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view/download model file: cell.nlogo

WHAT IS IT?

This model is part of the Rep Tools suite of models, a model of cell respiration, as part of project which involves teaching about the respiratory system through a combined Structure-Behavior-Function and emergent perspective.

The model uses the the code from the NetLogo sample models GasLab suite of models: Gas in a box. It is made up of the same basic rules for simulating the behavior of gases.

The basic principle of the models is that gas particles are assumed to have two elementary actions: they move and they collide - either with other particles or with any other objects such as walls. In addition, oxygen can react to form carbon dioxide. All the gases pass through the membrane of the cell with a given permeability. When gas leaves the cell, it is bound to red blood cells and slow down.

HOW IT WORKS

The particles are modeled as hard balls with no collisions, except those with the cell's membrane.

The basic principles are the following:

1. A particle moves in a straight line , unless it bounces off the membrane.
2. When a particle reaches the membrane, it goes through with the permeability probability or bounces back.
3. If a particle finds itself on or very close to a wall of the container, and it's not going through, it "bounces" -- that is, reflects its direction and keeps its same speed.
4. Energy consumption determines the rate at which oxygen reacts to form CO2 in the cell.
5.
When a gaseous oxygen molecule crosses the membrane in turns into bound oxygen on a red blood cell.
When a gaseous CO2 molecule crosses the membrane in turns into bound CO2 on a red blood cell.
When bound oxygen crosses the membrane in turns into free oxygen gas.
When bound CO2 crosses the membrane in turns into free CO2 gas.

HOW TO USE IT

Initial settings:
- INITIAL-NUMBER-BOUND-OXYGEN-BLOOD: number of oxygen moleucles in the blood (bound form)
- CELL-SIZE: size of the cell. (percentage of the screen size)

The SETUP button will set the initial conditions.
The GO/STOP button will run the simulation and stop it.

Other settings:
- ENERGY-CONSUMPTION: The rate at which energy is formed by the cell to service the body. This determines the probabity of oxygen reacting to form CO2.
- MEMBRANE-PERMEABILITY: The probability that if one of the molecules or blood cells reaches the membrane, it will go through.
- NUMBER-OXYGEN-ADD: The number of oxygen molecules that are added into the blood stream, upon pressing the ADD OXYGEN TO BLOOD button.

Monitors:
- CLOCK: time
- OXYGEN IN CELL: number of gaseous oxygen molecules in cell
- OXYGEN IN BLOOD: number of liquid bound-oxygen molecules in blood
- CO2 IN CELL: number of gaseous carbon-dioxide molecules in cell
- CO2 IN BLOOD: number of liquid bound-carbon-dioxide molecules in blood

CREDITS AND REFERENCES

Sharona T. Levi
Cindy E. Hmelo-Silver
Lei Liu
2005

Supported by the National Science Foundation