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--- tutorials:radiation-model-in-crop_model9 [2025/10/31 14:11] – barley1965
+++ tutorials:radiation-model-in-crop_model9 [2025/11/01 15:40] (current) – barley1965
@@ Line 16: / Line 16: @@
 </code>
-Note that we now track assimilates (''as'') in three types of modules: leaves (where they are produced), internodes (where they are transported), and fruits (where they accumulate).
+Assimilates are monitored in three types of modules: leaves (where they are produced), internodes (where they are transported), and fruits (where they accumulate).
 ===== Maintenance Respiration =====
@@ Line 36: / Line 36: @@
 </code>
-Note that internode length is incremented up to a fixed length of 1, however, we vary the speed of elongation as a function of sugar available in the internode, ''itn[as]''.
+Internode length is incremented up to a fixed length of 1, however, we vary the speed of elongation as a function of sugar available in the internode, ''itn[as]''.
 ===== Transport Mechanism =====
@@ Line 79: / Line 79: @@
 </code>
-This rule ensures leaves retain a minimum amount (0.01) for maintenance while exporting the surplus. In fact, if you look closely, assimilates can also go the other way, from an internode to a (young) leaf, because the latter is a sugar sink before it has reached its final size and becomes a net exporter of assimilates!
+This rule ensures leaves retain a minimum amount (0.01) for maintenance while exporting the surplus. As you can see from the second half of the rule, assimilates can also go the other way, from an internode to a (young) leaf, because the latter is a sugar sink before it has reached its final size and becomes a net exporter of assimilates!
 **b) Internode to Internode Transport** (L. 260-268):
@@ Line 110: / Line 110: @@
 }
 </code>
-This final rule expresses transport in only one direction, i.e. fruits are //absolute sinks// (which is wrong, because young fruit are often green and have been shown to carry out photosynthesis).
+This final rule expresses transport in only one direction, i.e. fruits are //absolute sinks// (as usual, we simplify things here, because young fruit are often green and have been shown to carry out photosynthesis).
 ===== Fruit Set Decision Based on Sugar Availability =====
-The model now makes fruit formation dependent on sugar available in the nearest leaf (L. 169-174):
+The model now makes fruit formation dependent on the availability of a threshold amount of sugar in the nearest leaf (L. 169-174):
 <code java>
-fl:Flower(t, m), (t >= m && t<m+2) ==>
+fl:Flower(t, m)(* <-minDescendants-Node-minDescendants->lf:Leaf *),(t >= m && t<m+2) ==>
-		{float sugar = first((* Leaf *)[as]);
+		{float sugar = lf[as];
 		println("sugar: " + sugar);
 		}
-		if(sugar>0.0005) ({noFrts++;} Fruit(0.01,1,0.1,noFrts))
+		if(sugar>0) ({noFrts++;} Fruit(0.01,1,0.1,noFrts))
 		else (fl);
 </code>
 Note that a ''Flower'' that has not yet become a ''Fruit'', has two more chances to become one.
-Availability of sugar is calculated by querying ''as'' of the nearest ''Leaf'' before deciding on fruit formation.
+Availability of sugar is calculated by querying ''as'' of the nearest ''Leaf'' before deciding on fruit formation. This query uses two ''minDescendants'' edges, first down to the next lower Node module, then up to the attached Leaf.
 ===== Fruit Growth Competition =====
@@ Line 148: / Line 148: @@
 Internodes change color based on their sugar content, providing visual feedback of the transport process:
 <code java>
-itn.(setShader(new RGBAShader(itn[as]*2000.0, itn[as]*1000, itn[as])));
+itn.(setShader(new RGBAShader(itn[as]*20.0, itn[as]*10, itn[as])));
 </code>
+{{:tutorials:transport.png?direct&400|}}
+===== Fruit growth: graphical output =====
+In order to see the development in time of each fruit, we have created a graph "Fruit growth. Here is how the associated data table (fruitdata) is filled:
+<code java>
+fruitdata.(setColumnKey((int)fr[no]-1, fr[no]));
+    if(time>0) {fruitdata.addRow().set((int)fr[no]-1,time,fr[size]);}
+</code>
+{{:tutorials:fruitgrowth.png?direct&400|}}
+{{:tutorials:fruitgrowth2.png?direct&400|}}
+{{:tutorials:fruitgrowth3.png?direct&400|}}
+{{:tutorials:fruitgrowth4.png?direct&400|}}
 ===== Tasks for Exploration =====
-  - Run the model and observe sugar flow: Watch how internodes change color as sugar moves through them.
+  - Run the model and observe sugar flow: Watch how internodes change color as sugar moves through them!
-  - Modify DIFF_CONST: Try values between 0.0001 and 0.01. How does this affect:
+  - Modify DIFF_CONST: Try values between 0.0001 and 0.01. How does this affect: Speed of sugar movement? Final fruit size? Number of successfully developed fruits?
-  *     Speed of sugar movement?
-  * 	Final fruit size?
-  * 	Number of successfully developed fruits?
   - Change transport frequency: Modify the condition if(time % 24 == 0) to different values (e.g., % 12 for twice-daily transport). What impact does this have?
   - Adjust maintenance respiration: Change MR from 0.01 to 0.05. How does increased respiration affect fruit development?
+  - The different Fruit growth graphs have been produced by modifying a single parameter: which one could that have been? (Hint: have a look at the run method, where new lateral buds are inserted).
 ===== Biological Relevance =====
 This transport model introduces key physiological concepts:
-•	Source-sink relationships: Leaves act as sources, fruits as sinks
+  - Source-sink relationships: Leaves act as sources, fruits as sinks
-•	Phloem transport: Simplified as diffusion along concentration gradients
+  - Phloem transport: Simplified as diffusion along concentration gradients
-•	Competition for resources: Multiple sinks compete for limited assimilates
+  - Competition for resources: Multiple sinks compete for limited assimilates
-•	Maintenance respiration: Realistic metabolic costs
+  - Maintenance respiration: Realistic metabolic costs
-•	Sink strength: Younger fruits have stronger sink strength
+  - Sink strength: Younger fruits have stronger sink affinity