Several species of fish swim upstream into the area of greatest turbulence in artificially created currents of water. This reaction is most pronounced with young salmon and trout. Treatment with thyroxine, testosterone and three oestrogen compounds slightly increases the rate at which coho and sockeye salmon smolt jump upstream over a dam. Elevated temperatures increase the amount of negative rheotaxis shown by chum fry and coho smolt in circular currents. / Science, Faculty of / Zoology, Department of / Graduate

Thesis (Ph. D.)--University of Chicago, 1912. / "Reprinted from the Journal of experimental zoology, vol. 13, no. 2, August 1912." Bibliography: p. 343-344.

Behaviour to increased water velocity is examined in fast stream fish (Otocinclus, Hypostomus, Pterygoplichthys, Chaetostoma and Gyrinocheilus) and a slow water form (Farlowella). Behaviour can be divided into two stages; resting and adhesion (Chapter I). In Otocinclus a third fin extension stage is apparent. Based on the slipping velocity of live and dead fish it is determined that Gyrinocheilus has the greatest station holding ability on a smooth perspex surface. This is attributed to a complete seal produced by its oral sucker lips (closed sucker). Station-holding ability is also examined on rougher surfaces. Slipping does not occur in any of the genera at water velocities up to 90 cm s⁻¹. Morphological adaptations (eg. oral sucker, pectoral fins, frictional pad and odontodes) that may contribute to increasing slipping velocity are examined. In Otocinclus these structures are analyzed using a Scanning Electron Microscope. Otocinclus is the only genera with the ventral dermal plates between the pelvic and pectoral fins organized laterally into a frictional pad. Drag on fish is directly measured with strain gauges and used to calculate drag coefficients (0.10 - 0.94; Chapter II). Drag coefficients for low fineness ratio (length/height < 10) forms at Reynold's numbers below 10⁴ compare poorly with literature values for technical bodies. Drag coefficients determined for fish are high due to roughness and interference drag produced by the fins. Using morphological measurements, dead slipping velocities, drag coefficients, static frictional coefficients and submerged body weight, lift coefficients (-0.55 - 1.23) calculated. Fast stream fish maximize slipping speed by having high frictional coefficients (0.67 - 0.95, on a smooth perspex surface), density (1.03 -1.10 g cm⁻³), rheotactic suction pressure (13 - 173 N m⁻²) and negative lift Although Farlowella has high density (1.129 g cm⁻³) and a low drag coefficient (0.23), its lift to drag ratio is high (6.71) and rheotactic suction pressures (2 - 27 N m⁻²) are low. In general Farlowella does not exhibit hydrodynamic, behavioural or morphological characteristics that enhance station-holding. / Science, Faculty of / Zoology, Department of / Graduate

No description available.

No description available.

