Feat: Implement interconnected organ simulation

This commit refactors the organ simulation to enable dynamic interactions between organs, replacing the previous "faked" or hardcoded connections.

Key changes include:
- Major Refactoring: Changed the `Organ::update` method signature to `update(Patient& patient, double deltaTime_s)`, allowing organs to access the shared patient state and other organs. This was propagated to all organ classes.
- Blood Chemistry Model: Introduced a central `Blood` struct in the `Patient` model to track shared resources like oxygen, CO2, glucose, and toxins.
- Organ System Interconnections:
    - Lungs & Brain: Lungs now perform gas exchange affecting the blood. The brain consumes O2, produces CO2, and its GCS is affected by hypoxia/hypercapnia.
    - Liver-Gallbladder: Gallbladder now receives bile directly from the liver's production rate.
    - Digestive System: Stomach passes chyme to the intestines, which absorb glucose into the blood. The pancreas responds to blood glucose changes.
    - Renal System: Kidneys' GFR is now influenced by the heart's aortic pressure, and they produce urine that fills the bladder directly.
    - Cardiovascular & Neurological: The heart rate responds to hypoxia, and the brain uses live aortic pressure from the heart.
- Comprehensive Test Scenario: Updated the main example to include a 60-second simulation with a meal and a lung injury event to verify the new interconnected system.

This creates a more realistic and scalable physiological simulation framework where organ behaviors are emergent from their interactions.

examples/main.cpp

@@ -8,31 +8,69 @@
 #include "MedicalLib/Patient.h"
 #include "MedicalLib/Organ.h"
 #include "MedicalLib/Heart.h"
+#include "MedicalLib/Stomach.h"
+#include "MedicalLib/Lungs.h"
 
 int main() {
     // Initialize a new patient with a 12-lead heart
     Patient patient = initializePatient(1, 12);
     std::cout << "Patient created with ID: " << patient.patientId << std::endl;
 
+    // Introduce a toxin load to the blood for the liver to clear
+    patient.blood.toxins_au = 100.0;
+    std::cout << "Initial toxin load of 100.0 a.u. introduced.\n" << std::endl;
+
     // Simulate time passing and print a live summary
-    const double simulationTime_s = 10.0;
+    const double simulationTime_s = 60.0; // Run for a longer time to see effects
-    const double deltaTime_s = 0.05; // 20 Hz update rate for display
+    const double deltaTime_s = 0.1;
     const int numSteps = static_cast<int>(simulationTime_s / deltaTime_s);
 
-    std::cout << "\n--- Simulating " << simulationTime_s << " seconds of heart activity... ---" << std::endl;
+    // Get pointers to organs we want to interact with
+    Stomach* stomach = getOrgan<Stomach>(patient);
+    if(stomach) {
+        stomach->addSubstance(300.0); // Simulate eating a meal
+        std::cout << "A 300mL meal has been consumed." << std::endl;
+    }
+    Lungs* lungs = getOrgan<Lungs>(patient);
+
+
+    std::cout << "\n--- Simulating " << simulationTime_s << " seconds... ---" << std::endl;
 
     for (int i = 0; i < numSteps; ++i) {
+        double currentTime = i * deltaTime_s;
         // Clear console on systems that support ANSI escape codes
         #if defined(__linux__) || defined(__APPLE__)
         std::cout << "\033[2J\033[1;1H";
         #endif
 
+        // --- Event scripting ---
+        if (std::abs(currentTime - 20.0) < deltaTime_s/2.0) {
+            if (lungs) {
+                std::cout << "\n*** LUNG INJURY EVENT ***\n" << std::endl;
+                lungs->inflictDamage(0.8); // 80% damage
+            }
+        }
+
         updatePatient(patient, deltaTime_s);
 
-        std::cout << "Time: " << i * deltaTime_s << "s / " << simulationTime_s << "s\n" << std::endl;
+        std::cout << "Time: " << currentTime << "s / " << simulationTime_s << "s\n" << std::endl;
-        std::cout << getOrganSummary(patient, "Heart") << std::endl;
+        std::cout << "--- Blood Chemistry ---\n"
+                  << "SpO2: " << patient.blood.oxygenSaturation << " %\n"
+                  << "PaCO2: " << patient.blood.co2PartialPressure_mmHg << " mmHg\n"
+                  << "Glucose: " << patient.blood.glucose_mg_per_dL << " mg/dL\n"
+                  << "Toxins: " << patient.blood.toxins_au << " a.u.\n\n";
 
