NetLogo User Community Models
by Gary An, MD (Submitted: 06/08/2006)
WHAT IS IT?
This is a simple model that looks at diffusion of molecules with and without the presence of a membrane with variable permeability. It also includes a very abstracted active transport pump that counteracts the permeability limitations of the membrane. Of note, this model is "intentionally" not refined, to allow for planned input/improvement via student interactions. Of note, this version uses a membrane made from turtles.
HOW IT WORKS
The "world" is a container that can be divided into two by adding a membrane. Molecules are represented by circular agents that are added at the bottom screen edge via a button "add-molecule1" or "-2". The molecules have a random movement pattern, and upon initial addition of molecules they will diffuse to fill the space. With the addition of the membrane there is a barrier to this initial diffusion, and dependent upon the set permeability for the membrane it will take longer or shorter to reach equilibrium. The permeability represents a percentage likelyhood that a molecule will pass. The additon of the "Molecule1-pump" allows uni-drectional (from "above" to "below") complete permeability to molecule1.
HOW TO USE IT
To start, use the "molecule-amount" sliders to set the number of molecules created per patch. Then hit "setup," "add-molecules" to set initial conditions. You can add the membrane and molecule1-pump at the same time. You can set the "mode" to the right of the screen. Hit "go" to go. You can also add molecules during the run as well. You can also change the membrane permeability to either molecule during the run as well.
THINGS TO NOTICE
Notice the diffusion pattern after initial addition of molecule. The movement of the front egde of the particle "wave" looks volitional, but it is a byproduct of the random movement of particles from a higher concentration to a lower one.
THINGS TO TRY
You can add different numbers of molecules to see if there is a change in the time to equilibrium (would you expect there to be any effect?)
EXTENDING THE MODEL
Note that in this model the calculations for "osmolality-above" and "osmolality-below" assume the fixed sizes of the two chambers. Similarly, in "mode" = 1 the areas scaled to osmolality are constant. However, you can adjust the placement of the membrane to see the effect of unequal chambers.
This model uses the classic "wiggle" code for random movement.
CREDITS AND REFERENCES
This model was developed by Gary An, MD. At time of development he was in the Department of Trauma, Cook County Hospital, Chicago, IL, USA. Email any questions or comments to firstname.lastname@example.org
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