, such systems behave in a very different way with respect to equilibrium Browinan colloids. We have analyzed the role of different swimming patterns on the concentration distribution of bacterial suspensions confined between two flat walls, by considering wild-type E. coli and P. aeruginosa, which perform Run and Tumble and Run and Reverse patterns, respectively. The concentration profiles have been obtained by counting motile bacteria at different distances from the bottom wall. In agreement with previous studies, an accumulation of motile bacteria close to the walls was observed. Different fraction of motile bacteria and different wall separations, ranging from 100 μm to 250 μm, have been tested. The concentration profiles resulted to be independent on the walls separation and on the different kind of motility and to scale with the motile fraction. These results are confirmed by numerical simulations, based on a collection of self-propelled rod-like particles interacting only through steric interactions.
Questa tesi di dottorato prende in esame il ruolo delle interfacce che caratterizzano i sistemi microfluidici, come ad esempio l’interfaccia libera aria/acqua delle gocce o l’interfaccia liquido/solido di fluidi racchiusi in microcanali. Questo lavoro ha un duplice carattere: da una parte, abbiamo studiato la dinamica di gocce sessili soggette ad oscillazioni del substrato; dall’altra, abbiamo investigato come la distribuzione spaziale della concentrazione in sospensioni batteriche, prese come sistema modello per colloidi attivi, venga alterata da un confinamento geometrico. Dinamica di gocce sessili. Il primo argomento rientra nel campo dei fenomeni di bagnabilità e della microfluidica aperta, che tratta il comportamento di gocce, tipicamente nel range dei nano- /microlitri, depositate su superfici aperte. A tali scale di lunghezza, questi sistemi sono dominati dalla capillarità a possono produrre effetti inaspettati che non vengono comunemente osservati alle scale macroscopiche a cui siamo abituati. I nostri studi sono volti al raggiungimento del controllo attivo del moto e della forma delle gocce per mezzo di vibrazioni del substrato, con applicazioni dalla Chimica alla Biologia. In particolare, è stato considerato il moto di gocce su in substrato inclinato sottoposto ad oscillazioni armoniche verticali. Normalmente, su superfici inclinate le goccioline rimangono ferme a causa dell’isteresi dell’angolo di contatto. Quando vengono applicate oscillazioni verticali le goccioline si sbloccano e scivolano giù. Sorprendentemente, per ampiezze di oscillazioni sufficientemente grandi le goccioline si muovono verso l’atro contro la forza di gravità. Un’analisi della risposta delle gocce al variare dell’accelerazione di picco e della frequenza di oscillazione, prendendo in esame fluidi con diverse tensioni superficiali e viscosità, ha permesso il controllo del moto unidimensionale lungo il pianoinclinato. Inoltre, abbiamo studiato le morfologie interfacciali di gocce d’acqua confinate sulla faccia superiore idrofilica di post rettangolari con larghezza 0.5 mm e varie lunghezze. Per piccoli volumi, il film liquido prende la forma di un filamento omogeneo con una cross-section uniforme simile ad un segmento circolare. Per volumi più grandi, l’interfaccia acqua/aria forma un rigonfiamento centrale, che cresce con il volume. Nel caso di post più lunghi di una lunghezza caratteristica, la transizione tra le due forme al variare del volume discontinua e mostra la bistabilità dei due stati morfologici associata ad un fenomeno di isteresi. Applicando al post, con volume d’acqua fissato corrispondente alla bistabilità, vibrazioni verticali con determinate frequenze si più indurre una transizione irreversibile dallo stato di filamento omogeneo a quello rigonfiato. Particelle auto-propulse sotto confinamento geometrico. Il secondo argomento riguarda il comportamento di fluidi attivi, cioè sospensioni di colloidi auto-propulsi che costituiscono sistemi intrinsecamente fuori equilibrio (Materia Attiva). In particolare, in presenza di strutture geometriche, tali sistemi si comportano in modo molto differente rispetto a colloidi Browniani all’equilibrio. Abbiamo analizzato il ruolo di diversi schemi di motilità sulla distribuzione di concentrazione di sospensioni batteriche confinate tra due pareti solide. considerando E. coli a P. aeruginosa wild-type, che si muovono secondo gli schemi Run and Tumble e Run and Reverse, rispettivamente. I profili di concentrazione sono tati ottenuti contando i batteri motili a diverse distanze dalle pareti. In accordo con studi precedenti, si osservato un accumulo di batteri motili in prossimit delle pareti. Sono state testate diverse frazioni di batteri motili e diverse distanze di separazione tra le pareti, nel range tra 100μm e 250 μm. I profili di concentrazione risultano indipendenti dalla distanza tra le pareti e dai differenti schemi di motilità e scalano con la frazione di batteri motili. Questi risultati sono confermati da simulazioni numeriche, basate su una collezione di particelle allungate auto-propulse che interagiscono solo tramite interazioni steriche.
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36

Spelman, Tamsin Anne. "Artificial micro-devices : armoured microbubbles and a magnetically driven cilium." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/269647.

