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--- 02_user_tutorials:from_photosynthesis_to_transport [2026/09/25 15:44] – created barley1965
+++ 02_user_tutorials:from_photosynthesis_to_transport [2026/09/28 09:48] (current) – removed barley1965
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-====== Exercise: Sources, sinks and assimilate transport in a virtual plant ======
-//Master 2, specialties "Seed Science and Plant Propagation" and "Plant Health". Duration: about 2 hours. Work in pairs.//
-===== Learning objectives =====
-At the end of this session you should be able to:
-  * explain how a functional–structural plant model (FSPM) links **light interception → photosynthesis → transport → growth of sinks**;
-  * identify, in real model code, where each of these processes is computed and which organs act as **sources** or **sinks**;
-  * run a model experiment rigorously: **predict, run, observe, explain**;
-  * modify the model to represent a situation from your own field (a pest or disease, or seed/fruit set);
-  * critically judge what a model does and does not represent.
-You do **not** need to be a programmer. Every code change you are asked to make is given or guided step by step.
-===== Schedule =====
-^ Part ^ Content ^ Time ^
-| 0 | Setup: open and run the model | 10 min |
-| 1 | The biology in brief | 10 min |
-| 2 | The model at a glance | 15 min |
-| 3 | Run and observe | 15 min |
-| 4 | Reading the code: production, transport, use | 25 min |
-| 5 | Virtual experiments | 25 min |
-| 6 | Your specialty: plant health **or** seed science | 15 min |
-| 7 | Synthesis | 5 min |
-| (Bonus) | Connect transport to fruit growth | for fast groups |
-----
-===== Part 0 – Setup (10 min) =====
-  - Start GroIMP and open the project ''Transport.gsz'' (//File → Open//).
-  - The model code is in the file ''Example1.rgg''. Open it in the text editor (//Panels → Explorers → Files//, then double-click the file).
-  - In the toolbar of the 3D view you will find buttons for the **public** methods of the model. Here there is one: ''grow''. Each click on ''grow'' = **one time step = one hour** of simulated time.
-  - To reset the plant to its initial state, use the reset/"init" button (this executes the ''init()'' method). **Also, every time you save the code (Ctrl+S), the model is recompiled and reset.**
-  - Click ''grow'' a few times, then run it repeatedly (run/loop button) and stop it after ~100 steps.
-Three charts open automatically:
-^ Chart ^ What it shows ^
-| //Light intercepted by canopy// | total light absorbed by all leaves during the last hour |
-| //Canopy photosynthesis// | total amount of sugar **stored** in all leaves (stock, not the hourly production!) |
-| //Fruit growth// | size of every fruit over time (one series per fruit) |
-**Colour code in the 3D view** (false colours, for display only):
-  * Leaves: colour depends on the light they absorbed.
-  * Internodes: colour depends on their sugar content – the brighter, the more sugar.
-  * The brown floor is made of light-absorbing tiles; bright tiles receive more light.
-The ''println'' messages (e.g. "sugar import into fruit") appear in the **XL Console** window.
-===== Part 1 – The biology in brief (10 min) =====
-Plants produce sugars (assimilates) in **source** organs – mainly mature leaves – and use them in **sink** organs – young leaves, stems, roots, flowers, fruits and seeds. Sugars travel through the **phloem**. In the widely accepted Münch model, sugar loading at the source raises the osmotic pressure there, unloading at the sink lowers it, and the resulting pressure difference drives a mass flow from source to sink. A young leaf is first a sink and becomes a source when it reaches roughly a third to half of its final size (**sink–source transition**).
-**Questions (answer in 2–3 lines each):**
-  - **Q1.** Name three sources and three sinks in a tomato plant bearing fruit.
-  - **Q2.** Give one example of a pest or pathogen that changes the source–sink balance of a crop, and say whether it mainly reduces the source, adds a sink, or blocks transport.
-  - **Q3.** In a seed crop, why can the number of fruits/seeds set early in the season limit the final seed size?
