Understanding the locomotion of microorganisms is essential for insights into microbial ecology, infection, and colonization processes. Although two-dimensional microscopy has been widely used to study microswimmer motility, it does not capture the full extent of their three-dimensional (3D) movement. Recent advances in defocused particle tracking, holographic tracking velocimetry, and stereo-microscopy face challenges in achieving high resolution at larger particle densities and tracking multiple microswimmers in suspension. In this work, we introduce a novel multi-camera microscopy system that significantly improves the accuracy of 3D microswimmer tracking. Our system uses four sCMOS cameras to image microorganisms within a 2.5 × 2.5 × 2 mm3. We assess the performance of our microscopy system by tracking a population of the unicellular motile algae Chlamydomonas reinhardtii. An in-house tracking algorithm based on the projective geometry framework enables tracking with reprojection errors below 0.3 body lengths. This system supports imaging and tracking particle source densities of 0.32, higher than other existing single camera 3D microscopy techniques. Analysis of C. reinhardtii trajectories in 3D reveals a predominance of left-handed chirality and helical swimming patterns. Moreover, our 3D tracking data provide translational and rotational diffusion coefficients that differ from those obtained using traditional two-dimensional methods.

This thesis presents a novel 3D tracking system for studying microorganism locomotion in complex fluid environments, addressing the limitations of current 2D and 3D techniques . The multi-camera microscopy system developed allows for high-resolution tracking of microswimmers like Chlamydomonas reinhardtii, providing new insights into their helical swimming patterns and interactions. The work includes the study of pairwise interactions and the impact of non-Newtonian fluids on motility, revealing key differences in swimming behavior and fluid dynamics in different media type.

The accumulation of motile cells at solid interfaces increases the rate of surface encounters and the likelihood of surface attachment, leading to surface colonization and biofilm formation. The cell density distribution in the vicinity of a physical boundary is influenced by the interactions between the microswimmers and their physical environment, including hydrodynamic and steric interactions, as well as by stochastic effects. Disentangling the contributions of these effects remains an experimental challenge. Here, we use a custom-made four-camera view microscope to track a population of motile puller-type Chlamydomonas reinhardtii in a relatively unconstrained three-dimensional (3D) domain. Our experiments yield an extensive sample of 3D trajectories including cell-surface encounters with a planar wall, from which we extract a full description of the dynamics and the stochasticity of swimming cells. We use this large data sample and combine it with Monte Carlo simulations to determine the link between the dynamics at the single-cell level and the cell density. Our experiments demonstrate that the near-wall scattering is bimodal, corresponding to steric and hydrodynamic effects. We find, however, that this near-wall dynamics has little influence on the cell accumulation at the surface. On the other hand, we present evidence of a cell-induced surface-directed rotation leading to a vertical orbiting behavior and hopping trajectories, consistent with long-range hydrodynamic effects. We identify this long-range effect to be at the origin of the significant surface accumulation of cells.

The rheology of suspensions of high-inertia (or granular) non-spherical particles characterized by high particle Stokes and Reynolds numbers is rarely investigated. In this study, we investigate the rheology of suspensions of inertial rod-like particles of aspect ratio 4 subjected to shear flow. In particular, the effect of fluid medium (air, water) against dry granular simulations on the developed stresses is assessed. CFD-DEM simulations are performed for a periodic shear box for a range of shear rates and volume fractions of particles. The dependence of rheological properties like shear stress, normal stress difference, pressure and relative viscosity on volume fraction, shear rate, granular temperature and the particle orientation are discussed. These results provide insight into the macroscopic rheology of suspensions of rods and demonstrate that the effect of particle shape and surrounding fluid cannot be completely ignored. Air as a fluid medium shows similar scaling as compared to dry granular simulations, but the stress values are generally lower. We observe drastic change in both scaling and values for water as fluid medium. In all cases, the rods show strong alignment in the direction of shear. This study can be further extended to develop stress closures for use in Eulerian flow models.