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Micro-devices are developed for uses in targeted drug delivery and microscale manipulation. Here we numerically and analytically study two promising devices in early stages of development. Firstly, we study Armoured Microbubbles (AMBs) which can self-propel as artificial microswimmers or facilitate microfluidic mixing in a channel when held stationary on a wall. Secondly, we study an artificial cilium, which due to its unique design, when placed in an array, easily produces a metachronal wave for fluid transportation. The Armoured Microbubble was designed by our experimental collaborators (group of Philippe Marmottant, University Grenoble Alpes) and consists of a partial hollow sphere, inside which a bubble is caught. Under ultrasound the bubble oscillates, generating a streaming flow in the surrounding fluid and producing a net force. Motivated by the AMB but considering initially a general setup, using matched asymptotic expansions we calculate the streaming flow around a spherical body undergoing arbitrary, but known, small-amplitude surface shape oscillations. We then specialise back to the AMB and consider its excitation under ultrasound, using a potential flow model with mixed boundary conditions, to identify the resonant frequencies and mode shapes, including the dependence of the resonance on the AMB shape parameters. Returning to our general streaming model, we applied the mixed boundary conditions directly to this model, calculating the streaming around the AMB, in good agreement with experiments. Using hydrodynamic images and linear superposition, this model was extended to incorporate one wall, and AMB compounds. We then study the streaming flows generated by arrays of AMBs in confined channels, by modelling each AMB as its leading order behaviour (with corrections where required) and superposing the individual flow fields of all the AMBs. We identified the importance of two confining walls on the streaming flow around the array, and compared these flows to experiments in five cases. Motivated by this setup, we theoretically considered the extension of a two fluid interface passing through an AMB array to quickly identify good AMB arrays for mixing. We then studied the second artificial micro-device: an artificial cilium. Tsumori et. al. produced a cilium of PDMS containing aligned ferromagnetic filings, which beat under a rotating magnetic field. We modelled a similar cilium but assumed paramagnetic filings, using a force model balancing elastic, magnetic and hydrodynamic forces identifying the cilium beat pattern. This agreed with our equilibrium model and asymptotic analysis. We then successfully identified that the cilium applies the most force to the surrounding fluid at an intermediate value of the two dimensionless numbers quantifying the dynamics.
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37

Martin, Matthieu. "Etude des processus de concentration et de dispersion d'une suspension de micro-algues : effet des interactions hydrodynamiques sur la dynamique de la suspension." Thesis, Université Grenoble Alpes (ComUE), 2017. http://www.theses.fr/2017GREAY008/document.

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Le sujet de cette thèse s'inscrit dans le cadre de l'étude de la matière active. Ces systèmes sont composés de "particules actives" capables de s'organiser spontanément (transition de phase), et de manière autonome (sans application d'un champs extérieur), créant ainsi des dynamiques complexes comme les transition de phase dynamiques, synchronisation, instabilités etc...De nombreuses études tendent à montrer le rôle important des interactions entre particules active dans l'émergence de ces dynamiques. Nous avons abordé ces questions à travers l'étude d'une suspension de micro-algues Chlamydomonas reinhardtii. Il s'agit d'un système modèle de micro-nageur couramment utilisé pour l'étude des suspensions actives. Nous avons notamment étudié un phénomène de migration spontanée de la suspension, permettant de concentrer des micro-algues grâce à une source de lumière. Puis nous avons étudié le processus de dispersion d'un amas concentré de micro-algues. Nous avons notamment mis en évidence le rôle des interactions hydrodynamiques entre micro-algues dans cette dynamique de dispersion
The subject of this thesis is part of the study of the active matter. These systems are composed of "active particles" capable of organizing themselves spontaneously (phase transition), and autonomously (without application of an external field), thus creating complex dynamics such as dynamical phase transition, synchronization, instabilities etc ...Numerous studies tend to show the important role of interactions between active particles in the emergence of these dynamics. We have addressed these issues through the study of a suspension of microalgae Chlamydomonas reinhardtii. It is a model system of micro-swimmer commonly used for the study of active suspensions. We studied in particular a phenomenon of spontaneous migration of the suspension, allowing to concentrate micro-algae thanks to a light source. We then studied the dispersal process of a concentrated bloom of microalgae. In particular, we have highlighted the role of hydrodynamic interactions between micro-algae in this dispersion dynamics
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38

Katsamba, Panayiota. "Biophysics of helices : devices, bacteria and viruses." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/283006.

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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.
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39

Wu, Kuan-Ting, and 吳冠廷. "Accumulation of microswimmers near a no-slip surface." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/67s7se.