-===== Part 2 – The model at a glance (15 min) =====
-==== 2.1 The organs (modules) ====
-^ Module ^ Role ^ Important attributes ^
-| ''Bud'' | apical meristem; produces new metamers | ''rank'' (position on the axis), ''phyllo'' (countdown until next metamer), ''order'' (1 = main stem, 2 = branch, 3 = dormant bud) |
-| ''Internode'' | stem segment; **transport pathway and small sink** | ''length'', ''age'', ''rank'', ''as'' (assimilate content) |
-| ''Node'' | attachment point of a leaf and a lateral bud | – |
-| ''Leaf'' | **source** (and sink while young) | ''length'', ''width'', ''al'' (absorbed light), ''age'', ''as'' (assimilate content) |
-| ''Flower'' | becomes a fruit if enough sugar is available | ''age'', ''max_age'' |
-| ''Fruit'' | **main sink** | ''size'', ''age'', ''as'', ''no'' (fruit number) |
-| ''Tile'' | light-absorbing ground | ''al'' |
-| ''MyLight'' | a 200 W spotlight 50 units above the plant | – |
-==== 2.2 What happens during one call of grow() ====
-<code java>
-public void grow () {
-    run();            // 1. architecture: new metamers, flowers, fruits, leaf death
-    lm.compute();     // 2. light model: ray tracing of the whole scene
-    absorbAndGrow();  // 3. light absorption, photosynthesis, organ growth
-    if (time % 24 == 0) {                       // 4. once every 24 steps ...
-        for (int hour = 0; hour < 24; hour++) {
-            transport();                        //    ... 24 rounds of transport
-        }
-    }
-    updateChart();    // 5. charts
-    time++;
-}
-</code>
-**Q4.** One step represents one hour (constant ''DURATION'' = 3600 s). How often is sugar actually transported in this model? Is this realistic? What could be the reason for this choice?
-==== 2.3 How the plant is built ====
-The rule that makes a bud produce a new metamer is:
-<code java>
-Bud(r, p, o), (r < 10 && p == 0 && o < 3) ==>
-    RV(-0.1) Internode(0.1, 1, r, 0.1) Node
-    [ RL(BRANCH_ANGLE) Bud(r, PHYLLOCHRON, o+1) ]   // lateral bud -> branch
-    [ LFA(1) Leaf(0.1, 0.07, 0, 1, 0, r) ]          // leaf
-    RH(GOLDEN_ANGLE) RV(-0.1) Internode(0.1, 1, r, 0.1)
-    Bud(r+1, PHYLLOCHRON, o);                       // the apex continues
-</code>
-**Q5.** Draw (on paper) one metamer as produced by this rule: which organs, in which order, and what is inside the square brackets ''[ ]''?
-**Q6.** When ''rank'' reaches 10, the bud turns into a ''Flower''. How many flowers do you expect on the plant? (Hint: look at the condition ''o < 3'' and at the order given to the main stem in ''init()''.)
-===== Part 3 – Run and observe (15 min) =====
-Reset the model and run it for about **300 steps** (≈ 12 days). Observe the 3D view, the charts and the console.
-Fill in:
-^ Observation ^ Your answer ^
-| Step at which the first flower appears | |
-| Step at which the first fruit appears | |
-| Number of fruits at step 300 | |
-| Shape of the fruit growth curves (linear? S-shaped? all the same?) | |
-| Where are the internodes brightest (most sugar)? Top, bottom, main stem, branches? | |
-| Which leaves absorb the most light? | |
-**Q7.** Do all flowers become fruits at the same time? Why not? (You will find the rule in Part 4.4.)
-===== Part 4 – Reading the code: production, transport, use (25 min) =====
-We now follow a sugar molecule from where it is made to where it is used.
-==== 4.1 Production: the light response curve ====
-<code java>
-float calculateCER(float ppfd) {
-    return ((FMAX + DARK_RESPIRATION_RATE) * PHOTO_EFFICIENCY * ppfd)
-         / (PHOTO_EFFICIENCY * ppfd + FMAX + DARK_RESPIRATION_RATE)
-         - DARK_RESPIRATION_RATE;
-}
-</code>
-''ppfd'' is the photon flux density received by the leaf (µmol photons m⁻² s⁻¹), CER is the CO₂ exchange rate (µmol CO₂ m⁻² s⁻¹). ''FMAX'' = 20, ''DARK_RESPIRATION_RATE'' = 0.5, ''PHOTO_EFFICIENCY'' = 0.85.
-  * **Q8.** What is the value of CER in darkness (ppfd = 0)? What does a negative value mean for the leaf?
-  * **Q9.** What value does CER approach when ppfd becomes very large? Sketch the curve.
-  * **Q10.** The function ''calculatePS'' then converts CER into kilograms of glucose produced by one leaf in one hour. Which three quantities is CER multiplied by? (Look at the code.)
-In ''absorbAndGrow()'', every leaf adds its production to its own stock: ''lf[as] += calculatePS(...)''.
-==== 4.2 Transport ====
-The method ''transport()'' contains three rules. Read them carefully.