Swimming is a fundamental feature in many living systems. Biological microorganisms move in the search of food, appropriate pH, temperature, mate and for many other elements crucial for life. A classic example is sperm cell, which travels thousands of its body length in the complex genital tract of females to reach the egg. Inspired by such unique character and diversified motion abilities of the biological world, researchers have always been intrigued to create small artificial microbots which could swim and perform complex tasks. In his famous talk ’There is plenty of room at the bottom’ in 1960, Richard Feynman suggested designing swallowable doctors which could travel in the blood vessels and perform the surgery. Although seemingly exquisite and far-fetched, this idea laid the foundation stone to pave the path towards building autonomously propelled artificial machines with applications ranging from targeted drug delivery to environmental remediation. However, considerable challenges are yet to be addressed before developing fully functional artificial machines, especially in the biomedical applications. For instance, directed transport in vivo, using man-made artificial machines face many obstacles starting from their fabrication, fuels for powering them and their interactions with the surroundings. Rapid changes in the environment in vivo, would make it difficult in selecting the ideal material and shape design of the microswimmer and would most probably require a flexible structure which could potentially squeeze itself and easily pass through small cavities. With most of the swimmers, in the past, being designed from inorganic materials, leave them unsuitable for biological applications. In addition, the environments inside an animal body is dominated by various complexity such as flows of bodily fluids, cavities and soft tissues. In laboratory settings, often these peculiarities are ignored as mostly the motion behavior is tested in stagnant conditions on solid substrates and it is unclear how would an artificial machine will behave in such complex environments. In this thesis, we combined the advances in microfluidics to benefit the microswimmer research manifold. In the last few years, microfluidics and micromotors have been used together in various instances because of their co-sharing regime of low Reynolds number and excellent fluid manipulation abilities at the microscale. In addition, microfluidics offer unique opportunities in designing structures with well-engineered shapes. With these points in mind, in this thesis, we used microfluidics to fabricate microswimmers and design custom made environments to mimic the complexity present in vivo, and to study the feedback of artificial swimmers in them. Specifically, in the first part of the thesis, two microfluidic strategies namely droplet microfluidics and stop-flow lithography were investigated to design hydrogel-based micromotors. Besides, in the next part, we developed complex environments and studied the motion behavior of conventional microswimmers in them. In the first subpart of the thesis, using droplet microfluidics, we designed polyacrylamide and poly (ethylene glycol) diacrylate (PEGDA) based Janus droplets using co-flowing phases with enzyme immobilized in one of the phases to confer asymmetry. The droplets were polymerized on-chip using UV polymerization. We found that the polyacrylamide and PEGDA 565 particles did not result into efficient bubble production when suspended in H2O2 solution and we explain this behaviour using the analogy of smaller pore size and possible poisoning of the enzyme by acrylamide. But, when a 10 v/v% PEGDA 700 was selected as the polymer material, it resulted in very efficient bubble evolution, although the Janus geometry was compromised which restricted swimming for these particles. The second subpart dealt with applying stop-flow lithography technique for designing hydrogel micromotors with different shapes and these shapes corresponded to different swimming modes. Exploiting laminar flow in the low Reynolds number region in the microfluidics channels, we fabricated micromotors with variable composition, shape and controlled active regions. Furthermore, we studied the different trajectories resulting from the complex interactions between swimmer body and fluid dynamics around it and connected them to the theoretical findings. We found close agreement between the experimental results and the theoretical outcomes: I-shaped structure behaved as a pump, U-shaped as a propeller and S-shaped as a rotor. Post fabrication, during real applications, the micromotors will be exposed to complex environments for instance interfaces and flows. To evaluate the feedback of microswimmers in these situations, in the next two sections, we designed custom made environments using microfluidics and we studied the response of well-studied Janus microswimmers in them. It should be noted that in the following two sections we used Janus particles rather than the bubble driven swimmers (fabricated in the first section) for simplicity. In this section, we designed an oil-water interface using a special microfluidic trap design and explored the motion behaviour of a very well-studied Pt@SiO2 Janus micromotors on them. The chip geometry facilitated on-demand merging of a droplet of particles and the ‘fuel’ (H2O2) inside the trap. Additionally, the large surface of the trap resulted in high surface energy which was compensated by partial wetting of the glass substrate. This partial wetting created patches of oil on the glass which we refer to as ‘oil dimples’. The dimples gave us the unique opportunity to directly compare the propulsion and performance of Janus motors at both interfaces (oil-water and solid-water) within the same setup and under similar experimental conditions. The swimming pattern and the speed values were found to be similar at the two interfaces and we conjecture an interplay of various factors such as microscale friction, lubrication, surface locking by the surfactant, reaction product absorption by oil and potential Marangoni influences for this similarity. In the next section, we designed a laminar flowing system using a square glass capillary and studied the response of a spherically symmetrical Janus micromotor in the conditions of flow. Previously, in the literature the response of Pt@SiO2, which is a model pusher-type micromotor, has been studied and they have been demonstrated to migrate cross-stream when the flow is imposed. In this thesis, we introduce a Cu@SiO2 colloid which we hypothesize to resemble a puller-type configuration based on theoretical flow field calculations. Additionally, in the literature, it has been predicted that pullers would exhibit upstream migration when placed under the conditions of flow. Indeed, when placed under flow, these particles migrate upstream, resembling many of the swimmers from biological world. These experimental findings are recovered theoretically using a simple squirmer model in puller configuration. The model also predicted a unique jumping behaviour for these particles, at very high flow rate. When increasing the flow rate in the experiments, we actually capture this characteristics. Finally, based on the theoretical flow field calculations and particularly their upstream response in the imposed flow, we conjecture a puller configuration for Cu@SiO2 micromotors. To sum up, this thesis made important advances by creating a number of different shapes of microswimmers and designing complex environments using microfluidics in which microswimmers can be placed and their response can be studied. Although, in this thesis we emphasized on Janus particles, in future, these custom-made environments can be used to assess the behaviour of other microswimmers including biological ones. While still many engineering and medical problems need to be solved before fully functional applications of artificial microswimmers are realized, manifestations of various shape designs and understanding their behaviours in complex surroundings are the first crucial steps.:Contents: Acknowledgements List of Abbreviations 1. Introduction 2. Fundamentals of active matter and microfluidics 2.1. Active matter 2.1.1. Physical fundamentals of motion at microscale 2.1.2. Biological microswimmers 2.2. Review Paper: Microfluidics for microswimmers 3. Aims and Motivation 4. Results and Discussion 4.1. Microfluidics for fabrication of microswimmers 4.1.1. Introduction 4.1.2. Droplet microfluidics 4.1.3. Stop-flow lithography 4.1.4. Paper - Fundamental Modes of Swimming Correspond to Fundamental Modes of Shape: Engineering I–, U–, and S– Shaped Swimmers 4.2. Microfluidics for specific environments: Interfaces 4.2.1. Introduction 4.2.2. Paper - Study of Active Janus Particles in the Presence of an Engineered Oil–Water Interface 4.3. Microfluidics for specific environments: Flow 4.3.1. Introduction 4.3.2. Paper - Upstream rheotaxis of catalytic Janus spheres 5. Summary and Final Remarks 6. Experimental Details 6.1. Fabrication of hydrogel particles using droplet microfluidics 6.2. Characterization of the hydrogel particles 6.3. Motion studies of the hydrogel particles A. Appendix A.1. Droplet microfluidics A.2. Stop-flow lithography A.3. Microfluidics for specific environments: Interfaces A.4. Microfluidics for specific environments: Flow B. List of publications Bibliography C. Erklärung