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碩士
國立中央大學
物理學系
105
Microbial processes including biofilm formation or bio-fouling are ubiquitous and influence human extensively from daily lives to various industrial systems. For decades, researchers studied the processes and strategies of bacteria accumulation on surfaces. Considering the initial stage of biofilm formation, before the cell adhesion, swimming cells were reported swim along the surface for a long time. To describe the phenomenon, models of different perspectives of physics had been established, including far and near field hydrodynamic, steric effects and diffusion. To reach a more complete picture for the cell-surface interaction, we manipulated the swimming characteristic of single polar-flagellated bacteria, Vibrio. Alginolyticus, with mutant strains at different swimming speed. Observing the steady-state bacteria distribution within 20µm from a surface, contributions of each mechanism can be evaluated. Our results show that surface accumulation of microswimmers depends on both swimming speed and swimming characteristic. Accumulation of pusher bacteria is reduced as the speed increases. In contrast, accumulation of puller bacteria increases strongly with the speed. None of a previous model can fully explain our observations. By a closer look, the contribution of each mechanisms are assigned. Finally, we show that a microswimmer in nature can accumulate near a surface by a run and reverse swimming characteristic.
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40

Krüger, Carsten. "Liquid Crystal Microswimmers - from single entities to collective dynamics." Doctoral thesis, 2016. http://hdl.handle.net/11858/00-1735-0000-002B-7CA4-2.

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41

Sandoval, Bojorquez Diana Isabel. "Microswimmer-driven agglutination assay." 2019. https://tud.qucosa.de/id/qucosa%3A71668.

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Lab-on-a-chip systems for point-of-care testing demonstrate a promising development towards more accurate diagnostic tests that are of extreme importance for the future global health. This work presents an agglutination assay performed in micrometer sized well using Janus PS/Ag/AgCl micromotors to enhance the interactions between goat anti-human IgM functionalized particles and Human IgM. The fabricated microwell chips are a suitable platform to analyze the interaction between different particles and to perform the agglutination assays. The interaction between active Janus particles and passive and functionalized particles is studied, as well as the influence of ions on the motion of the Janus particles. Agglutination assays are performed with and without the presence of Janus particles, and in different PBS concentrations. Once illuminated with blue light, passive SiO2 particles were effectively excluded from Janus particles, while SiO2 NH2 particles revealed attraction. In contrast, functionalized SiO2 NH2 Ab particles suspended in PBS did not show any interaction. It was found that the optimal working conditions for antibodies and Janus particles differed and, as a result, the Janus particles did not reveal a desirable interaction between the functionalized particles and IgM. Further experiments should be performed to find the proper conditions in which the antibodies and the Janus particles maintain their activities. It is believed that an effective interaction between the functionalized and Janus particles could be achieved by modifying the parameters that affect their interaction such as the zeta potential and the medium in which the assay is being performed. This preliminary work provides the first steps towards the development of a fully integrated lab on a chip system for point of care testing.:Abstract ........................................................................................................................ iii Acknowledgments.......................................................................................................... v Table of Contents .......................................................................................................... vi List of Tables ............................................................................................................. viii List of Figures ............................................................................................................... ix Abbreviations ................................................................................................................. x 1. Introduction ............................................................................................................ 1 1.1 In vitro diagnostic tests ........................................................................................ 1 1.1.1 Point-of-care tests ......................................................................................... 2 1.2 Agglutination assay .............................................................................................. 2 1.3 Lab-on-a-chip ....................................................................................................... 5 1.4 Self-propelled particles ........................................................................................ 6 1.4.1 Light-driven Ag/AgCl micromotors ............................................................. 6 1.5 Aim ...................................................................................................................... 9 2. Materials and Methods ......................................................................................... 11 2.1 Microwell fabrication .................................................................................... 11 2.2 Microswimmers fabrication .......................................................................... 12 2.3 Functionalization of particles ........................................................................ 12 2.4.1 Scanning electron microscope ............................................................... 14 2.4.2 UV-vis spectroscopy .............................................................................. 14 2.4.3 Zeta potential ......................................................................................... 14 2.4.4 Optical microscopy ................................................................................ 15 2.5 Motion Experiments ...................................................................................... 15 2.6 Agglutination assay ....................................................................................... 16 2.7 Effect of PBS ................................................................................................. 16 2.7.1 Janus particles ........................................................................................ 16 2.7.2 Agglutination assay ................................................................................ 17 2.7.3 Exclusion of functionalized particles ..................................................... 17 3. Results and Discussion ........................................................................................ 18 3.1 Microwell chip with integrated Janus particles ................................................. 18 3.2 Characterization of particles .............................................................................. 19 3.2.1 UV-vis spectroscopy ................................................................................... 19 3.2.2 Zeta potential .............................................................................................. 21 3.2.3 Agglutination assay in PEG-covered glass slides ....................................... 22 3.3 Motion experiments ........................................................................................... 23 3.3.1 Exclusion time ............................................................................................ 23 3.3.2 On/off light cycles....................................................................................... 26 3.4 Agglutination assay ............................................................................................ 28 3.4.1 Assay performed in wells............................................................................ 28 3.4.2 Assay performed in wells with Janus particles ........................................... 29 3.5 Effect of PBS concentration............................................................................... 30 3.5.1 Janus particles ............................................................................................. 30 3.5.2 Agglutination assay ..................................................................................... 32 3.5.3 Exclusion of functionalized particles .......................................................... 33 4. Conclusions .......................................................................................................... 35 References .................................................................................................................... 37 Declaration of Research Integrity and Good Scientific Practice ................................. 42
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42

Mokhtari, Zahra. "Study of active particles in heterogeneous media." Doctoral thesis, 2018. http://hdl.handle.net/11858/00-1735-0000-002E-E4A1-8.