-        std::this_thread::sleep_for(std::chrono::milliseconds(50));
+        std::cout << getOrganSummary(patient, "Heart") << std::endl;
+        std::cout << getOrganSummary(patient, "Lungs") << std::endl;
+        std::cout << getOrganSummary(patient, "Brain") << std::endl;
+        std::cout << getOrganSummary(patient, "Stomach") << std::endl;
+        std::cout << getOrganSummary(patient, "Intestines") << std::endl;
+        std::cout << getOrganSummary(patient, "Pancreas") << std::endl;
+        std::cout << getOrganSummary(patient, "Kidneys") << std::endl;
+        std::cout << getOrganSummary(patient, "Bladder") << std::endl;
+
+
+        std::this_thread::sleep_for(std::chrono::milliseconds(100));
     }
 
     std::cout << "\n--- Simulation Complete. Final State: ---\n" << std::endl;

include/MedicalLib/Bladder.h

@@ -25,9 +25,10 @@ public:
 
     /**
      * @brief Updates the bladder's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the bladder's state.

include/MedicalLib/Brain.h

@@ -28,9 +28,10 @@ public:
 
     /**
      * @brief Updates the brain's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the brain's vitals.

include/MedicalLib/Esophagus.h

@@ -34,9 +34,10 @@ public:
 
     /**
      * @brief Updates the esophagus state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the esophagus's state.

include/MedicalLib/Gallbladder.h

@@ -24,9 +24,10 @@ public:
 
     /**
      * @brief Updates the gallbladder's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the gallbladder's state.

include/MedicalLib/Heart.h

@@ -52,9 +52,10 @@ public:
 
     /**
      * @brief Updates the heart's state over time, simulating the cardiac cycle.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the heart's vitals, including EKG and mechanical data.

include/MedicalLib/Intestines.h

@@ -28,9 +28,10 @@ public:
 
     /**
      * @brief Updates the intestines' state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the intestines' state.

include/MedicalLib/Kidneys.h

@@ -26,9 +26,10 @@ public:
 
     /**
      * @brief Updates the kidneys' state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the kidneys' state.

include/MedicalLib/Liver.h

@@ -26,9 +26,10 @@ public:
 
     /**
      * @brief Updates the liver's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the liver's vitals.

include/MedicalLib/Lungs.h

@@ -44,9 +44,10 @@ public:
 
     /**
      * @brief Updates the lungs' state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the lungs' vitals.
@@ -54,6 +55,12 @@ public:
      */
     std::string getSummary() const override;
 
+    /**
+     * @brief Inflicts damage on the lungs, reducing their compliance.
+     * @param damage The amount of damage to inflict (0-1).
+     */
+    void inflictDamage(double damage);
+
     // --- Getters for Key Respiratory Vitals ---
 
     /** @brief Gets the current respiration rate in breaths per minute. */

include/MedicalLib/Organ.h

@@ -3,6 +3,9 @@
 #include <string>
 #include <vector>
 
+// Forward-declare to avoid circular dependency
+struct Patient;
+
 // Define MEDICAL_LIB_EXPORT for exporting symbols from the DLL
 #if defined(_WIN32)
     #if defined(MEDICAL_LIB_EXPORT)
@@ -33,9 +36,10 @@ public:
 
     /**
      * @brief Pure virtual function to update the organ's state over time.
+     * @param patient A reference to the patient object for inter-organ communication.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    virtual void update(double deltaTime_s) = 0;
+    virtual void update(Patient& patient, double deltaTime_s) = 0;
 
     /**
      * @brief Pure virtual function to get a string summary of the organ's vitals.

include/MedicalLib/Pancreas.h

@@ -16,9 +16,10 @@ public:
 
     /**
      * @brief Updates the pancreas's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the pancreas's state.

include/MedicalLib/Patient.h

@@ -7,11 +7,22 @@
 // Forward-declare the Organ class to avoid circular dependencies
 class Organ;
 
