This study presents the development of a pro grammable microfluidic device designed for precise hydrodynamic manipulation of particles and fluids. Utilising femtosecond laser ablation and cold oxygen plasma bonding, the device features highly accurate microfluidic inlets with minimal surface rough ness, ensuring consistent flow dynamics. Experimental validation confirmed the device’s ability to generate uniform flow fields and half Rankine bodies, demonstrating its potential for real time reconfigurability in various applications, including particle manipulation and flow field analysis. The research lays the groundwork for future advancements in microfluidic technology, emphasising high precision and structural integrity.

Algae remains a focal point of scientific inquiry with its wide-ranging environmental, health, and energy applications. Among model organisms, the unicellular green alga Chlamydomonas reinhardtii holds significance, particularly in light of its responsiveness to temperature alterations impacting swimming velocity. Notably, this study investigates the intriguing ability of live Chlamydomonas cells to modulate suspension viscosity compared to non-living particles.

Under shear flow conditions, a captivating phenomenon termed "heat thickening" is unveiled in live algae suspensions. Unlike conventional fluids, heightened temperatures uniquely enhance viscosity in these suspensions due to the interplay between cell-generated stresslets and shear flow. This study aims to characterize the influence of temperature on microalgal swimming speeds, flagella beating frequencies, and its role in viscosity modulation.

An experimental setup with precise temperature control and water circulation is employed to achieve this. Both 2D and 3D tracking methods measure motility and inform the findings. Results demonstrate that swimming velocity and beating frequency increase with temperature until 35 degrees Celsius, followed by a decline. This trend aligns with the observed live cell suspension viscosity measurements, indicating the impact of motility on suspension rheology.

Quantitative research has indicated the simultaneous influence of beating frequency and swimming velocity on suspension viscosity, underscoring the importance of investigating motility's role. This study suggests that the motility of live algae cells holds the potential for interpreting and modulating suspension rheology, warranting further exploration under various temperature conditions. Such insights contribute to understanding algae behavior and its applications across environmental and industrial contexts.

This thesis describes methods and first analyses to study the shape and motion of a large school of approximately 2000 Harengula clupeola (false herring) in three-dimensional space. This school of fish was present at the large-scale and publicly accessible ocean aquarium of the Rotterdam zoo, in the Netherlands known as Diergaarde Blijdorp, from spring 2017 to summer 2020.@en

Life at low-Reynolds numbers regime is intriguing. Single motile bacteria are known to exhibit erratic behaviour; they swim in what is known as a random walk, alternating between periods of swimming straight and abrupt moments of re-orientation. Yet in dense populations, cells of E.coli have been reported to exhibit weak synchronization and self-organize into collective oscillatory motion patterns. However, the origin of this rhythmic behaviour remains largely unknown. Here, we present a method of inducing self-sustained oscillations over minute timescales in single E.coli cells by trapping them in circular microcavities. By engineering the size of these microwells, we show that the velocity of single E.coli can be tuned between speeds ranging from a few to 20 um/s. Furthermore, we show that by connecting the microwells via on-chip channels, E.coli tend to coordinate their motion through hydrodynamic interaction and exhibit collective dynamics. Using analytical modeling, we extract the coupling strength and design the channels to mediate synchronized oscillation between two bacterial oscillators. Our work not only advances our understanding of the collective dynamics of swarming bacteria but also provides the first evidence for single-cell bacterial oscillators, paving the way to using micro-organism-inspired oscillations in applications as varied as antibiotic screening, scientific computing and micro-swimmers.

Emulsions, characterized as a metastable dispersion of one liquid into a second one in the presence of surface-active agents, have complex rheology that interests both physicists and industries. Depending on the volume fraction of the dispersed phase ($\phi$), emulsions can display both solid-like and liquid-like behavior. Rheometrical measurements of complex fluids usually yield several flow curves, each corresponding to a certain volume fraction. Scaling analysis assists in investigating the fundamental traits of those flow curves by rescaling the rheometrical data onto several master curves described by a few non-dimensional variables.

Whereas experiments successfully scaled the data onto master curves are usually of three-dimensional complex fluids, many numerical simulations are of low-cost two-dimensional flows, lacking direct referable experimental data. Additionally, scenarios involving droplets, bubbles, and particles trapped at the interface of two fluids inherently constitute a two-dimensional system. Motivated by these considerations, the project aims to measure the rheology of emulsion monolayers.

