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--- tutorials:radiation-model-in-crop_model9 [2025/10/30 22:10] – barley1965
+++ tutorials:radiation-model-in-crop_model9 [2025/10/31 14:11] (current) – barley1965
@@ Line 1: / Line 1: @@
 ====== Assimilate Transport and Fruit Development ======
-The Transport model extends the FlowerAging model by implementing a physiologically-based system for sugar transport from photosynthetically active leaves through the plant architecture to developing fruits. This creates a more realistic simulation of source-sink relationships in the virtual plant.
+//Open {{ :tutorials:advanced:Transport.gsz |Transport.gsz}}//
+The Transport model extends the [[:Tutorials:Radiation-model-in-crop model7|Flower aging model]] by implementing a physiologically-based system for sugar transport from photosynthetically active leaves through the plant architecture to developing fruits. This creates a more realistic simulation of source-sink relationships in the virtual plant.
 ===== Assimilate Storage and Transport Parameters =====
-The model introduces a new parameter ''as'' (assimilate storage) to track sugar content in different organs:
+The model introduces a new parameter ''as'' (assimilate storage) to track sugar content in different organs (L. 9, 12, 43):
 <code java>
-module Internode(super.length, int age, int rank, float as)
+module Internode(super.length, int age, int rank, float as) extends Cylinder(length, 0.1);
-	extends Cylinder(length, 0.1);
+module Leaf(super.length, super.width, float al, int age, float as, int rank) extends Box(length, width, 0.01);
+module Fruit(float size, int age, float as) ==> Sphere(size).(setShader(RED));
+</code>
-module Leaf(super.length, super.width, float al, int age, float as,
+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).
-    int rank) extends Box(length, width, 0.01);
-module Fruit(float size, int age, float as) ==>
+===== Maintenance Respiration =====
-	Sphere(size).(setShader(RED));
+A maintenance respiration constant has been added to simulate the metabolic cost of keeping tissues alive (L. 96):
-<\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).
+<code java>
-) Maintenance Respiration
-A maintenance respiration constant has been added to simulate the metabolic cost of keeping tissues alive (L. 78):
 const float MR = 0.01; //maintenance respiration
-This is applied to internodes during growth to simulate sugar consumption:
+</code>
+This is applied to internodes during growth to simulate sugar consumption (L. 207 ff):
+<code java>
 itn:Internode ::> {
-    itn[age]++;
+		itn[age]++;
-    if(itn[as]>0) {itn[as] *= (1-MR); }
+		if(itn[as]>0) {itn[as] *= (1-MR); }
-    itn[length] += logistic(1, itn[age], 10, 0.1);
+		itn[length] += logistic(1, itn[age], 10, itn[as]);
-}
+		itn.(setShader(new RGBAShader(itn[as]*15.0, itn[as]*7.5, itn[as])));
-) Transport Mechanism
+	}
-The core innovation is the implementation of a diffusion-based transport system. The transport occurs with a diffusion constant that controls the rate (L. 75):
+</code>
-const float DIFF_CONST = 0.001;
-The transport is invoked periodically in the grow() method - every 24 timesteps to simulate hourly transport (L. 138-143):
+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]''.
+===== Transport Mechanism =====
+The main novelty of the present model is the implementation of a diffusion-based transport system. The transport occurs with a diffusion constant that controls the rate (L. 94):
+<code java>
+const float DIFF_CONST = 0.002;
+</code>
+Transport is invoked periodically in the ''grow()'' method - every 24 timesteps to simulate hourly transport (L. 145-149):
+<code java>
 if(time % 24 == 0) {
     for(int hour = 0; hour < 24; hour++) {
@@ Line 36: / Line 53: @@
     }
 }
-) Transport Rules
+</code>
+===== Transport Rules =====
 Three types of transport are implemented using user-defined edge relations:
-a) Leaf to Internode Transport (L. 251-258):
+**a) Leaf to Internode Transport, and vice versa ** (L. 256-280):
+<code java>
 lf:Leaf <-minDescendants- itn:Internode ::> {
-    if(lf[as] > 0.01) { // Keep minimum for leaf maintenance
+		if(lf[as] > 0.01 && lf[age]>=10) { // Keep minimum for leaf maintenance
         float exportable = lf[as] - 0.01;
         float r = DIFF_CONST * exportable;
         lf[as] -= r;
         itn[as] += r;
-    }
+		//println("transport from leaf to internode");
-}
+		} else
-This rule ensures leaves retain a minimum amount (0.01) for maintenance while exporting the surplus.