+/**
+ * @brief Represents the composition of the patient's blood.
+ */
+struct Blood {
+    double oxygenSaturation = 98.0;      // Normal SpO2
+    double co2PartialPressure_mmHg = 40.0; // Normal PaCO2
+    double glucose_mg_per_dL = 100.0;    // Normal fasting glucose
+    double toxins_au = 0.0;              // Arbitrary units, 0 is clean
+};
+
 /**
  * @brief Holds all the vital signs and other medical information for a patient.
  */
 struct Patient {
     int patientId;
+    Blood blood;
     std::vector<std::unique_ptr<Organ>> organs;
 };
 
@@ -67,6 +78,22 @@ MEDICAL_LIB_API std::string getPatientSummary(const Patient& patient);
  * @brief Gets a pointer to a specific organ by its type.
  * @tparam T The type of the organ to get.
  * @param patient The patient to get the organ from.
+ * @return A pointer to the organ if found, otherwise nullptr.
+ */
+template<typename T>
+T* getOrgan(Patient& patient) {
+    for (auto& organ : patient.organs) {
+        if (T* specificOrgan = dynamic_cast<T*>(organ.get())) {
+            return specificOrgan;
+        }
+    }
+    return nullptr;
+}
+
+/**
+ * @brief Gets a const pointer to a specific organ by its type.
+ * @tparam T The type of the organ to get.
+ * @param patient The patient to get the organ from.
  * @return A const pointer to the organ if found, otherwise nullptr.
  */
 template<typename T>

include/MedicalLib/SpinalCord.h

@@ -35,9 +35,10 @@ public:
 
     /**
      * @brief Updates the spinal cord's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the spinal cord's vitals.

include/MedicalLib/Spleen.h

@@ -32,9 +32,10 @@ public:
 
     /**
      * @brief Updates the spleen's state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the spleen's state.

include/MedicalLib/Stomach.h

@@ -35,9 +35,10 @@ public:
 
     /**
      * @brief Updates the stomach state over a time interval.
+     * @param patient A reference to the patient object.
      * @param deltaTime_s The time elapsed in seconds.
      */
-    void update(double deltaTime_s) override;
+    void update(Patient& patient, double deltaTime_s) override;
 
     /**
      * @brief Gets a string summary of the stomach's state.

src/Bladder.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Bladder.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -11,14 +12,7 @@ Bladder::Bladder(int id)
       pressure_cmH2O(5.0),
       internalSphincterClosed(true) {}
 
-void Bladder::update(double deltaTime_s) {
+void Bladder::update(Patient& patient, double deltaTime_s) {
-    // In a connected model, this would be called by the Kidneys.
-    // For now, simulate a constant fill rate from the kidneys.
-    const double urineInflow_ml_per_s = 0.02;
-    if (currentState != MicturitionState::VOIDING) {
-        addUrine(urineInflow_ml_per_s * deltaTime_s);
-    }
-
     // Simple pressure model: pressure increases with volume
     pressure_cmH2O = (currentVolume_mL / capacity_mL) * 60.0;
 

src/Brain.cpp

@@ -1,4 +1,6 @@
 #include "MedicalLib/Brain.h"
+#include "MedicalLib/Patient.h" // For Blood struct
+#include "MedicalLib/Heart.h"   // For Heart data
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -29,13 +31,17 @@ Brain::Brain(int id)
     cerebellum = {"Cerebellum", 0.6, 60.0};
 }
 
-void Brain::update(double deltaTime_s) {
+void Brain::update(Patient& patient, double deltaTime_s) {
     totalTime_s += deltaTime_s;
 
-    // In a real scenario, MAP would be provided by the circulatory system (Heart)
+    // Get Mean Arterial Pressure from the Heart
-    // For now, we'll just keep it stable with minor fluctuations.
+    if (const Heart* heart = getOrgan<Heart>(patient)) {
-    meanArterialPressure_mmHg += getFluctuation(0.1);
+        meanArterialPressure_mmHg = heart->getAorticPressure();
-    meanArterialPressure_mmHg = std::clamp(meanArterialPressure_mmHg, 85.0, 95.0);
+    } else {
+        // If no heart, use a default stable value
+        meanArterialPressure_mmHg += getFluctuation(0.1);
+        meanArterialPressure_mmHg = std::clamp(meanArterialPressure_mmHg, 85.0, 95.0);
+    }
 