A cylindrical Couette ring configuration was built to facilitate the generation of monolayers and rheometrical measurements. The image processing method was developed to deal with three distinct scenarios, high $\phi$, medium $\phi$, and low $\phi$, depending on the concentration of droplets. The steady velocity profiles and the averaged packing fractions were acquired through image analysis. Subsequently, the local rheology was deduced and compared with the macroscopic rheological measurement at various packing fractions. While the densely packed emulsion monolayer is a shear-thinning yield stress material, the spatial cooperativity (non-local effect) and capillary force (wall effect) were found to have a profound influence on the rheology.

The precise manipulation of particles and droplets is crucial to many microfluidic applications in engineering. The design of microfluidic devices is generally tailored to perform a specific task, with each specific application requiring a unique and fixed design. In this way, using a single device to perform multiple analyses of a wide range of specimens, from biological to chemical specimens, is unfeasible. Here, we address this issue and present a microfluidic approach that dynamically controls the hydrodynamic flow and the streamlines to realize complex multi-particle manipulations within a single device. Our approach combines the design of a flow-through microfluidic flow cell together with an optimization procedure to find a priori optimal particle path-lines, and a Proportion-Integral-Derivative-based (PID) feedback controller to provide real time control over the particle manipulations. In our device, particles are manipulated with hydrodynamic forces, by using a uniform flow through the flow cell and three inlets perpendicular to the flow cell. The streamlines within the device are manipulated by injecting or extracting fluid through the three inlets. We demonstrate the robustness of our approach by performing multiple functions within the device, including particle trapping, particle sorting, particle separation and assembly. We show that the real time control procedure affords accurate particle manipulation, with a maximum error on the order of the diameter of the particle. Our particle manipulation approach is particularly well suited to biological samples and living cells.@en

Dense suspensions can be found in various industrial and natural processes. A relatively new technique uses the principle of additive manufacturing to produce products from a wide variety of materials by printing with dense suspensions. To reach a high print quality the suspension rheology must be understood very well. Current knowledge about suspension rheology however lacks the capability of predicting the exact behaviour of a predefined suspension, especially for dense suspensions. Direct numerical simulation (DNS) in combination with a second order accurate immersed boundary method (IBM) (Breugem, 2012) can be a useful tool to research suspension rheology. However, currently no numerical results are known for suspensions close to the jamming limit produced with this method.
The current work validates the capability of the IBM to simulate dense suspensions by comparing produced results with existing numerical and experimental data. This is done by simulating a plane Couette flow for a range of particle volume fractions 𝜙=0.2−0.6, all of which are simulated with two friction coefficients (𝜇𝑐=0 and 0.39). Furthermore, the focus is on Stokes flow of neutrally buoyant non-colloidal suspensions with monodisperse spherical particles and the channel height was chosen equal to 13.5 particle diameters. DNS has been used to analyse the suspension rheology in terms of mean concentration profiles, velocity profiles, interactions in the microstructure and particle stress profiles. Steady-state concentration profiles of the simulated cases show a particle layering effect close to the confining walls. This layering effect alters the suspension rheology significantly and for that reason the wall regions are analysed separately from the core region. For both regions the microstructure, the relative viscosity and the normal particle stresses are analysed. The results agree well with existing numerical results (Gallier et al., 2016) (Yeo & Maxey, 2010a). Comparison with experimental work (Dbouk et al., 2013) (Zarraga et al., 2000) shows that results for the relative viscosities of the unlayered core regions are lower in general, reasons for this difference can be higher friction factors or the use of non-spherical particles in experiments. However, the same asymptotic trend is observed for increasing 𝜙. The maximum packing fraction 𝜙𝑚 was found by fitting the relative viscosities to the Marron & Pierce equation (Maron & Pierce, 1956), which gave 𝜙𝑚=0.69 for 𝜇𝑐=0 and 𝜙𝑚=0.635 for 𝜇𝑐=0.39. These results for 𝜙𝑚 are in good agreement with results from (Gallier et al., 2014).
In general the IBM turns out to be capable of reproducing existing numerical data. Furthermore, results have been obtained for suspensions closer to the jamming limit than known so far in numerical work on this particular flow regime. Besides that, the present results are obtained with an advanced soft-sphere collision model, including lubrication corrections for close approach of particles, which has been extensively validated with collision experiments in a previous study. Comparison of the results from this work with experimental data shows larger differences. The reason for this can be that the suspensions in experimental set-ups deviate from the idealized suspension in the simulations. Besides that experimental results differ significantly from each other, indicating that differences also exist between the experimental suspensions. These differences have to be clearly defined in order to make a valuable comparison. Therefore it is currently difficult to determine how accurately the IBM simulates suspension rheology.

