Biosilicification mechanisms: An investigation using computational modeling and experimentation

Biomineralization is the deposition of minerals by living organisms. The question of how and by which mechanisms nature has developed biominerals can be addressed via several complementary approaches. This dissertation investigates these mechanisms from several perspectives using both computational and experimental methods. The emphasis of this work is on silicification in diatoms, eukaryotic unicellular algae, with a complex biosilica structure.
One of the approaches taken in this thesis is to study the events that lead to silica formation, such as reactions and the transportation of chemical components. For this purpose a computational model with several cell compartments was designed, on which parameter estimation methods were applied. This model explains the different regimes in silicon uptake by cells that were previously observed in experiments. The presented computational framework was also used to investigate the silicon uptake regulation in close relation with other cell processes such as silicification. Moreover, an experiment was performed on the same species of diatom under different temperatures and different levels of silicic acid supply to address the effect of physical and chemical control on the silica morphology. Using SEM imaging and machine learning analysis on the data extracted from images of silica, it was concluded that the different temperatures changed the cell population dynamics and, consequently, the silica pattern.