Purple Membrane Simulation Model

Purple Membrane (bacterioRhodopsin) Network Model

Description: This model simulates the biological pathway that produces bacterioRhodopsin in halobacterium. BacterioRhodopsin helps to give halobacterium its pink and purple hues. Please note that the intention of this model is only to represent the qualitative changes in the physical amounts of each compound. The graphical appearance of the nodes is not meant to be quantitative measures of those physical amounts. Also, this model is a simplified depiction of purple membrane creation. We have left out many details and focused on only the major components.

This model is generally used with Lesson 4 of the Environmental Influence on Gene Networks curriculum module.  Please use the above links for more information, lesson plans, and for teacher and student resources, such as this worksheet used to guide students through using the model.

To access the model, please click this link or type this address into a browser - http://bit.ly/PurpleMemSim.

Instructions: Click 'start/reset' to set up the model. Next, click 'go' to begin the model. You can now change the amounts of oxygen and light in the environment using the slider bars on the top left. As you can see, these environmental changes will affect the model in various ways. To find out more about a particular node, hover your mouse over the center of that node and a short description will print in the output window. Next, try knocking out one of the four proteins (the white squares) and observe the effect on the rest of the nodes. You can do this by either clicking on one of the knockout buttons on the left side or by hovering the mouse over the protein and holding down the mouse button. To reactivate a protein, click the corresponding reactivate button. You can also reactivate all deactivated proteins by clicking on 'reactivate all'.

If there are any issues with the above online simulation, you can instead download free NetLogo Software and run the model from your computer.  


  • Download, run, and/or save NetLogo 5.3.1 onto your PC, Mac, or Linux machine.
  • Download this zipped file: purple_membrane_5.3.1.
  • Extract the file from the zipped folder by either dragging it into a new folder or saving it into a new folder.  Do not change the file name from "purple_membrane_5.3.1.nlogo".
  • Launch NetLogo 5.3.1 from your machine.
    • Navigate to the "File" tab and then select the "Open" subsection.
    • Browse and select the "purple_membrane_5.3.1.nlogo" file you saved.  
    • Click the start button to begin using the model.  Or follow the instructions included in the worksheet to use the network model.

Acknowledgments: This model was developed for high school education through a grant from the National Science Foundation to ISB.

Created with NetLogo