Eukaryotic cilia and flagella are some of the best conserved biological structures across species. Giventhe pressure natural selection imposes onto living beings to optimize their body plans, eukaryotic flagella have demonstrated to be an optimal organelle for propulsion at low Reynolds numbers. Therefore, understanding how cilia beat is of central importance to understand any biological process involving the motion of a fluid. The well conserved internal structure of cilia, the axoneme, has been thoroughly reported but there is still no scientific agreement on how oscillations can emerge from the combina-
tion of the myriad different components forming the axoneme. Current theories base their approaches on complex control mechanism to control the activity of the axonemal molecular motors, the dyneins. In the present thesis we propose a much simpler mechanism, demonstrating that no dyneins activity regulation mechanism is required since oscillations naturally emerge from the axoneme undergoing a dynamic buckling instability triggered by a system of follower forces exerted by the molecular motors.

Here, we first derive a numerical spectral methods solver to resolve the dynamics of a slender filament immersed in a low Reynolds fluid. We then use the solver to explain the emergence of oscillations in simplified synthetic versions of cilia. The structural simplicity of these experiments helps to identify the presence of follower forces and to model the structure, observing that our predictions based on the mechanical instability are in agreement with the experimental results. Given that a follower force can explain the dynamics of synthetic cilia, we then apply the model to study possible configurations of forces in the axoneme which can trigger the instability even if it is an isolated system, finding that the axoneme can indeed undergo a dynamic buckling instability leading to self-sustained oscillations reminiscent of cilia.

We finally build a minimal version of the model to capture the dynamics of cilia, simplifying the axoneme as a filament subject to a tip concentrated, tangential and compressive follower force. We use it to study the synchronization of cilia with external hydrodynamic and mechanical forcings and with another cilium, being able to capture non-linear features of flagellar dynamics which has been experimentally observed but previous simpler flagellar models fail to capture.

Flagellar locomotion is one of the first forms of locomotion on our planet. Microorganisms use their flagella to reorientate or generate movement in search for nutrients or gradients in light intensity. These microscopic swimmers are able to adapt their swimming gait to the circumstances they encounter. Motile microorganisms such as the Chlamydomonas reinhardtii are used as a source of inspiration in biomimetics and used in biological, pharmaceutical and industrial applications to produce for example biofuels or medication. The fluids in which these microscopic cells swim are often of complex rheology, containing macromolecules such as synthetic polymers of proteins, which influences the
motile behaviour of these cells. The motile behaviour is mostly studied in a quasi 2D environment which might be different from the behavior in a more natural 3D environment. Therefore, our aim is to analyse the motility of microorganisms in a 3D environment in fluids with different rheological properties.

To gain more insight in the influence of rheology on the motility of microorganisms, the model microorganism Chlamydomonas reinhardtii is observed in fluids of various levels of elasticity. An in-house 3D microscopic setup, consisting of 4 LaVision sCMOS cameras, is used to observe the motility of the cells. A Lagrangian tracking algorithm is used to detect and follow many individual motile cells simultaneously. We focused on the velocity of the cells, their helical motions (radius and pitch) which they use to scan their surroundings, and their flagellar beating frequency.

We observed a velocity and pitch independent of the Deborah number, whereas decreasing values for these metrics were found in Newtonian fluids of equal viscosity. The radius of the helical motion showed to be independent of elasticity or viscosity. The beating frequency of the cells shows to be constant in a viscoelastic fluid independent on the viscosity or elasticity, whereas it tends to decrease in Newtonian fluids of increasing viscosity.

