Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Doctor of Philosophy


Civil and Environmental Engineering


Hassan Peerhossaini

2nd Supervisor

Christopher Thomas DeGroot

Joint Supervisor


To have better control over photobioreactors at various operating conditions, it is necessary to characterize microorganisms’ motion, optimize light distribution, and investigate efficient mixing methods in photobioreactors.

The second chapter of this thesis aims to develop a theoretical model for the calculation of microorganisms’ optical characteristics. Modeling light transfer in photobioreactors needs accurate input data to solve Maxwell’s equations. Here, input data include absorption properties of the microorganism’s pigment, pigment-content measurement, and the details of the shape and size of the microorganism cells. These input data predicted the optical characteristics of microorganism cells with homogeneous, coated, and heterogeneous geometries.

The third chapter reports on experiments that were carried out to investigate the effect of two mixing methods, turbulent stirring and orbitally shaking, on the growth metrics of Synechocystis sp. CPCC 534, and compare them with stationary cultures. The study revealed that stirring Synechocystis cultures can enhance the growth rate, doubling per day, yield, and Chla production in contrast to cultures without any mixing.

In the fourth chapter, the motility of wild-type Synechocystis sp. CPCC 534 was investigated to establish a correlation between the evolution of cell motility and cell growth phases during the complete growth cycle of 78 days. Average cell velocity, mean squared displacement (MSD), diffusion coefficient, and displacement probability density function (PDF) were calculated to assess the dynamics of Synechocystis sp. CPCC 534 during the growth period. The obtained results indicate that the age of microorganisms has a notable influence on different aspects of cell motility. Consequently, this can affect the transport characteristics of active suspension.

In the final chapter of this thesis, we aimed to examine the transport characteristics of active fluids and passive fluids in a bifurcated microchannel with a rectangular cross-section. A PDMS microchannel was designed and fabricated to investigate the behavior of two fluids in the bifurcated microchannel. Finally, our investigation revealed that passive fluids exhibit higher velocity than active fluids. This difference arises due to the minimal movement of active fluids caused by their run-and-tumble motion.

Summary for Lay Audience

An active fluid is a type of fluid that contains tiny living elements such as bacteria, algae, and sperm cells, which can move around. Active fluids have unique behaviors that distinguish them from regular fluids (passive fluids). Unlike regular fluids (passive fluids), which require gradients of pressure, velocity, or temperature to create flow, the motion of active fluids is driven by the microorganisms’cells. Microorganisms cells convert chemical energy from nutrients into mechanical energy to move around. Understanding the motion of microorganisms is crucial due to their significant impact on human life, and the environment, and their widespread applications in various fields, including industry, medicine, food, and energy.

In the second chapter of this thesis, theoretical methods were used to assess the suitability of various sphere geometries (homogenous-sphere, coated-sphere, and heterogenous sphere) in simulating the optical properties of photosynthetic microorganism (Chlamydomonas reinhardtii). This was completed using the finite difference time domain (FDTD) method and a precise geometric model. These results showed that more accurate input data were required to correctly determine the optical properties of Chlamydomonas reinhardtii, including the absorption properties of pigments, the real part of refractive indices of each cell component, and the shape of the cells.

The third chapter focuses on the experiments, that were conducted on the impact of different mixing modes on the cultivation of the cyanobacterium Synechocystis sp. CPCC 534, and compared with simple molecular diffusion (motionless mode). The study showed that applying mixing in the culture can enhance both the growth rate and biomass yield production in comparison to relying solely on molecular diffusion (motionless mode).

In the fourth chapter, experiments were performed on how microbial growth and aging affect microorganism movement. The focus is on studying the motility behavior of Synechocystis sp. CPCC 534 and its relationship with aging in a closed microfluidic chip. The findings of the study explained a clear connection between the cell growth phase and cell motility. Specifically, the motility of cells increased steadily during the exponential linear growth phases and declined during the stationary phase until it reached a constant value.

In the final chapter, an experimental investigation was carried out to study the flows of suspension fluids containing live (active fluid) and dead (passive fluid) Synechocystis sp. bacteria in a bifurcating microchannel at different flow rates. Analyzing the average flow velocities of active and passive fluids, showed that the passive fluid's average velocity exceeded that of the active fluid at various flow rates. This difference can be attributed to the tiny movement of active fluids caused by their run-and-tumble motion.