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43

Thutupalli, Shashi. "Towards autonomous soft matter systems: Experiments on membranes and active emulsions." Doctoral thesis, 2011. http://hdl.handle.net/11858/00-1735-0000-0006-B530-E.

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44

Breier, Rebekka Elisabeth. "Three-dimensional nonequilibrium steady state of active particles: symmetry breaking and clustering." Doctoral thesis, 2017. http://hdl.handle.net/11858/00-1735-0000-0023-3EC4-6.

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45

Klindt, Gary. "Hydrodynamics of flagellar swimming and synchronization." Doctoral thesis, 2017. https://tud.qucosa.de/id/qucosa%3A29698.

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What is flagellar swimming? Cilia and flagella are whip-like cell appendages that can exhibit regular bending waves. This active process emerges from the non-equilibrium dynamics of molecular motors distributed along the length of cilia and flagella. Eukaryotic cells can possess many cilia and flagella that beat in a coordinated fashion, thus transporting fluids, as in mammalian airways or the ventricular system inside the brain. Many unicellular organisms posses just one or two flagella, rendering them microswimmers that are propelled through fluids by the flagellar beat including sperm cells and the biflagellate green alga Chlamydomonas. Objectives. In this thesis in theoretical biological physics, we seek to understand the nonlinear dynamics of flagellar swimming and synchronization. We investigate the flow fields induced by beating flagella and how in turn external hydrodynamic flows change speed and shape of the flagellar beat. This flagellar load-response is a prerequisite for flagellar synchronization. We want to find the physical principals underlying stable synchronization of the two flagella of Chlamydomonas cells. Results. First, we employed realistic hydrodynamic simulations of flagellar swimming based on experimentally measured beat patterns. For this, we developed analysis tools to extract flagellar shapes from high-speed videoscopy data. Flow-signatures of flagellated swimmers are analysed and their effect on a neighboring swimmer is compared to the effect of active noise of the flagellar beat. We were able to estimate a chemomechanical energy efficiency of the flagellar beat and determine its waveform compliance by comparing findings from experiments, in which a clamped Chlamydomonas is exposed to external flow, to predictions from an effective theory that we designed. These mechanical properties have interesting consequences for the synchronization dynamics of Chlamydomonas, which are revealed by computer simulations. We propose that direct elastic coupling between the two flagella of Chlamydomonas, as suggested by recent experiments, in combination with waveform compliance is crucial to facilitate in-phase synchronization of the two flagella of Chlamydomonas.:1 Introduction 1.1 Physics of cell motility: flagellated swimmers as model system 2 1.1.1 Tissue cells and unicellular eukaryotic organisms have cilia and flagella 2 1.1.2 The conserved architecture of flagella 3 1.1.3 Synchronization in collections of flagella 5 1.2 Hydrodynamics at the microscale 9 1.2.1 Navier-Stokes equation 10 1.2.2 The limit of low Reynolds number 10 1.2.3 Multipole expansion of flow fields 11 1.3 Self-propulsion by viscous forces 13 1.3.1 Self propulsion requires broken symmetries 13 1.3.2 Signatures of flowfields: pusher & puller 15 1.4 Overview of the thesis 16 2 Flow signatures of flagellar swimming 2.1 Self-propulsion of flagellated swimmers 20 2.1.1 Representation of flagellar shapes 20 2.1.2 Computation of hydrodynamic friction forces 21 2.1.3 Material frame and rigid-body transformations 22 2.1.4 The grand friction matrix 23 2.1.5 