     updateActivity(deltaTime_s);
     updatePressures(meanArterialPressure_mmHg);
@@ -45,6 +51,37 @@ void Brain::update(double deltaTime_s) {
     if (eegData.size() > eegHistorySize) {
         eegData.pop_back();
     }
+
+    // --- Blood Interaction ---
+    Blood& blood = patient.blood;
+    // Brain consumes O2 and produces CO2. Rate depends on activity.
+    double totalActivity = (frontalLobe.activityLevel + temporalLobe.activityLevel +
+                           parietalLobe.activityLevel + occipitalLobe.activityLevel +
+                           cerebellum.activityLevel) / 5.0;
+
+    // O2 consumption
+    double o2_consumption = 0.1 * totalActivity * deltaTime_s; // % per second
+    blood.oxygenSaturation -= o2_consumption;
+
+    // CO2 production
+    double co2_production = 0.08 * totalActivity * deltaTime_s; // mmHg per second
+    blood.co2PartialPressure_mmHg += co2_production;
+
+    // Update GCS based on blood gas levels
+    if (blood.oxygenSaturation < 85.0) {
+        gcsScore = 10;
+    } else if (blood.oxygenSaturation < 75.0) {
+        gcsScore = 6;
+    } else {
+        gcsScore = 15;
+    }
+
+    if (blood.co2PartialPressure_mmHg > 60.0) {
+        gcsScore = std::min(gcsScore, 12); // CO2 narcosis
+    }
+    if (blood.co2PartialPressure_mmHg > 80.0) {
+        gcsScore = std::min(gcsScore, 8);
+    }
 }
 
 void Brain::updateActivity(double deltaTime_s) {
@@ -52,9 +89,12 @@ void Brain::updateActivity(double deltaTime_s) {
     frontalLobe.activityLevel += getFluctuation(0.005);
     frontalLobe.activityLevel = std::clamp(frontalLobe.activityLevel, 0.7, 0.9);
 
-    // GCS is a clinical score, doesn't typically change second-to-second.
+    // GCS is a clinical score, doesn't typically change second-to-second,
-    // This is a placeholder for future, more complex pathology simulation.
+    // but it will be affected by severe hypoxia or hypercapnia.
-    gcsScore = 15;
+    // This is a simplified model.
+    if (gcsScore > 8) { // Only check if not already severely impaired
+        if (cerebralPerfusionPressure_mmHg < 50) gcsScore = 8; // Reduced perfusion
+    }
 }
 
 void Brain::updatePressures(double meanArterialPressure) {

src/Esophagus.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Esophagus.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -9,7 +10,7 @@ Esophagus::Esophagus(int id)
       currentState(PeristalsisState::IDLE),
       lowerEsophagealSphincterTone(20.0) {}
 
-void Esophagus::update(double deltaTime_s) {
+void Esophagus::update(Patient& patient, double deltaTime_s) {
     // Simulate a swallow every 15 seconds for demonstration
     static double timeSinceLastSwallow = 0.0;
     timeSinceLastSwallow += deltaTime_s;

src/Gallbladder.cpp

@@ -1,4 +1,6 @@
 #include "MedicalLib/Gallbladder.h"
+#include "MedicalLib/Patient.h"
+#include "MedicalLib/Liver.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -10,12 +12,15 @@ Gallbladder::Gallbladder(int id)
       storedBile_mL(30.0),
       bileConcentrationFactor(5.0) {}
 
-void Gallbladder::update(double deltaTime_s) {
+void Gallbladder::update(Patient& patient, double deltaTime_s) {
-    // A real model would be driven by liver output and CCK hormone for contraction.
+    // Get bile from the liver
-    // For now, simulate slow storage and concentration, with a periodic contraction.
+    if (const Liver* liver = getOrgan<Liver>(patient)) {
+        double bileProduced_mL = liver->getBileProductionRate() * deltaTime_s;
+        storeBile(bileProduced_mL);
+    }
 
-    // Simulate bile coming from the liver
+    // A real model would also be driven by CCK hormone for contraction.
-    storeBile(0.005 * deltaTime_s); // Slow constant trickle
+    // For now, simulate slow storage and concentration, with a periodic contraction.
 