-**Rule 1 – between a leaf and the internode that carries it**
-<code java>
-lf:Leaf <-minDescendants- itn:Internode ::> {
-    if (lf[as] > 0.01 && lf[age] >= 10) {        // mature leaf: EXPORT
-        float exportable = lf[as] - 0.01;
-        float r = DIFF_CONST * exportable;
-        lf[as] -= r;   itn[as] += r;
-    } else if (itn[as] > 0.01 && lf[age] < 10) { // young leaf: IMPORT
-        float exportable = itn[as] - 0.01;
-        float r = DIFF_CONST * exportable;
-        lf[as] += r;   itn[as] -= r;
-    }
-}
-</code>
-**Rule 2 – between two successive internodes** (simplified here, same meaning as in the model)
-<code java>
-i_top:Internode <-minDescendants- i_bottom:Internode ::> {
-    float r = DIFF_CONST * (i_top[as] - i_bottom[as]);
-    i_bottom[as] :+= r;
-    i_top[as]    :-= r;
-}
-</code>
-**Rule 3 – from an internode to a fruit**
-<code java>
-itn:Internode -minDescendants-> fr:Fruit ::> {
-    if (itn[as] > 0) {
-        float r = DIFF_CONST * itn[as];
-        itn[as] :-= r;   fr[as] :+= r;
-    }
-}
-</code>
-//Reading tip:// ''a:Leaf <-minDescendants- b:Internode'' means "b is an Internode found by going **down** from the leaf a towards the base" – i.e. the internode below the leaf. ''DIFF_CONST'' = 0.002 is the fraction of the difference (or of the stock) that moves per transport round.
-  * **Q11.** At what age does a leaf switch from sink to source in this model? Why do leaves keep a reserve of 0.01?
-  * **Q12.** In Rule 2, can sugar move **upwards** as well as **downwards**? What decides the direction? Which physical process does this rule resemble (hint: Fick's law)?
-  * **Q13.** Compare Rule 1 (export) and Rule 2. Does the export of a mature leaf depend on how much sugar is already in the internode? Is that consistent with the Münch model?
-  * **Q14.** In Rule 3, which quantity drives the flux into the fruit: the fruit's demand, or the internode's stock? What would a "strong" sink look like in this model?
-==== 4.3 Use: maintenance and growth ====
-  * Internodes lose 1 % of their sugar per step (''MR'', maintenance respiration) and grow in length depending on their sugar content (''itn[as]'').
-  * Leaves grow following a logistic curve (look at the leaf part of ''absorbAndGrow()'').
-  * Fruits grow in the ''fr:Fruit ::> { ... }'' block of ''absorbAndGrow()''.
-**Q15 – Detective question.** Look closely at the fruit block. Where does the variable ''sugar'' that drives fruit growth come from? Is it the sugar ''fr[as]'' delivered by transport (Rule 3)? Is the sugar used by the fruit removed from anywhere?
-**Q16.** Does leaf growth depend on the amount of sugar in the leaf? (Read the comment in the code, then read the code itself.)
-==== 4.4 Fruit set ====
-<code java>
-fl:Flower(t, m)(* <-minDescendants- Node -minDescendants-> lf:Leaf *),
-    (t >= m && t < m+2) ==>
-    { float sugar = lf[as]; }
-    if (sugar > 0) ( {noFrts++;} Fruit(0.01, 1, 0.1, noFrts) )
-    else (fl);
-</code>
-**Q17.** In words: under which condition does a flower become a fruit? Which leaf is checked? What happens to a flower when the condition is not met?
-===== Part 5 – Virtual experiments (25 min) =====
-Method, for **each** experiment:
-  - Write your **prediction** //before// running (effect on fruit number, fruit size, internode sugar, total leaf sugar).
-  - Change **one** value only, save (the model resets), run 300 steps.
-  - Record the result, then **restore the original value**.
-Every group does **E1**, plus **two** other experiments of its choice.
-^ Exp. ^ What to change ^ Where ^
-| E1 | ''DIFF_CONST'': 0.002 → 0.02, then → 0.0002 | constants at the top |
-| E2 | Lamp power: ''setPower(200.0)'' → 50.0 | module ''MyLamp'' |
-| E3 | Sink–source transition: leaf age ''10'' → ''30'' (two places in Rule 1) | ''transport()'' |
-| E4 | Maintenance respiration ''MR'': 0.01 → 0.05 | constants |
-| E5 | Transport every hour instead of 24 rounds once a day: in ''grow()'', replace the whole ''if (time % 24 == 0) {...}'' block by a single line ''transport();'' | ''grow()'' |
-| E6 | Phyllochron: ''PHYLLOCHRON'' 25 → 15 | constants |
-Results table (one line per run):
-^ Exp. ^ Value ^ Prediction ^ Nb fruits (step 300) ^ Size of largest fruit ^ Internode colour ^ Total leaf sugar (chart) ^ Explanation ^
-| Ref | – | – | | | | | |
-| E1 | 0.02 | | | | | | |
-| E1 | 0.0002 | | | | | | |
-| | | | | | | | |
-| | | | | | | | |
-**Q18.** Was any result the opposite of your prediction? Use your answer to Q15 to explain it.