Dynamics of swimming 23 2.2 The hydrodynamic far field: pusher and puller 26 2.2.1 The flow generated by a swimmer 26 2.2.2 Force dipole characterization 27 2.2.3 Flagellated swimmers alternate between pusher and puller 29 2.2.4 Implications for two interacting Chlamydomonas cells 31 2.3 Inertial screening of oscillatory flows 32 2.3.1 Convection and oscillatory acceleration 33 2.3.2 The oscilet: fundamental solution of unsteady flow 35 2.3.3 Screening length of oscillatory flows 35 2.4 Energetics of flagellar self-propulsion 36 2.4.1 Impact of inertial screening on hydrodynamic dissipation 37 2.4.2 Case study: the green alga Chlamydomonas 38 2.4.3 Discussion: evolutionary optimization and the number of molecular motors 38 2.5 Summary 39 3 The load-response of the flagellar beat 3.1 Experimental collaboration: flagellated swimmers exposed to flows 41 3.1.1 Description of the experimental setup 42 3.1.2 Computed flow profile in the micro-fluidic device 43 3.1.3 Image processing and flagellar tracking 43 3.1.4 Mode decomposition and limit-cycle reconstruction 47 3.1.5 Changes of limit-cycle dynamics: deformation, translation, acceleration 49 3.2 An effective theory of flagellar oscillations 50 3.2.1 A balance of generalized forces 50 3.2.2 Hydrodynamic friction in generalized coordinates 51 3.2.3 Intra-flagellar friction 52 3.2.4 Calibration of active flagellar driving forces 52 3.2.5 Stability of the limit cycle of the flagellar beat 53 3.2.6 Equations of motion 55 3.3 Comparison of theory and experiment 56 3.3.1 Flagellar mean curvature 57 3.3.2 Susceptibilities of phase speed and amplitude 57 3.3.3 Higher modes and stalling of the flagellar beat at high external load 59 3.3.4 Non-isochrony of flagellar oscillations 63 3.4 Summary 63 4 Flagellar load-response facilitates synchronization 4.1 Synchronization to external driving 65 4.2 Inter-flagellar synchronization in the green alga Chlamydomonas 67 4.2.1 Equations of motion for inter-flagellar synchronization 68 4.2.2 Synchronization strength for free-swimming and clamped cells 70 4.2.3 The synchronization strength depends on energy efficiency and waveform compliance 73 4.2.4 The case of an elastically clamped cell 74 4.2.5 Basal body coupling facilitates in-phase synchronization 75 4.2.6 Predictions for experiments 78 4.3 Summary 80 5 Active flagellar fluctuations 5.1 Effective description of flagellar oscillations 84 5.2 Measuring flagellar noise 84 5.2.1 Active phase fluctuations are much larger than thermal noise 84 5.2.2 Amplitude fluctuations are correlated 85 5.3 Active flagellar fluctuations result in noisy swimming paths 86 5.3.1 Effective diffusion of swimming circles of sperm cell 86 5.3.2 Comparison of the effect of noise and hydrodynamic interactions 87 5.4 Summary 88 6 Summary and outlook 6.1 Summary of our results 89 6.2 Outlook on future work 90 A Solving the Stokes equation A.1 Multipole expansion 95 A.2 Resistive-force theory 96 A.3 Fast multipole boundary element method 97 B Linearized Navier-Stokes equation B.1 Linearized Navier-Stokes equation 101 B.2 The case of an oscillating sphere 102 B.3 The small radius limit 103 B.4 Greens function 104 C Hydrodynamic friction C.1 A passive particle 107 C.2 Multiple Particles 107 C.3 Generalized coordinates 108 D Data analysis methods D.1 Nematic filter 111 D.1.1 Nemat 111 D.1.2 Nematic correlation 111 D.2 Principal-component analysis 112 D.3 The quality of the limit-cycle projections of experimental data 113 E Adler equation F Sensitivity analysis for computational results F.1 The distance function of basal coupling 117 F.2 Computed synchronization strength for alternative waveform 118 F.3 Insensitivity of computed load-response to amplitude correlation time 118 List of Symbols List of Figures Bibliography
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46