     switch (currentState) {
         case GallbladderState::STORING:

src/Heart.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Heart.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -57,11 +58,21 @@ Heart::Heart(int id, int numLeads)
     }
 }
 
-void Heart::update(double deltaTime_s) {
+void Heart::update(Patient& patient, double deltaTime_s) {
     // --- Electrical Simulation Update ---
     totalTime_s += deltaTime_s;
+
+    // Compensatory response to hypoxia
+    double o2_saturation = patient.blood.oxygenSaturation;
+    double targetHeartRate = 75.0;
+    if (o2_saturation < 90.0) {
+        targetHeartRate = 75.0 + (90.0 - o2_saturation) * 2.0; // Increase HR as SpO2 drops
+    }
+
+    // Move current heart rate towards the target
+    heartRate += (targetHeartRate - heartRate) * 0.1 * deltaTime_s;
     heartRate += getFluctuation(0.01); // Slow variation in underlying rate
-    heartRate = std::max(60.0, std::min(heartRate, 100.0));
+    heartRate = std::max(60.0, std::min(heartRate, 140.0));
     double cycleDuration_s = 60.0 / heartRate;
 
     double oldCyclePosition = cardiacCyclePosition_s;

src/Intestines.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Intestines.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -23,20 +24,16 @@ Intestines::Intestines(int id)
     colon = {"Colon", 1.5, 0.5, 0.1, 1.0}; // High water absorption
 }
 
-void Intestines::update(double deltaTime_s) {
+void Intestines::update(Patient& patient, double deltaTime_s) {
-    // For demonstration, simulate chyme arriving from the stomach
-    static double timeSinceChyme = 0.0;
-    timeSinceChyme += deltaTime_s;
-    if (timeSinceChyme > 25.0) {
-        receiveChyme(10.0); // Receive 10mL of chyme
-        timeSinceChyme = 0.0;
-    }
-
     if (chymeVolume_mL > 0) {
         // Simplified absorption model: total absorption is an average of all segments
         double totalNutrientAbsorption = (duodenum.nutrientAbsorptionRate + jejunum.nutrientAbsorptionRate + ileum.nutrientAbsorptionRate + colon.nutrientAbsorptionRate) / 4.0;
         double totalWaterAbsorption = (duodenum.waterAbsorptionRate + jejunum.waterAbsorptionRate + ileum.waterAbsorptionRate + colon.waterAbsorptionRate) / 4.0;
 
+        // Absorb glucose into the blood
+        double glucoseAbsorption = totalNutrientAbsorption * chymeVolume_mL * 0.001 * deltaTime_s;
+        patient.blood.glucose_mg_per_dL += glucoseAbsorption;
+
         // Reduce chyme volume based on absorption
         double absorbedVolume = (totalNutrientAbsorption * 0.01 + totalWaterAbsorption * 0.1) * deltaTime_s;
         chymeVolume_mL -= absorbedVolume;

src/Kidneys.cpp

@@ -1,4 +1,7 @@
 #include "MedicalLib/Kidneys.h"
+#include "MedicalLib/Patient.h"
+#include "MedicalLib/Heart.h"
+#include "MedicalLib/Bladder.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -28,7 +31,7 @@ Kidneys::Kidneys(int id)
     }
 }
 
-void Kidneys::update(double deltaTime_s) {
+void Kidneys::update(Patient& patient, double deltaTime_s) {
     // Recalculate total capacity based on nephron health
     totalFiltrationCapacity = 0.0;
     for (const auto& nephron : nephrons) {
@@ -38,14 +41,25 @@ void Kidneys::update(double deltaTime_s) {
     }
     totalFiltrationCapacity /= nephrons.size();
 
-    // GFR is dependent on overall health
+    // GFR is dependent on blood pressure from the heart
-    const double baseline_gfr = 125.0 * totalFiltrationCapacity;
+    double perfusionPressure = 90.0; // Assume normal MAP if heart is not present
+    if (const Heart* heart = getOrgan<Heart>(patient)) {
+        perfusionPressure = heart->getAorticPressure();
+    }
+    double pressureModifier = std::clamp(perfusionPressure / 90.0, 0.5, 1.2);
+
+    const double baseline_gfr = 125.0 * totalFiltrationCapacity * pressureModifier;
     gfr_mL_per_min += 0.1 * (baseline_gfr - gfr_mL_per_min) * deltaTime_s + getFluctuation(0.5);
 