-===== Part 6 – Your specialty (15 min) =====
-Choose **one** track and do at least one task.
-==== Track A – Plant Health ====
-**A1. Aphids: a new phloem sink.** Aphids feed directly on phloem sap. Add a colony on the internodes of rank 3, starting at step 100.
-At the top of the file, next to the other constants, add:
-<code java>
-const float APHID_RATE = 0.02;   // fraction of internode sugar taken per transport round
-float aphidSugar = 0;            // total sugar taken by the aphids
-</code>
-Inside ''transport()'', add a fourth rule (before the closing '']''):
-<code java>
-itn:Internode, (itn[rank] == 3 && time > 100) ::> {
-    float r = APHID_RATE * itn[as];
-    itn[as] :-= r;
-    aphidSugar += r;
-}
-</code>
-Print the total at each step: add ''println("aphids: " + aphidSugar);'' in ''grow()''. Compare with the reference run. Then try rank 8 instead of 3 (closer to the flowers).
-**A2. Defoliation by a leaf disease.** Remove all leaves of rank ≤ 4 at step 150. Add this rule in ''run()'':
-<code java>
-lf:Leaf, (time == 150 && lf[rank] <= 4) ==> ;
-</code>
-**A3. A pathogen that lowers photosynthetic capacity** (e.g. a leaf spot or a virus): reduce ''FMAX'' from 20 to 10.
-**Questions:**
-  * **QA1.** Which intervention reduced fruit set / fruit growth the most? Was the position of the aphid colony important? Why?
-  * **QA2.** Which of A1, A2, A3 reduces the //source//, which adds a //sink//? Why is it useful for a plant pathologist to make this distinction?
-  * **QA3.** What would you need to add to the model to represent the aphid population growing over time?
-==== Track B – Seed Science and Plant Propagation ====
-**B1. Fruit thinning.** Remove every second fruit at step 250. Add this rule in ''run()'':
-<code java>
-fr:Fruit, (time == 250 && fr[no] % 2 == 0) ==> ;
-</code>
-Compare the size of the remaining fruits with the reference run.
-**B2. Fruit abortion threshold.** In the fruit-set rule (Part 4.4), a flower sets fruit as soon as ''sugar > 0''. Replace ''0'' with a threshold, e.g. ''sugar > 0.05'', and then with a larger value. Record how the number of fruits and the time of fruit set change.
-**B3. Competition among fruits.** In the fruit block of ''absorbAndGrow()'', the sugar share of each fruit is weighted by ''Math.exp(-0.05 * fr[age])''. This gives **younger** fruits priority. Set the factor to ''0'' (equal shares), then to ''+0.05'' (older fruits get priority).
-**Questions:**
-  * **QB1.** Is there a trade-off between the number and the size of fruits? Show it with your results.
-  * **QB2.** In real plants, the first-set fruits usually dominate later ones. Which setting of B3 is closest to this? What are the consequences for seed-lot uniformity?
-  * **QB3.** A seed producer wants large, uniform seeds. Based on the model, what would you advise, and what is missing from the model to give a reliable answer?
-===== Part 7 – Synthesis (5 min) =====
-  * **Q19.** Draw a diagram (boxes and arrows) of the sugar flows in the model **as it is coded**: production → stocks → transport → use. Mark any place where sugar appears or disappears without an arrow.
-  * **Q20.** List two strengths and two limitations of this model for studying source–sink relations.
-===== Bonus – Make fruits grow on the sugar they actually receive =====
-For fast groups (this is a "new functionality" task). At present, fruits grow from the sugar stored in //all// leaves, which is never consumed (see Q15), while the sugar delivered by Rule 3 (''fr[as]'') is not used.
-Modify the fruit block in ''absorbAndGrow()'' so that:
-  - the fruit computes its **potential** growth for this step (you can keep the ''logistic(...)'' call with a fixed maximum),
-  - it converts potential growth into a **sugar demand** (introduce a constant, e.g. ''SUGAR_PER_SIZE''),
-  - it grows only as much as its stock ''fr[as]'' allows, and **removes** the sugar used from ''fr[as]''.
-Then repeat experiment E1. Do the results now match your original predictions?
-===== Before the exam =====
-This exercise is not handed in, but the questions above cover the kind of reasoning expected in the exam: explaining source–sink relations, reading a simple model rule, and predicting and interpreting the outcome of a virtual experiment. Keep your answers and tables as revision notes.