Les microorganismes présentent des comportements collectifs qui émergent des interactions qui se produisent à l’échelle individuelle. Dans le cas des suspensions concentrées (fraction volumique > 50%) les effets stériques deviennent dominants. C’est le cas du sperme de bélier sur lequel cette étude a principalement porté. Nous avons étudié certains aspects hydrodynamiques liés à la rhéologie du sperme et à la rhéotaxie. Nous montrons un comportement rhéo-fluidifiant en loi de puissance du liquide séminal reproductible d’un in- dividu à l’autre. Nous avons aussi mis en évidence qu’un contrôle chimique peut fortement affecter le comportement rhéotactique des spermatozoı̈des chez l’ovin et chez l’homme. Nous avons par ailleurs étudié la dynamique collective de la semence confinée dans des chambres d’épaisseur contrôlée en apportant des éclaircissements sur l’origine et la caractérisation du comportement turbulent observé. Nos résultats montrent que certaines caractéristiques de la turbulence bidimensionnelle se manifestent (loi de puissance du spectre d’énergie des vitesses, loi de séparation des traceurs passifs) que nous interprétons comme résultant d’une stratification laminée de l’écoulement par les interactions stériques à forte concentration. Enfin, nous avons développé et breveté un système micro-fluidique dans lequel une mise en rotation spontanée de la semence apparaı̂t. Nous avons analysé ce phénomène et l’avons relié à une transition de phase d’orientation cohérente avec une modélisation de type Self-Organized-Hydrodynamics. De plus nos résultats montrent une bonne corrélation entre la vitesse de rotation et la note de mobilité massale, donnant des perspectives d’applications pour la prédiction de la fertilité à ce dispositif. / Microorganisms exhibit collective behaviors that emerge from interactions occurring at the individual scale. In the case of high concentrated suspensions (volume fraction > 50%) steric effects become dominant. This is the case of ram semen on which this study focused. We first studied some hydrodynamic aspects related to the semen rheology and rheotaxis. We show a reproducible seminal plasma power law shear-thinning behavior from one subject to another. We have also highlighted that a chemical control can strongly affect the rheotactic behavior of sperms in the ovine and humans. We also studied the collective dynamics of the semen in chambers of control depth by providing clarification on the origin and characterization of the observed turbulent behavior. Our results show that some characteristics of two-dimensional turbulence occur (power law of the velocity energy spectrum, the pair-particles separation law ) that we interpret as the result of a stratification laminated flow induced by steric interactions at high concentration. Finally, we have developed and patented a micro-fluidic system in which a spontaneous spin-up appears. We analyzed this phenomenon and we connect it to a coherent orientation phase transition with a Self-Organized-Hydrodynamics modeling. In addition, our results show a good correlation between the speed and scoring of mass mobility, giving opportunities for application of the prediction of fertility for this device.

