This is my attempt at the rules to try and get at what we were talking about. 
I. My attempt to break down the science into steps to help us think about rules for the model. 

There are two reactions to photosynthesis - the light dependent and the light independent (Calvin Cycle).   The light dependent reaction takes in light and water to make an energy rich molecule called NADPH and releases O2. The light independent reaction takes the energy from the energy NADPH by breaking the H bond and also CO2 and makes sugar and releases water. # Light energy is absorbed by the chloroplasts in a leaf.  Water enters the plant via the roots, travels through the stem, into the viens of the leaf and disperses across the leaf's cells. 

1. The light energy that got absorbed excited molecules in the choloroplasts, this drives the transfer of electrons and hydrogen from water to an acceptor called NADP+.  The addition of a H to NADP+ makes this molecule NADPH and temporarly stores the energized electrons.  Water is split in this reaction and the H goes to the NADP+ and O2 is released. Oxygen given off by plants is from the splitting of water not carbon dioxide.
2. During the light reaction an ADP is converted into an ATP.
3. Calvin Cycle - The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplasts.  To reduce CO2 it takes the energy from the ATP molecule and NADPH generated in the light dependent reaction. 
   "The Calvin cycle in most plants occurs during the daylight, for only then can the light reactions regenerate the NADPH and ATP spent in the reduction of CO2 to sugar." 
    
   II. Potential Rules for NL model
   
   
   Water

-         there is a certain amount of water that is allowed in the stem and the leaf.  If those amounts are not met then the blue turtles (water) in the vase are allowed to move up the stem and into the leave to keep the water amounts in the leaf constant. Each area has a certain number of turtles it needs with the stem needing to fill their needs first and then the leaves.

-         If there is no water in the cup then the chloroplast turtles first turn brown (this assuming the sun is kept constant), and if they still do not get water, the stem turtles all move over on square to show wilting, if after extended part of time without water, a leaf falls off and then another leaf, etc.. until the plant dies.

-         When a water turtle runs into an excited chloroplast turtle then they connect, and a water turtle is subtracted from the total number of water turtles in the leaf.  A call for another turtle to fill its space is sent out.

-         The water turtles in the leave move through the veins and then randomly disperse into the bigger section of the leaf.

-         There is a slider to determine how much water you start with. 
Chloroplasts

-         The leaf is a designated space.  But the leaf is actually made up of a number of chloroplasts.  I would actually use an emergent behavior to construct the leaf.  Start with the molecules inside the chloroplasts.  For example, say 10 turtles = one chloroplasts.  We need 100 chloroplasts to appear in area x to y.

-         Inside each of the chloroplasts are green turtles. They are moving around slowly.

-         when a chloroplasts turtle meets up with a sun turtle then the chloroplast turtle gets turned into an excited chloroplast turtle.  An excited chloroplast turtle moves around its determined area faster and alters its shading to visually show it is excited.

-         When an excited chloroplast turtle runs into a water molecule, one oxygen is releases and the excited chloroplast turtle changes its shade again to be ready to receive a carbon dioxide. 

-         If a non-excited chloroplast turtle runs into water, nothing happens.

-         When the excited chloroplast turtle with water runs into carbon dioxide - sugar is produced and the number of carbon dioxide molecules is down by one, the cholorplast turtle gets returned to non-excited state.  
Sun

-         the sun turtles move out from the sun in a trajectory type of motion until they hit something and then they disappear.

-         We could still use your moving sun idea to simulate day and night. That could be a very interesting behavior.

-         Slider options could be (in full sunlight all day, overcast, partial sun during the day, shade most of the day..very little sun) 
Carbon Dioxide

-         CO2 turtles are randomly running around outside of the plant.  We need to figure out some way that they enter into the leaf. 

-         There is a slider to determine how many CO2 molecules you start with.

-         Ed question - what happens to a plant if it does not get CO2?  For example, if our model has a set number of CO2 turtles and they get used up, what happens?  Do we just want to keep this constant?  I think it could be interesting if we wanted to keep it variable.  
Display or Output Boxes

-         CO2 levels

-         Sugar levels

-         H20 available for the plant

-         H20 released from the plant

-         Sunlight levels 
Sliders

-         sunlight

-         CO2

-         H20

NL Leaf Model.pdf.jpg (image/pjpeg)
Photo equat w arrows.pdf (application/pdf)
NL Leaf Model.pdf.jpg (image/pjpeg)
Photo equat w arrows.pdf (application/pdf)
Photo equat w arrows.jpeg.pdf (application/pdf)
Photo equat w arrows.pdf (application/pdf)
arrow pic.pdf.pdf (application/pdf)
arrow pic.jpeg.pdf (application/pdf)