-    // Urine output is related to GFR but also hydration status (not modeled yet)
+    // Urine output is related to GFR
     urineOutput_mL_per_s = gfr_mL_per_min / 60.0 * 0.01; // Simplified relationship
     urineOutput_mL_per_s += getFluctuation(0.001);
 
+    // Pass urine to the bladder
+    if (Bladder* bladder = getOrgan<Bladder>(patient)) {
+        bladder->addUrine(urineOutput_mL_per_s * deltaTime_s);
+    }
+
     // Simulate electrolyte balance
     bloodSodium_mEq_per_L += getFluctuation(0.05);
     bloodPotassium_mEq_per_L += getFluctuation(0.01);

src/Liver.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Liver.h"
+#include "MedicalLib/Patient.h" // For Blood struct
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -28,7 +29,7 @@ Liver::Liver(int id)
     }
 }
 
-void Liver::update(double deltaTime_s) {
+void Liver::update(Patient& patient, double deltaTime_s) {
     // Recalculate total capacity based on lobule health (for future use)
     totalMetabolicCapacity = 0.0;
     for (const auto& lobule : lobules) {
@@ -58,6 +59,23 @@ void Liver::update(double deltaTime_s) {
     alt_U_per_L = std::clamp(alt_U_per_L, 10.0, 40.0);
     ast_U_per_L = std::clamp(ast_U_per_L, 10.0, 40.0);
     bilirubin_mg_per_dL = std::clamp(bilirubin_mg_per_dL, 0.3, 1.2);
+
+    // --- Blood Interaction ---
+    Blood& blood = patient.blood;
+    // 1. Toxin Filtration
+    double toxinFiltrationRate = 0.1 * totalMetabolicCapacity * deltaTime_s; // a.u. per second
+    double toxinsRemoved = blood.toxins_au * toxinFiltrationRate;
+    blood.toxins_au -= toxinsRemoved;
+    blood.toxins_au = std::max(0.0, blood.toxins_au);
+
+    // 2. Glucose regulation (Gluconeogenesis / Glycogenolysis)
+    const double highGlucose = 120.0;
+    const double lowGlucose = 80.0;
+    if (patient.blood.glucose_mg_per_dL > highGlucose) {
+        patient.blood.glucose_mg_per_dL -= (patient.blood.glucose_mg_per_dL - highGlucose) * 0.1 * totalMetabolicCapacity * deltaTime_s;
+    } else if (patient.blood.glucose_mg_per_dL < lowGlucose) {
+        patient.blood.glucose_mg_per_dL += (lowGlucose - patient.blood.glucose_mg_per_dL) * 0.1 * totalMetabolicCapacity * deltaTime_s;
+    }
 }
 
 std::string Liver::getSummary() const {

src/Lungs.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Lungs.h"
+#include "MedicalLib/Patient.h" // For Blood struct
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -37,7 +38,7 @@ Lungs::Lungs(int id)
     mainBronchus = {"Main Bronchus", 0.8};
 }
 
-void Lungs::update(double deltaTime_s) {
+void Lungs::update(Patient& patient, double deltaTime_s) {
     totalTime_s += deltaTime_s;
 
     updateRespiratoryMechanics(deltaTime_s);
@@ -48,6 +49,24 @@ void Lungs::update(double deltaTime_s) {
     if (capnographyData.size() > capnographyHistorySize) {
         capnographyData.pop_back();
     }
+
+    // --- Blood Interaction ---
+    Blood& blood = patient.blood;
+    // Gas exchange is driven by the pressure gradient between alveoli and blood
+    double ventilationFactor = (tidalVolume_mL / 500.0) * (respirationRate / 16.0);
+    ventilationFactor = std::clamp(ventilationFactor, 0.5, 1.5); // Clamp effect
+
+    // Oxygenation: Blood O2 moves towards the lung's O2 level
+    double o2_gradient = oxygenSaturation - blood.oxygenSaturation;
+    blood.oxygenSaturation += o2_gradient * 0.8 * ventilationFactor * deltaTime_s;
+	blood.oxygenSaturation = std::clamp(blood.oxygenSaturation, 0.0, 100.0);
+
+    // CO2 Removal: Blood CO2 moves towards the lung's (low) CO2 level
+    // We'll model the lung's CO2 as being lower than the blood's target
+    double effectiveAlveolarCO2 = 40.0 / ventilationFactor;
+    double co2_gradient = blood.co2PartialPressure_mmHg - effectiveAlveolarCO2;
+    blood.co2PartialPressure_mmHg -= co2_gradient * 0.5 * deltaTime_s;
+	blood.co2PartialPressure_mmHg = std::clamp(blood.co2PartialPressure_mmHg, 0.0, 200.0);
 }
 
