A mathematical model and numerical method for studying the collective dynamics of
geotactic, gyrotactic and chemotactic micro-organisms immersed in a viscous fluid is
presented. The Navier–Stokes equations of fluid dynamics are solved in the presence
of a discrete collection of micro-organisms. These microbes act as point sources
of gravitational force in the fluid equations, and thus affect the fluid flow. Physical
factors, e.g. vorticity and gravity, as well as sensory factors affect swimming speed and
direction. In the case of chemotactic microbes, the swimming orientation is a function
of a molecular field. In the model considered here, the molecules are a nutrient whose
consumption results in an upward gradient of concentration that drives its downward
diffusion. The resultant upward chemotactically induced accumulation of cells results
in (Rayleigh–Taylor) instability and eventually in steady or chaotic convection that
transports molecules and affects the translocation of organisms. Computational results
that examine the long-time behaviour of the full nonlinear system are presented.
The actual dynamical system consisting of fluid and suspended swimming
organisms is obviously three-dimensional, as are the basic modelling equations. While
the computations presented in this paper are two-dimensional, they provide results
that match remarkably well the spatial patterns and long-time temporal dynamics
of actual experiments; various physically applicable assumptions yield steady states,
chaotic states, and bottom-standing plumes. The simplified representation of microbes
as point particles allows the variation of input parameters and modelling details, while
performing calculations with very large numbers of particles (≈104–105), enough so
that realistic cell concentrations and macroscopic fluid effects can be modelled with
one particle representing one microbe, rather than some collection of microbes. It
is demonstrated that this modelling framework can be used to test hypotheses concerning
the coupled effects of microbial behaviour, fluid dynamics and molecular
mixing. Thus, not only are insights provided into the differing dynamics concerning
purely geotactic and gyrotactic microbes, the dynamics of competing strategies for
chemotaxis, but it is demonstrated that relatively economical explorations in two
dimensions can deliver striking insights and distinguish among hypotheses.