Ghosh, Arijit. "Dynamics, Fluctuations and Rheological Applications of Magnetic Nanopropellers." Thesis, 2014. http://etd.iisc.ac.in/handle/2005/2984.

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Micron scale robots going inside our body and curing various ailments is a technolog¬ical dream that easily captures our imagination. However, with the advent of novel nanofabrication and nanocharacterization tools there has been a surge in the research in this field over the last decade. In order to achieve locomotion (swim) at these small length scales, special strategies need to be adopted, that is able to overcome the large viscous damping that these microbots have to face while moving in the various bod¬ily fluids. Thus researchers have looked into the swimming strategies found in nature like that of bacteria like E.coli found in our gut or spermatozoa in the reproductive mucus. Biomimetic swimmers that replicate the motion of these small microorganisms hold tremendous promise in a host of biomedical applications like targeted drug delivery, microsurgery, biochemical sensing and disease diagnosis. In one such method of swimming at very low Reynolds numbers, a micron scale helix has been fabricated and rendered magnetic by putting a magnetic material on it. Small rotating magnetic fields could be used then to rotate the helix, which translated as a result of the intrinsic translation rotation coupling in a helix. The present work focussed on the development of such a system of nanopropellers, a few microns in length, the characterization of its dynamics and velocity fluctuations originating from thermal noise. The work has also showed a possible application of the nanopropellers in microrheology where it could be used as a new tool to measure the rheological characteristics of a complex heterogeneous environment with very high spatial and temporal resolutions. A generalized study of the dynamics of these propellers under a rotating field, has showed the existence of a variety of different dynamical configurations. Rigid body dynamics simulations have been carried out to understand the behaviour. Significant amount of insight has been gained by solving the equations of motion of the object analytically and it has helped to obtain a complete understanding, along with providing closed form expressions of the various characteristics frequencies and parameters that has defined the motion. A study of the velocity fluctuations of these chiral nanopropellers has been carried out, where the nearby wall of the microfluidic cell was found to have a dominant effect on the fluctuations. The wall has been found to enhance the average level of fluctuations apart from bringing in significant non Gaussian effects. The experimentally obtained fluctuations has been corroborated by a simulation in which a time evolution study of the governing 3D Langevin dynamics equations has been done. A closer look at the various sources of velocity fluctuations and a causality study thereof has brought out a minimum length scale below which helical propulsion has become impractical to achieve because of the increased effect of the orientational fluctuations of the propeller at those small length scales. An interesting bistable dynamics of the propeller has been observed under certain experimental conditions, in which the propeller randomly switched between the different dynamical states. This defied common sense because of the inherent deterministic nature of the governing Stokes equation. Rigid body dynamics simulations and stability analysis has shown the existence of time scales in which two different dynamical states of the propeller have become stable. Thus the intrinsic dynamics of the system has been found to be the reason behind the bistable behaviour, randomness being brought about by the thermal fluctuations present in the system. Finally, in a novel application of the propellers, they have been demonstrated as a tool for microrheological mapping in a complex fluidic environment. The studies done in this work have helped to develop this method of active microrheology in which the measurement times are orders of magnitude smaller than its existing counterparts.
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47

Ghosh, Arijit. "Dynamics, Fluctuations and Rheological Applications of Magnetic Nanopropellers." Thesis, 2014. http://hdl.handle.net/2005/2984.

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Abstract:
Micron scale robots going inside our body and curing various ailments is a technolog¬ical dream that easily captures our imagination. However, with the advent of novel nanofabrication and nanocharacterization tools there has been a surge in the research in this field over the last decade. In order to achieve locomotion (swim) at these small length scales, special strategies need to be adopted, that is able to overcome the large viscous damping that these microbots have to face while moving in the various bod¬ily fluids. Thus researchers have looked into the swimming strategies found in nature like that of bacteria like E.coli found in our gut or spermatozoa in the reproductive mucus. Biomimetic swimmers that replicate the motion of these small microorganisms hold tremendous promise in a host of biomedical applications like targeted drug delivery, microsurgery, biochemical sensing and disease diagnosis. In one such method of swimming at very low Reynolds numbers, a micron scale helix has been fabricated and rendered magnetic by putting a magnetic material on it. Small rotating magnetic fields could be used then to rotate the helix, which translated as a result of the intrinsic translation rotation coupling in a helix. The present work focussed on the development of such a system of nanopropellers, a few microns in length, the characterization of its dynamics and velocity fluctuations originating from thermal noise. The work has also showed a possible application of the nanopropellers in microrheology where it could be used as a new tool to measure the rheological characteristics of a complex heterogeneous environment with very high spatial and temporal resolutions. A generalized study of the dynamics of these propellers under a rotating field, has showed the existence of a variety of different dynamical configurations. Rigid body dynamics simulations have been carried out to understand the behaviour. Significant amount of insight has been gained by solving the equations of motion of the object analytically and it has helped to obtain a complete understanding, along with providing closed form expressions of the various characteristics frequencies and parameters that has defined the motion. A study of the velocity fluctuations of these chiral nanopropellers has been carried out, where the nearby wall of the microfluidic cell was found to have a dominant effect on the fluctuations. The wall has been found to enhance the average level of fluctuations apart from bringing in significant non Gaussian effects. The experimentally obtained fluctuations has been corroborated by a simulation in which a time evolution study of the governing 3D Langevin dynamics equations has been done. A closer look at the various sources of velocity fluctuations and a causality study thereof has brought out a minimum length scale below which helical propulsion has become impractical to achieve because of the increased effect of the orientational fluctuations of the propeller at those small length scales. An interesting bistable dynamics of the propeller has been observed under certain experimental conditions, in which the propeller randomly switched between the different dynamical states. This defied common sense because of the inherent deterministic nature of the governing Stokes equation. Rigid body dynamics simulations and stability analysis has shown the existence of time scales in which two different dynamical states of the propeller have become stable. Thus the intrinsic dynamics of the system has been found to be the reason behind the bistable behaviour, randomness being brought about by the thermal fluctuations present in the system. Finally, in a novel application of the propellers, they have been demonstrated as a tool for microrheological mapping in a complex fluidic environment. The studies done in this work have helped to develop this method of active microrheology in which the measurement times are orders of magnitude smaller than its existing counterparts.
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48

Mondal, Debasmita. "Role of Friction in Microswimmer and Active Filament Motion." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5634.