Chlamydomonas reinhardtii might have developed a more efficient swimming gait to propel themselves in a viscoelastic fluid compared to a Newtonian fluid, especially in high viscosities. Moreover, we argued that motile microorganisms that are allowed to swim freely in a 3D confinement, show a different motile behaviour than when their motility is constricted by a quasi 2D plane. To validate these findings we recommend to perform experiments both in quasi 2D and 3D, while using the same cell culture.

The coalescence of two droplets suspended in a viscous fluid is the focus of this study. When two droplets that are suspended in a shearing flow come in contact with each other, it is currently uncertain if the contact would result in coalescence. To be able to make such predictions, it is necessary to study the effects of the system parameters, such as the angle of collision between the droplets and the properties of the flow and the two fluids, on the process of coalescence. This necessitates the need for a robust experimental setup in which such studies can be performed.

The characteristic of a systematic study is repeatability and control over experimental conditions. In coalescence studies, the impact angle between the droplets is a parameter that has proved difficult to control. In this study, a microfluidic device is developed that uses the concept of surface energy wells to achieve repeatability in the impact angles of droplet collisions. Using the device, droplet coalescence experiments were performed. An interesting observation was made from the experiments which guided the further course of this research work. It was seen that the droplets did not coalesce upon approach, but coalescence was driven by the separation of the droplets. In the literature, this phenomenon is referred to as 'separation-driven coalescence'. Furthermore, it was suspected that an experimental condition could be defined based on a non-dimensional parameter, namely, the Capillary number Ca, such that for Ca > Ca_cr, separation of droplets ceases to trigger coalescence.

The effect of the system parameters, namely the impact angle, θ_i, and the viscosity ratio, λ, over the Ca_cr was investigated. In this study, the presence of a Ca_cr for separation-driven coalescence is confirmed, both experimentally and through a scaling argument. The results of the study indicate that the thickness of the film on the onset of separation influences the Ca_cr. However, a dependency between Ca_cr and λ was not found experimentally. Large experimental uncertainties prevent any further conclusions to be made regarding the Ca_cr.

In this thesis, a framework is developed for the investigation of the Ca_cr for separation-driven coalescence. With more experimental data, a deeper understanding of separation-driven coalescence can be obtained.

The interfacial tension is a fundamental property of liquid-liquid systems and governs the mixing potential of two immiscible fluids. For two fluids to form a stable mixture, their interfacial tension needs to be very low. Applications of systems with a low interfacial tension find a plethora of applications: for example, in the food industry, for generating oil-water emulsions, or in the pharmaceutical industry, where characterising the mixture is important for the drug delivery. Despite the numerous industrial applications, characterising low interfacial tension remains a challenge. Traditional direct force measurement techniques, such as the Wilhelmy Plate method, have difficulties resolving the small forces involved. Other conventional drop distortion techniques, such as spinning drop tensiometry, require long calibration time and can have error margins up to 60%. This thesis investigates the potential of utilising the optical tweezers for studying low interfacial tensions and developed a method to do so. In this set-up, a highly focused laser beam holds a micron-sized sphere: similar to a pair of tweezers. As light refracts through the bead, momentum is transfered and thus exerts a force. The light refraction is also used for position detection, allowing for a spatial resolution of 0.1-2 nm. As a micro-sphere, which is hold by the optical tweezers, is pushed against an interface, the forces exerted on the bead are probed allowing for the interfacial tension to be determined. Combining the excellent spatial resolution of the optical tweezers with fitting a minimal surface model, the set-up has the potential to measure the interfacial tension over a range of decades. We have researched the dodecane-water interface, where we added glycerol to the aqueous phase to match the index of refraction. The interfacial tension was lowered by adding Span-80 or the combination of Span-80 and SDS. We have been able to conduct several measurements on interfaces with estimated values of O(-6) - O(-3) N/m. We find that the system is highly dependent on the different in index of refraction between the two fluids as well as the curvature of the interface. However, discrepancies between literature values and measurements arise due to the altering of the fluid properties and interfacial dimensions. We conclude that the use of optical tweezers to measure low interfacial tension is promising, however its speed and accuracy are reduced due to the strong requirement to match the index of refraction.