+	if(itn[as] > 0.01 && lf[age]<10) { // Keep minimum for internode maintenance
-b) Internode to Internode Transport (L. 260-268):
+        float exportable = itn[as] - 0.01;
+        float r = DIFF_CONST * exportable;
+        lf[as] += r;
+        itn[as] -= r;
+		//println("transport from internode to leaf");
+		}
+	}
+</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!
+**b) Internode to Internode Transport** (L. 260-268):
+<code java>
 i_top:Internode <-minDescendants- i_bottom:Internode ::> {
     if((i_bottom[as] - i_top[as])<=0) {
@@ Line 61: / Line 95: @@
     }
 }
-This bidirectional transport follows the concentration gradient between successive internodes.
+</code>
-c) Internode to Fruit Transport (L. 269-275):
+This bidirectional transport follows the concentration gradient between successive internodes.
+**c) Internode to Fruit Transport** (L. 269-275):
+<code java>
 itn:Internode -minDescendants-> fr:Fruit ::> {
     if(itn[as]>0) {
@@ Line 71: / Line 109: @@
     }
 }
-) Fruit Set Decision Based on Sugar Availability
+</code>
-The model now makes fruit formation dependent on available sugar in the plant (L. 165-172):
+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).
-fl:Flower(t, m), (t >= m) ==>
-    {float sugar = sum((* lf:Leaf *)[as]);
+===== Fruit Set Decision Based on Sugar Availability =====
-    println(sugar);
+The model now makes fruit formation dependent on sugar available in the nearest leaf (L. 169-174):
-    }
+<code java>
-    if(probability(0.6)) (Fruit(0.01,1,0.1))
+fl:Flower(t, m), (t >= m && t<m+2) ==>
-    else if(probability(0.4)) ();
+		{float sugar = first((* Leaf *)[as]);
-The sugar availability is calculated by summing all leaf assimilates before deciding on fruit formation.
+		println("sugar: " + sugar);
-) Fruit Growth Competition
+		}
-Multiple fruits compete for available resources using an age-based weighting system (L. 209-225):
+		if(sugar>0.0005) ({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.
+===== Fruit Growth Competition =====
+Multiple fruits compete for available resources using an age-based weighting system (L. 214-226):
+<code java>
 fr:Fruit ::> {
     float totalSugar = sum((* lf1:Leaf *)[as]);
@@ Line 95: / Line 141: @@
     float sugar = (totalAgeWeight > 0) ?
         (totalSugar * ageWeight) / totalAgeWeight : totalSugar / fruitCount;
-Younger fruits receive proportionally more resources through exponential age weighting, simulating their stronger sink strength.
+    </code>
-) Visual Feedback
+Younger fruits receive proportionally more resources through exponential age weighting, simulating their stronger sink affinity (thereby compensating their smaller size).
+===== Visual Feedback =====
 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])));
-Tasks for Exploration
+</code>
-.	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:
+===== Tasks for Exploration =====
-o	Speed of sugar movement?
+  - Run the model and observe sugar flow: Watch how internodes change color as sugar moves through them.
-o	Final fruit size?
+  - Modify DIFF_CONST: Try values between 0.0001 and 0.01. How does this affect:
-o	Number of successfully developed fruits?
+  *     Speed of sugar movement?
-.	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?
+  * 	Final fruit size?
-.	Adjust maintenance respiration: Change MR from 0.01 to 0.05. How does increased respiration affect fruit development?
+  * 	Number of successfully developed fruits?
-Key Improvements Over FlowerAging Model
+  - 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?
-Feature	FlowerAging	Transport
+  - Adjust maintenance respiration: Change MR from 0.01 to 0.05. How does increased respiration affect fruit development?
-Sugar tracking	Only in leaves	Leaves, internodes, and fruits
-Transport	None	Diffusion-based with user-defined edges
+===== Biological Relevance =====
-Fruit growth	Fixed size	Based on sugar availability
-Resource competition	None	Age-based weighting
-Maintenance costs	None	Respiration in internodes
-Visual feedback	Leaf color only	Leaf and internode color
-Biological Relevance
 This transport model introduces key physiological concepts:
 •	Source-sink relationships: Leaves act as sources, fruits as sinks
@@ Line 122: / Line 167: @@
 •	Maintenance respiration: Realistic metabolic costs
 •	Sink strength: Younger fruits have stronger sink strength
-The model provides a foundation for exploring how plant architecture and physiology interact to determine yield formation.