This model can be used to explore the dynamics of diffusion of aqueous particles between two compartments separated by a membrane.
When you click on "Run" you should see the particles diffuse around on the right side of the membrane, but only very rarely will they manage to cross the membrane. This is because the non-polar molecules of the membrane don't have energetic interactions with substances that dissolve easily in water. So the chance that an aqueous particle will give up it's energetic interactions with water and move into the membrane is very small.
If you click on "Stop" you can then choose the agent from the "Gallery" that is a yellow square. The yellow square agent represents a transporter protein. After you have selected the yellow agent, click on the pencil tool then click at a few positions along the grey membrane in the simulation area to place some transporter proteins there. Now what happens when you run the simulation?
A transporter protein has an outer surface that prefers to interact with the membrane, but it also provides sites of favorable interaction with the aqueous molecule, making it much more likely that the molecule will make its way across the membrane.
Note: The chart window should give you a sense of the number of particles that have crossed the membrane, you can see the actual counts by cicking on the button with the downward pointing arrowhead near teh top right corner of the siumlation area and selecting "Simulation Property Editor".
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