Le transport des micro-organismes, comme par exemple les bactéries, par un fluide se retrouve au centre de thématiques de recherche dans des domaines aussi variés que de la biologie, l’écologie, l’ingénierie et la médecine.Ce manuscrit résume mon étude expérimentale du couplage entre le mouvement microscopique de la nage des bactéries et le mouvement advectif de l’écoulement.La première partie du manuscrit porte sur la rhéologie des suspensions d’E. coli sous faible taux de cisaillement. Pour cette condition, j’ai montré que les perturbations hydrodynamiques induites par la nage réduisent fortement la viscosité. Cet effet peut-être si important pour qu’il soit suffisant pour compenser entièrement la perte visqueuse due au cisaillement.La seconde partie traite des expériences d’écoulement réalisées dans un canal capillaire. Pour cette géométrie, j’ai examiné le couplage pour des écoulements caractérisés par un plus fort taux de cisaillement. Le suivi des trajectoires et le dénombrement des bactéries m’ont permis de mettre en évidence l’existence d’une composante de vitesse normal à la direction de l’écoulement. Cette dernière montre que les bactéries suivent des trajectoires hélicoïdales qui s’enroulent autour du centre du capillaire d’une façon antihoraires. Cette nouvelle composante est corrélée à la migration préférentielle des bactéries dans une couche de localisation proche de la paroi du canal.Les couplages rhéotactiques bactéries/fluide que j’ai étudiés doivent avoir des conséquences potentielles sur le transport en géométries plus complexes qui mériteraient une étude particulière. / The question of transfer and spreading of living microorganisms, such as motile bacteria, is of interest in biology and ecology, but also in engineering and medicine.The way in which the background flow affects the behavior of these bacteria and how it impacts the bacterial transport through complex systems and on the macroscopic properties of the fluid remains unclear and little studied.In this thesis, I present an experimental investigation of the coupling between the local bacteria-driven motion and the fluid advection.In a first part, I investigate the rheological response of E. coli suspensions when subjected to weak flows (low shear rates). I show that, in particular conditions, the microscopic perturbations caused by the bacteria highly impact on the macroscopic viscosity of the suspension, leading to a striking viscosity decrease and eventually overcoming the dissipative effects due to viscous loss. I also identify the relevant time scales defining this viscosity decrease.In a second part, I perform experiments in a capillary channel and analyze the coupling for stronger flows (higher shear rates), at which bacteria were found not to impact on the macroscopic viscosity. Instead, by analyzing the bacterial trajectories under flow, I evidence a breakage of the symmetry of this trajectories which, characterized by a preferential migration, causes the localization of the bacteria in a layer that extends over a significant distance from the surface, and thus potentially influencing the bacterial transport in complex systems

No description available.

<p>The present dissertation focuses on two themes: (i) elastic instability of flow and (ii) elastic instability of microscopic filaments.</p> <p><br></p> <p>(i) The presence of macromolecules often leads to the viscoelastic nature of industrial and biological fluids. The flow of viscoelastic fluids in porous media is important in many industrial, geophysical, and biological applications such as enhanced oil recovery, groundwater remediation, biofilm formation, and drug delivery. The stretching of polymeric chains as the viscoelastic fluid passes through the microstructure of the porous media induces large elastic stresses, which leads to viscoelastic instability at the Weissenberg number greater than a critical value, where the Weissenberg number quantifies the ratio of elastic to viscous forces. Viscoelastic instability can lead to a time-dependent chaotic flow even at negligible inertia, which is sometimes also known as elastic turbulence due to its analogous features to traditional inertial turbulence. In the present thesis, we investigate the pore-scale viscoelastic instabilities and the flow states induced by the instabilities in symmetric and asymmetric geometries. We found that the topology of the polymeric stress field regulates the formation of different flow states during viscoelastic instabilities. Viscoelastic instability-induced flow states exhibit hysteresis due to the requirement of a finite time for the transformation of polymeric stress topology. Further, we study viscoelastic flows through ordered and disordered porous geometries and explore the effect of viscoelastic instability on sample-scale transport properties. Viscoelastic instability enhances transverse transport in ordered porous media and longitudinal transport in disordered porous media. We also derive a relationship between the polymeric stress field and the Lagrangian stretching field. The Lagrangian stretching field helps to predict the feature of flow states and transport in complex flows. The experimental measurement of the polymeric stress field is extremely challenging. The framework established here can be used to obtain the topology of the polymeric stress field directly from the easily measured velocity field.  </p> <p><br></p> <p><br></p> <p>(ii) The interaction between flow and elastic filaments plays an important role in sperm and bacterial motility and cell division. The sperm cells of many organisms use long elastic flagellum to propel themselves and also face complex flows and boundaries during their search for egg cells. Strong flows have the potential to mechanically inhibit flagellar motility through elastohydrodynamic interactions. We explore the effects of an extensional flow on the buckling dynamics of sperm flagella through detailed numerical simulations and microfluidic experiments. Compressional fluid forces lead to rich buckling dynamics of the sperm flagellum beyond a critical dimensionless sperm number, which represents the ratio of viscous force to elastic force. Shear flows navigate the sperm cells in complex geometries and flows. We have also studied the effect of flow strength and flagellar elastic deformation on the sperm trajectory in simple shear and Poiseuille flows.</p>