The microscopicworld is surprisingly busywith swimming micro-organisms. In a droplet of pondwater, there can be tens of thousands of microbes. They are predators and preys, producers and consumers, and they formthe bottom levels of the ecology of our world. The swimming micro-organisms can be in general classified into prokaryotes and eukaryotes. Eukaryotes come later in evolution. They are higher organisms than the prokaryotes as they possess more complex cellular structures such as the nucleus and mitochondria. Motile eukaryotic micro-organisms all use an active hair-like structure for swimming, known as flagella or cilia. Although nuanced difference exists between flagella (cilia) of different species, their general internal structure and driving mechanisms are mostly the same. In some sense, they are one of the bestselling machines for locomotion on themicron scale. Although flagella are the first-ever documented organelles in cell biology, our understanding of them is still limited. For example, we have only begun to appreciate how the conformational change of single protein motors results in the waveformon the scale of a flagellum. Our understanding of the flow generated by even a single flagellum is rudimentary: resolving the temporal features of such flow field remains experimentally challenging. On a larger scale, how thousands of cilia interact with each other to facilitate fluid transport is still elusive: theoretical models and simulations are waiting for experimental verification. In this thesis, I explore different topics centering around flagellar/ciliary motility by employing novel experimental and numerical techniques, and hence advance our understanding. My experimental investigation starts by resolving the flow generated by the beating cilia of single cells. Due to the high beating frequency, high temporal resolution is required to map the time-varying flow field, which conventional tracer particle-based flow velocimetry techniques cannot provide. To tackle this challenge, I implemented an optical tweezers-based flow velocimetry (OTV) technique. In this technique, a bead is trapped and placed at a particular location by a focused laser beam. The local flow displaces the bead from the trapping center. This displacement, although small, can be accurately monitored by laser interferometry and converted into an electrical signal by photoelectric detectors. Essentially,we gain the desired accuracy and temporal resolution by exploiting the high resolution and large bandwidth of interferometric and electrical measurements. With this technique, I revealed that the ciliary flow deviates fundamentally fromhow it is often modeled by Stokes equations. More specifically, the flow’s amplitude decays faster spatially, and its phase shifts over distance. These discrepancies are resolved by adding a linear unsteady term to Stokes equations. Furthermore, I systematically characterized the ciliary flow field created by captured C. reinhardtii cells. The flow field in different directions and over the ciliary beating plane are measured experimentally, modelled numerically, and analyzed theoretically. Results displayed excellent agreement with each other, and altogether increased our knowledge in the ciliary flow. With the OTV measurements, I not only studied the basic hydrodynamics of ciliary flowbut also addressed a long-standing hypothesis regarding the function of a ciliary appendage. Many cilia have fibrous ultrastructures called mastigoneme. These fibrous appendages are believed to help cells swim faster by increasing the ciliary surface area. Our experiments, together with numerical studies, completely refute this hypothesis: such fibrous hairs do not show any hydrodynamic significance in C. reinhardtii. Instead, its absence in genetically modifiedmutants appeared to result in some behavioral changes, causing the cells to turn abruptly more often than usual. Therefore, I have re-opened the question about the function of the fibrous mastigonemes. Future investigation towards this direction is needed and is likely to lead to more exciting findings. Lastly, I attempted to bridge the physics of ciliary flowwith the biology of ciliary beating. I focused on the ciliary difference and investigated it by selectively loading each cilium of C. reinhardtii with external flows. The ciliary difference is critical for the steering of biflagellates (micro-organisms swimming with two flagella/cilia). I observed an unreported functional difference between the two cilia, as I found that the coupling between the two cilia is unilateral. One cilium serves as the coordinator of beating, and a cell is coupled to external hydrodynamic forces mostly through this coordinating cilium. Altogether, by introducing the OTV technique and incorporating different numerical methods, I was able to elucidate the ciliary flowin a time-resolvedway, updating the current understanding in these unsteady flows. The effectiveness of this methodology was demonstrated again by its application in studying the function of the fibrous ultrastructures. By further moving on to the biological aspect of ciliary beating, we found a new type of difference between the two cilia, which enriches our knowledge in inter-ciliary coupling. @en