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Friction is pervasive in all fields of science. It is the key factor that emerging technologies involving autonomous motion at micron scales such as micro-bots need to overcome in order to be efficient. They fall in the new paradigm of active matter which in its scope also covers the biological world. In this talk, I will present my thesis work on the role of frictional stresses in the motion of two model biological systems: (a) a microswimmer, Chlamydomonas which swims through the fluid by using the motion of its two anterior flagella/cilia, and (b) an active filament, the cell-free isolated cilium from the same microswimmer and reactivated in the presence of an external energy source. These prototypical active systems, driven by oscillatory motion of the cilia, generate fluid motion at the micron-scale. Naturally, these systems operating in low Reynolds number regime are expected to be governed by the ambient fluid friction. We, therefore, explore the role of hydrodynamics and other sources of friction, if any, in these model systems through simultaneous measurements of their motion and flow fields. In the first part of my thesis, I discuss the role of confinement in coupling cell motility and fluid flow of the microswimmer. Extreme confinement of this swimmer between rigid boundaries often arises in natural and technological contexts, yet measurements of its mechanics in this regime are absent. We show that strongly confining Chlamydomonas between two parallel plates not only inhibits its motility but also leads, for purely mechanical reasons, to inversion of the surrounding vortex flows due to contact friction with the walls. This contrasts with expectations based on the source-dipole description of confined swimmers. Insights from the experiment lead to a simplified theoretical description of flow fields based on a quasi-2D Brinkman approximation to the Stokes equation than the usual method of recursive images. We argue that this vortex flow inversion provides the advantage of enhanced fluid mixing despite higher friction. In the second part of the thesis, I study the mechanics of the active cilium which undergoes spontaneous oscillations by continuously consuming chemical energy and dissipating them through mechanical motion. Therefore, stable oscillations require that the elastic stresses due to the active energy input must be balanced by a significant source of dissipation. Conventionally, it stems from the external fluid. We show, in contrast, that external fluid friction is negligibly small to counteract the passive elastic stresses within the isolated and active Chlamydomonas cilium beating near the instability threshold. Consequently, internal friction emerges as the sole source of dissipation for ciliary oscillations. We combine these experimental insights with theoretical modeling of active filaments to show that an instability to oscillations takes place when active stresses are strain softening and shear thinning. Together, these results demonstrate that it is not always the external fluid friction, but friction from the external boundaries as well as internal degrees of freedom, which govern confined microswimmer motion and active ciliary oscillations, respectively.
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49

CARMONA, SOSA Viridiana. "3D microstructures for active and soft matter studies." Doctoral thesis, 2021. http://hdl.handle.net/11573/1563050.

