Bacterial chemotaxis in thin fluid layers with free surface

[[abstract]]Thin fluid layers are common natural habitats for various species of aerobic bacteria. Collective behaviors in bacterial colonies caused by chemotaxis can form complex bioconvection patterns, which often work in favor of the colony's survival and growth. The connection between the biology of bacterial aerotaxis and the physics of buoyancy effects caused by non-uniform suspension density is numerically investigated for a suspension of oxytactic bacteria placed in the Petri dish. The upper surface is free and open to the atmosphere, and through it oxygen diffuses into the suspension. Surface tension and dynamic contact line are incorporated into the mathematical and numerical models. A comparison has been made between dynamic free surface and fixed free surface models, and differences have been revealed. The parametric study in the case of dynamic free surface has been performed, and the non-linear dynamics of the phenomenon has been investigated. Resulting from upward aerotaxis and downward gravitational force, Rayleigh-Taylor-like instabilities develop between layers of different densities in the suspension. Bacterial plume patterns and their dynamics, such as sinking, merging, and birth of new plumes, characterize the phenomenon for particular intervals of dimensionless parameters. Accordingly, categorization of the phenomenon based on bacterial plume evolution has been made, and significant intervals of dimensionless parameters have been extracted