The progress made by microfabrication technologies has escalated the interest in particle manipulation on micron scale. Particles are not only limited to solid particles but also include cells, droplets and bubbles. Activities involved in manipulation are trapping, sorting, separation and so on. The devices designed to execute such activities are aimed for a particular application. However, there lies a gap in literature to design an all-in-one device. Microfluidics research carried out at the Laboratory for Aero and Hydrodynamics is currently working on designing such devices which can carry out different manipulation tasks.
This thesis is aimed at designing and fabricating such a device where two particles can be manipulated simultaneously. The application of designing such a device would be to study cell-cell interaction, droplet coalescence and so on. To achieve this, a microfluidic device is designed as a Hele-Shaw flow cell. Since the height-averaged velocity in a Hele-Shaw flow cell is irrotational, analytical solution is possible for such a design. Although a Hele-Shaw flow is viscous flow between two closely spaced plates, it produces same streamline patterns as a 2D ideal flow. This enables the use of basic building blocks of an ideal flow field such as sources, sinks, uniform flow and so on. In this case, sources and sinks are superimposed to get the flow field inside the microfluidic device. The microfluidic device is fabricated using Polydimethylsiloxane (PDMS), a commonly used polymer to fabricate microfluidic devices. The design of the device is validated by comparing experimental flow fields, streamlines and stagnation points to the corresponding analytical solution. Single particle manipulation activities are carried out in the device. This is executed by manually controlling the flow rates or the strength of sources and sinks. Firstly, the particle is trapped at the stagnation point for a certain timespan. Finally, some manipulation activities are carried out using a single particle with the aid of streamlines produced by the sources and sinks.

Considering the abundance of viscoelastic fluids in nature, growing attention has been received for the study of microorganisms in viscoelastic fluids. In Newtonian fluids, the flow of microorganisms is governed by the viscosity alone. But in viscoelastic fluids, the addition of the elastic component complicates the situation. The flow of the organism is now dictated by a combination of the two forces- viscous and elastic. Understanding the behaviour of these organisms is not only important because of the presence of such environments in nature, but also because of the potential pharmaceutical applications that such studies might lead to.
This thesis focuses on the experimental study of the swimming of Chlamydomonas reinhardtii, a model motile swimmer that swims at low Reynolds numbers. The main objective of the thesis is to characterize these differences in motility and hydrodynamic interactions of these cells in Newtonian and viscoelastic fluids of varying viscosities. This is accomplished by observing the motion of a dilute suspension of Chlamydomonas reinhardtii in 3D using four cameras. The cells are subsequently tracked using an in-house 3D particle tracking code that incorporates a recursive divide and conquer strategy to reconstruct the trajectories.
The experiments showed a drop in velocity in viscoelastic fluids as compared to its Newtonian counterparts, validating the results from existing literature. The cells also maintained their helical motion previously observed in TRIS, although with a drop in radius and pitch in viscoelastic fluids. The ratio of the radius to the pitch, however, remained constant for all the cases, indicating a tendency to retain its overall motion.
The study of cell-wall interactions is of prime importance because of the presence of confined surfaces encountered in nature. The concentration profile of the cells was observed to be similar in all the fluids, showing a non-uniform distribution with large concentration at the boundaries. The overall trajectories near the wall in TRIS revealed that the cells tend to arrive at steep angles in the contact region and leave at shallow angles, a phenomenon termed as asymmetric reflection. When the viscosity increased, however, this behaviour became less apparent as the incoming angles became less steep, while the outgoing angles remained shallow. For the viscoelastic case, the behaviour appears to become more symmetric with increase in viscoelasticity. Additionally, the data also points to a less steep drop in velocity in the contact region in solutions of higher viscosity as compared to the less viscous solutions. Though this might indicate a greater influence of hydrodynamics near the wall for more viscous fluids, more data is required to observe this behaviour deeply.
The obtained results show a clear effect of viscoelasticity on the motility and kinematics of the cells, confirming results and predictions from existing literature. For cell wall interactions, differences are certainly discerned, not only for the viscoelastic cases but also for the more viscous cases. More experiments on these fluids are recommended to give a clear indication of the change in wall interactions in fluids of higher viscosity and viscoelasticity.