 void Lungs::updateRespiratoryMechanics(double deltaTime_s) {
@@ -68,12 +87,14 @@ void Lungs::updateRespiratoryMechanics(double deltaTime_s) {
     }
 
     // Pressure and Volume dynamics
+    double totalCompliance = rightUpperLobe.compliance + rightMiddleLobe.compliance + rightLowerLobe.compliance + leftUpperLobe.compliance + leftLowerLobe.compliance;
+
     double flowRate_mL_s = 0;
     if (currentState == RespiratoryState::INSPIRATION) {
         // Simple sine wave for pressure generation
         double pressure_wave = sin(M_PI * (cyclePosition_s / inspirationDuration));
         peakInspiratoryPressure_cmH2O = 15.0 * pressure_wave; // 15 cmH2O peak
-        flowRate_mL_s = (peakInspiratoryPressure_cmH2O / mainBronchus.resistance) * 100;
+        flowRate_mL_s = (peakInspiratoryPressure_cmH2O / mainBronchus.resistance) * 100 * totalCompliance;
         tidalVolume_mL += flowRate_mL_s * deltaTime_s;
     } else { // EXPIRATION
         peakInspiratoryPressure_cmH2O = 0;
@@ -138,6 +159,15 @@ std::string Lungs::getSummary() const {
 }
 
 // --- Getters Implementation ---
+void Lungs::inflictDamage(double damage) {
+    double damageFactor = 1.0 - std::clamp(damage, 0.0, 1.0);
+    rightUpperLobe.compliance *= damageFactor;
+    rightMiddleLobe.compliance *= damageFactor;
+    rightLowerLobe.compliance *= damageFactor;
+    leftUpperLobe.compliance *= damageFactor;
+    leftLowerLobe.compliance *= damageFactor;
+}
+
 double Lungs::getRespirationRate() const { return respirationRate; }
 double Lungs::getOxygenSaturation() const { return oxygenSaturation; }
 double Lungs::getTidalVolume() const { return tidalVolume_mL; }

src/Pancreas.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Pancreas.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -19,22 +20,34 @@ Pancreas::Pancreas(int id)
       amylaseSecretion_U_per_L(80.0),
       lipaseSecretion_U_per_L(40.0) {}
 
-void Pancreas::update(double deltaTime_s) {
+void Pancreas::update(Patient& patient, double deltaTime_s) {
-    // In a real model, hormone secretion would be driven by blood glucose.
+    // Hormone secretion is driven by blood glucose.
-    // Enzyme secretion would be driven by food in the duodenum.
+    const double glucose = patient.blood.glucose_mg_per_dL;
+    const double highGlucoseThreshold = 120.0;
+    const double lowGlucoseThreshold = 80.0;
+
+    // Insulin response
+    if (glucose > highGlucoseThreshold) {
+        insulinSecretion_units_per_hr += (glucose - highGlucoseThreshold) * 0.1 * deltaTime_s;
+    } else {
+        insulinSecretion_units_per_hr -= 0.5 * deltaTime_s;
+    }
+
+    // Glucagon response
+    if (glucose < lowGlucoseThreshold) {
+        glucagonSecretion_ng_per_hr += (lowGlucoseThreshold - glucose) * 0.2 * deltaTime_s;
+    } else {
+        glucagonSecretion_ng_per_hr -= 1.0 * deltaTime_s;
+    }
+
+    // Enzyme secretion would be driven by food in the duodenum (not yet modeled).
     // For now, we just simulate minor fluctuations around a baseline.
-
-    // Endocrine fluctuations
-    insulinSecretion_units_per_hr += getFluctuation(0.05);
-    glucagonSecretion_ng_per_hr += getFluctuation(0.5);
-
-    // Exocrine fluctuations
     amylaseSecretion_U_per_L += getFluctuation(0.2);
     lipaseSecretion_U_per_L += getFluctuation(0.2);
 
