Microorganisms such as the E. coli bacterium swim in liquid media following a “run-and-tumble” pattern: a cell runs straight for some time, then stops and rotates randomly for a short time, then runs again etc. This leads to a Brownian-like motion of bacteria in “bulk” media, i.e. when there are no obstacles. The presence of obstacles such as a wall changes the motion of the bacteria substantially, see e.g. this paper.
I am interested in how interactions between the bacteria and their environment affect their swimming patters in heterogeneous environments. An example of such environments is soil which contains a complicated network of connected pores of various sizes.
With a big help from Michele Zagnoni, Dario Dell’arciprete and I have created microfluidic chips that contain a regular grid of microcompartments (diameter = 20um) with various degrees of connectivity ranging from a fully connected 2d network to a “percolating cluster” which barely connects two sides of the chip. The picture on the left shows a microscopic image of a small section of the chip (ca. 300um wide) filled with fluorescein (dye) in ethanol. Bright areas are the compartments and connections between them. A wide channel on the right is used to deliver nutrients/bacteria to the chip.
Statistical physics makes very specific predictions how the mean square displacement of a bacterium should increase in time if it behaved as a Brownian particle (“random walker”) on such clusters. If we see deviations from these predictions in the experiment, it means that bacteria do not move at random between the compartments.
This is an ongoing project – thus far we have only recorded a handful of videos and have not attempted any statistical analysis yet. The video on the left shows bacteria (green moving spots) invading the chip from the right. This video shows what happens after a couple hours – the bacteria invade all available space in “waves”. This is a similar phenomenon to the one reported in this paper.