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If clicking does not initiate a download, try right clicking or control clicking and choosing "Save" or "Download".(The run link is disabled because this model uses extensions.)

## WHAT IS IT?

This is an individual-based biofilm model. Cells can switch between two phenotypes: susceptible and persister. Persisters do not grow but are tolerant to the antibiotic. Different switching strategies between these two phenotypes are implemented. Antibiotic treatments can be simulated to study the survival and recovery of the biofilm.

For more information:
Carvalho et al. (2018), How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics?, npj Biofilms and Microbiomes 4:6, doi:10.1038/s41522-018-0049-2

## HOW IT WORKS

Cells are initialized on a surface and grow, divide and shove each other to generate a biofilm. Dissolved substrate and antibiotic diffuse and react with the cells in a diffusion-reaction fashion. They diffuse from a bulk liquid above the biofilm, where concentrations are maintained constant, across a boundary layer toward the biofilm. In the model, bacteria can be susceptible, persister or dead.

## HOW TO USE IT

Setup and go!

## THINGS TO NOTICE

The dynamics of survival and recovery of the biofilm vary greatly depending on the switching strategy selected and the parameters a and b.

## THINGS TO TRY

(suggested things for the user to try to do (move sliders, switches, etc.) with the model)

## EXTENDING THE MODEL

(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)

## NETLOGO FEATURES

(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features)

## RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

## CREDITS AND REFERENCES

Carvalho et al. (2018), How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics?, npj Biofilms and Microbiomes 4:6, doi:10.1038/s41522-018-0049-2

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