Synchronization of oscillators is an ubiquitous phenomenon that involves mechanical systems, like pendulum clocks, but also biological systems, like peacemaker cells in the heart or neural activity in the brain. If we consider biological systems at the microscale, namely at the scale of cells, we find that processes like locomotion and fluid transport often exploit synchronization of mechanical oscillators called flagella orcilia. These oscillators at the microscale are whip-like structures extending from the cell body. They are present in a number of micro-organisms like sperm cells, Paramecium or the algae C. reinhardtii. In human, cilia are found in the lungs, the respiratory tract and the middle ear. Cilia are activated in a coordinated way to effectively carry out their function, such as draining mucus. The mechanism behind this cilia coordination is still debated. It is not clear how very simple organisms lacking any feedback system have developed complex oscillatory patterns involving coordination among a multitude of cilia or flagella. There is high interest in understanding the fundamental principles ruling ciliary dynamics, since they would impact medical and engineering applications. The purpose of this thesis is to investigate the mechanisms regulating the synchronization of cilia and flagella.@en

The environment in which microscopic organisms live in is dominated by viscous forces because of their small length scales. Inertial forces are of little use to them in their propulsion mechanisms. As a consequence of this, an organism such as the scallop which moves through time-reversible deformations of its body would not propel itself in a regime dominated by visocus forces. Hence, microscopic organisms use appendages like cilia and flagella that are not time reversible to move forward. However, inertial effects become important to microscopic organisms at the relevant time and length scales. For example, inertia is used by a microscopic organism such as Paramecium to escape/attack its predator/prey.
The effects of inertia on the model of a spherically ciliated micro-organism are studied numerically using an Immersed Boundary Method (IBM) in the present work. In this model ,the distortions of the envelope that is generated by connecting all the tips of the cilia together, are prescribed. The unsteady Reynolds number which characterizes the influence of unsteady inertia that is generated by the beat of the organism, is varied from 0.025 to 18. The code which uses a Volume Penalization/Volume of Solid IBM to simulate the distorting sphere is validated for several test cases. The mean swimming velocity of the organism that is obtained numerically from the code is in agreement with the analytical model for two cases of the unsteady Reynolds number. The mean swimming velocity is found to decrease at increasing inertia. The flow pattern that is obtained in the near-field as a result of the distorting sphere is significantly different from those obtained with the existing models available in literature.

The interest in manipulating particles, droplets and bubbles have garnered significant attention in recent years, owing to the advantages offered by micro-fluidics and the advancement in micro-fabrication technologies. These manipulation activities have found its applications in myriad fields of engineering, ranging from medical diagnostics to chemical industry to drug discovery. This has increased demand for the development of devices such as 'Lab on a chip', which performs laboratory-sized experiments and analysis on a single small chip, with the same speed and accuracy as its room-sized counterpart. However, manipulation activities carried out in these devices has fixed channels, designed to serve purpose for specific manipulation tasks. This makes the device suitable for a specific application. Addressing this aspect, a device designed without having any real channels would give an opportunity to integrate multiple functionalities onto a single-chip in the long run. As a first step towards reaching this 'bigger picture', it is necessary to explore the feasibility of manipulating particles, droplets and bubbles by generating so called 'virtual channels'.
The present thesis focuses on an attempt to manipulate particles without the use of any real channels or external field. Although such manipulation is desired in the micro-scale, a top down approach is preferred and hence, the manipulation is carried out in a scaled up model. First, a Hele-Shaw flow cell is designed with sources and sinks in the millimeter scale to deviate streamlines in the same range. Thereafter, four different velocity fields are studied under different combination of sources and sinks, which are then compared to the computational ones. The property of a Hele-Shaw cell that the averaged velocity over the height of the channel is irrotational, makes it possible to compute velocity fields by the use of potential flow theory. The same velocity fields are hence, computed using a discrete source based Panel Method. A good agreement is found between computation and experiment, making PIV measurements not a necessary option for evaluation of velocity fields under these sources and sinks. Finally, individual particle is inserted into the Hele-Shaw cell and manipulated using unsteady fields. The manipulation includes tasks such as diverting particles having same initial position to different end locations; trapping particle for different instances of time and then releasing them into different directions; flipping positions of two particles; and deflecting a particle by ninety degrees. The individual particle trajectory for the above manipulation activities are tracked down using a particle tracking code and then compared with the ones generated using the Panel Method. This, however, excludes the activities where particles need to be trapped because of particle fluctuation near stagnation point. Overall, the Panel Method serves well in predicting particle path-lines and can be used as a tool for manipulating particles.