-    // Clamp to healthy ranges
+    // Clamp to healthy/possible ranges
-    insulinSecretion_units_per_hr = std::clamp(insulinSecretion_units_per_hr, 0.5, 2.0);
+    insulinSecretion_units_per_hr = std::clamp(insulinSecretion_units_per_hr, 0.5, 10.0);
-    glucagonSecretion_ng_per_hr = std::clamp(glucagonSecretion_ng_per_hr, 40.0, 60.0);
+    glucagonSecretion_ng_per_hr = std::clamp(glucagonSecretion_ng_per_hr, 20.0, 100.0);
     amylaseSecretion_U_per_L = std::clamp(amylaseSecretion_U_per_L, 60.0, 100.0);
     lipaseSecretion_U_per_L = std::clamp(lipaseSecretion_U_per_L, 20.0, 60.0);
 }

src/Patient.cpp

@@ -58,9 +58,10 @@ Patient initializePatient(int patientId) {
  * @param deltaTime_s The time elapsed in seconds.
  */
 void updatePatient(Patient& patient, double deltaTime_s) {
-    // Update all organs
+    // Update all organs. The new update function handles all internal state changes
+    // and inter-organ interactions.
     for (auto& organ : patient.organs) {
-        organ->update(deltaTime_s);
+        organ->update(patient, deltaTime_s);
     }
 }
 

src/SpinalCord.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/SpinalCord.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -21,7 +22,7 @@ SpinalCord::SpinalCord(int id)
     ascendingSensoryTract = {"Ascending Sensory Tract", SignalStatus::NORMAL, 65.0};
 }
 
-void SpinalCord::update(double deltaTime_s) {
+void SpinalCord::update(Patient& patient, double deltaTime_s) {
     // In a healthy state, status doesn't change.
     // Pathology models would alter these values.
     // For now, we just simulate minor fluctuations in a healthy velocity.

src/Spleen.cpp

@@ -1,4 +1,5 @@
 #include "MedicalLib/Spleen.h"
+#include "MedicalLib/Patient.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -18,7 +19,7 @@ Spleen::Spleen(int id) : Organ(id, "Spleen") {
     whitePulp = {1500.0, 500.0};
 }
 
-void Spleen::update(double deltaTime_s) {
+void Spleen::update(Patient& patient, double deltaTime_s) {
     // In a real model, these values would change in response to infection or disease.
     // For now, we just simulate minor fluctuations around a healthy baseline.
 

src/Stomach.cpp

@@ -1,4 +1,6 @@
 #include "MedicalLib/Stomach.h"
+#include "MedicalLib/Patient.h"
+#include "MedicalLib/Intestines.h"
 #include <random>
 #include <algorithm>
 #include <sstream>
@@ -20,17 +22,11 @@ Stomach::Stomach(int id)
       gastricJuiceSecretionRate_ml_per_s(0.1),
       emptyingRate_ml_per_s(0.5) {}
 
-void Stomach::update(double deltaTime_s) {
+void Stomach::update(Patient& patient, double deltaTime_s) {
     // --- State Machine Logic ---
     switch (currentState) {
         case GastricState::EMPTY:
-            // For demo, simulate food arriving every 20 seconds
+            // In a real simulation, addSubstance would be called externally (e.g., from Esophagus)
-            static double timeUntilFood = 0.0;
-            timeUntilFood += deltaTime_s;
-            if (timeUntilFood > 20.0) {
-                addSubstance(150.0); // Simulate arrival of a meal
-                timeUntilFood = 0.0;
-            }
             break;
 
         case GastricState::FILLING:
@@ -60,6 +56,11 @@ void Stomach::update(double deltaTime_s) {
         case GastricState::EMPTYING:
             // Empty chyme into intestines
             double amountToEmpty = emptyingRate_ml_per_s * deltaTime_s;
+
+            if (Intestines* intestines = getOrgan<Intestines>(patient)) {
+                intestines->receiveChyme(amountToEmpty);
+            }
+
             currentVolume_mL -= amountToEmpty;
 
             if (currentVolume_mL <= 0) {