by Dirk Brockmann

This explorable illustrates a dynamic model for pattern formation in a growing community of microbes. Many microbial organisms exhibit collective behavior when a community of them expands say on a surface with nutrients. These patterns are often very beautiful and rich in structure.

If you are interested in exploring the beauty of microbial pattern formation have a look at Life at the Edge of Sight - A Photographic Exploration of the Microbial World a recent book by Scott Chimileski and Roberto Kolter that contains amazing photography of these patterns (and much more).

The model below is a variant of a model introduced in a 1994 paper Generic Modeling of Cooperative Growth Patterns in Bacterial Colonies, by a pioneer of the field, Eshel Ben-Jacob, and co-authors to describe patterns observed in communities of Bacillus Subtilis under various growth conditions.

This is how it works

Microbes in this model are motile particles that move around in a two-dimensional petri dish that contains a substrate with nutrients. Microbes consume the nutrients. The acquired energy is used for moving around in the substrate and for replication.

Initially, we have a droplet of microbes in the center. In this occupied area, microbes can move around relatively easily and slowly deplete the nutrients. In the beginning, nutrients are distributed evenly throughout the medium, the overall amount of nutrients can be selected with the Initial Amount of Nutrient slider.

To expand microbes need to push the boundary outwards into regions with more nutrients. The difficulty of this is controlled by the Medium Resistance slider.

In addition to these parameters you can change how efficiently the microbes metabolize the nutrients to acquire energy and the speed at which they move around.

When microbes deplete the nutrients and locally run out of food, they will eventually stop moving and enter a resting e.g. a spore state in which they just stick and wait.

Observe this

If you turn the initial amount of nutrients to its maximum value and the medium’s resistance to its minimum and press play, a pattern emerges that pretty much covers the plane densely because there’s sufficient food and the microbes can expand easily.

Now try a system with less nutrients and a higher resistance. In this regime, the pattern will be dominated by branches and will be less dense. The pattern expands at the tips of the branches where microbes haven’t gone into the resting state.

Likewise you can explore what happens if you change the motility and the metabolic efficiency.


* This explorable is called Scott’s world as a token of appreciation to Scott Chimileski great photographic art of the microbial world.

Related Explorables:

Scott's World*

Microbial growth patterns


The spatial hypercycle model

Surfing a Gene Pool

Expansion of clones with idential fitness

Surfing a Gene Pool

Expansion of clones with idential fitness

Particularly Stuck

Diffusion Limited Aggregation

Particularly Stuck

Diffusion Limited Aggregation