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Microfabrication techniques have opened up new ways to study the dynamics of microsystems expanding the range of applications in microengineering and cell biology. Among three-dimensional microfabrication techniques, two-photon polymerization enjoys a unique set of characteristics that make it appealing for designing complex structures of arbitrary form. During the last decades, two-photon polymerization has evolved from the first structure fabricated with this technique, a coil with a diameter of 7 μm and a total length of approximately 34 μm (by Maruo et al.), to generate sophisticated systems like remotely driven micromachines. In the present thesis, we address two main applications of microfabrication. On the first line of research, the design, and fabrication of efficient and self-powered micro-robots have been a very active research topic. Motile micro-organisms like E. coli may provide an optimal solution to generate propulsion in artificial microsystems. It has been demonstrated that microstructures can be transported when released on a layer of swarming bacteria, suspended in a bacterial bath, or covered by surface adhering bacteria. Although it is possible to obtain a net movement in the mentioned cases, the displacement is stochastic and self-propulsion characteristics are hard to reproduce. In this thesis, we investigate possible design strategies for bio-hybrid micro shuttles having a defined number of propelling units that self-assemble onto precisely defined locations. One of the biggest issues involved in the optimization design process of the microshuttles is an irreversible adhesion of structures in the substrate, which often is caused by Van der Waals attraction. To overcome this problem we use different stabilization methods with unsuccessful results. Looking for a less invasive and biocompatible strategy we investigate the possibility of changing the sign of Van der Walls forces turning them from attractive to repulsive. To this aim, we develop a method that demonstrates to reduce the adhesion observed before. So, the final design aims at minimizing friction and adhesion with the substrate while optimizing propulsion speed and self-assembly efficiency. Finally, using a mutated strain of E. coli the microshuttle can be remotely controlled by dynamic structured light patterns for reaching an optimal control of the motion of the structures. In a different direction of microfabrication applications, 3D microstructures can also offer new opportunities to address more fundamental problems in the soft matter dynamic. On this second line of research, we have designed and used complex 3D microstructures to investigate the Brownian dynamics and hydrodynamics of propeller shaped particles, as well as to probe effective interactions in colloidal systems, like critical Casimir forces. In the dynamics of microhelices we use optical tweezers to study the mechanic and hydrodynamic properties of micro-fabricated helices suspended in a fluid. For the case of rigid helices, we track Brownian fluctuations around mean values with a high precision and over a long observation time. Through the statistical analysis of fluctuations in translational and rotational coordinates, we recover the full mobility matrix of the micro-helix including the off diagonal terms related with roto-translational coupling. Exploiting the high degree of spatial control provided by optical trapping, we can systematically study the effect of a nearby wall on the roto-translational coupling, and conclude that a rotating helical propeller moves faster near a no-slip boundary. We also study the relaxation dynamics of deformable micro-helices stretched by optical traps. We find that hydrodynamic drag only weakly depends on elongation resulting in an exponential relaxation to equilibrium. In connection with the versatility of microfabrication by two-photon polymerization, we find the study of interaction in colloidal systems. At macroscopic scales, thermal fluctuations of a physical property on a system are typically negligible, but at the micrometer and nanometer scales instead, fluctuations become generally relevant and they give rise to novel and intriguing phenomena such as critical Casimir effect. Critical Casimir forces are induced between colloidal objects suspended in a critical binary mixture undergoing strong thermal fluctuations. So far, most of the experiments and proposed models consider the interaction between simple geometrical objects such as two spheres, or a single sphere and a plate. In the last part of this thesis, we propose a novel 3D printed microprobes consisting of the main body and two handles that can be optically trapped to directly measure effective forces and torques between colloidal objects with non spherical shapes. The organization of this thesis is as follows. Chapter 1 gives a general introduction to the physical phenomenon behind the 3D microfabrication technique employed in our experiments, two-photon polymerization. We describe the differences between two phenomena: single-photon absorption and two-photon absorption, and explain the effectiveness of using two-photon polymerization for reaching a resolution of 100 nanometers in microfabrication. Then we present an experimental characterization of the voxel size of our custom-built two-photon polymerization set-up. We explain the sample preparation steps for microfabrication as well as the development of an innovative low-refractive index layer for eliminating irreversible adhesion of SU-8 microstructures. Chapter 2 provides a general introduction to E. coli motility, the propulsion mechanism of these bacteria, and the circular trajectory developed by the microorganism when swimming near a rigid boundary. Besides, we briefly explain the possibility of using synthetic biology to obtain light-driven strains of E. coli by the expression of Proteorhodopsin on the bacteria membrane. In Chapter 3 we combine two-photon polymerization technique and genetically modified bacteria to create a biohybrid microshuttle. We start with a basic microshuttle design whose propulsion is obtained from four E. coli bacteria. After integrating ramps in another microshuttle model for minimizing the circular trajectory showed in the microstructure trajectory, we make major changes in the distribution of microchambers inside the last model named catamaran microshuttle. Exploiting the ability of a mutated strain of E. coli expressing proteorhodopsin, we successfully control the microrobot steering by illuminating our sample with green light patterns. In Chapter 4 we design and use 3D microhelices from two different materials to investigate, through optical tweezers, Brownian dynamics, and hydrodynamics of this kind of chiral particles. Through the statistical analysis of fluctuations in translational and rotational coordinates, we study the roto-translational coupling element from the mobility matrix of the micro-helix. Besides, we conclude that a rotating helical propeller moves faster near a no-slip boundary. For the case of a deformable micro=helix, we find that hydrodynamic drag only depends on its elongation. Finally, Chapter 5 presents the design for a microprobe to measure critical Casimir forces using holographic optical tweezers. We show a characterization experiment for a micro-cube with two handles, concluding that a third handle will improve the stability of a microprobe inside the sample.
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50

(8816204), Nathaniel H. Brown. "Self-propulsion of Contaminated Microbubbles." Thesis, 2020.

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In many natural and industrial processes, bubbles are exposed to surface-active contaminants (surfactants) that may cover the whole or part of the bubble interface. A partial coverage of the bubble interface results in a spontaneous self-propulsion mechanism, which is yet poorly understood.
The main goal of this study is to enhance the understanding of the flow and interfacial mechanisms underlying the self-propulsion of small surfactant contaminated bubbles. The focus is on characterizing the self-propulsion regimes generated by the presence of surface-active species, and the influence of surfactant activity and surface coverage on the active bubble motion.
The study was developed by simultaneously solving the full system of partial differential equations governing the free-surface flow physics and the surfactant transport on the deforming bubble interface using multi-scale numerical simulation.
Results show in microscopic detail how surface tension gradients (Marangoni stresses) induced by the uneven interfacial coverage produce spontaneous hydrodynamics flows (Marangoni flows) on the surrounding liquid, leading to bubble motion. Results also establish the influence of both surfactant activity and interfacial coverage on total displacement and average bubble velocity at the macroscale.
Findings from this research improve the fundamental understanding of the free-surface dynamics of self-propulsion and the associated transport of surface-active species, which are critical to important natural and technological processes, ranging from the Marangoni propulsion of microorganisms to the active motion of bubbles and droplets in microfluidic devices. Overall, the findings advance our understanding of active matter behavior; that is, the behavior of material systems with members able to transduce surface energy and mass transport into active movement.
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