Purple Membrane Simulation 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 are 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.

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 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'.

Troubleshooting: Why doesn't anything appear in the applet above? The applet requires Java 1.4.1 or higher to run. It will not run on Windows 95 or Mac OS 8 or 9. Mac users must have OS X 10.2.6 or higher and use a browser that supports Java 1.4 applets. On other operating systems, you may obtain the latest Java plugin from Sun's Java site. If you still are not able to view network images above, please try using a different browser.

Author: Patrick Mar, Institute for Systems Biology

Principal Investigator: Nitin S. Baliga

Other Contributors: Marc Facciotti, Dan Gallagher, Paul Shannon, Kenia Whitehead

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

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view/download model file: PurpleMembrane.nlogo