ver inc

Introduce richer neuro-visceral coupling and signal integration across
organs to improve physiological realism:
- Add Brain, Esophagus, Bladder, Stomach, Spinal signal structs
- Couple bladder with spinal autonomics and brain state to drive
  parasympathetic/sympathetic/somatic outputs and thresholds
- Deliver esophageal bolus into stomach; update hiatal pressure and LES
  tone from stomach distension/acid/motility
- Move stomach emptying into intestines within patient update loop
- Replace spleen state penalty with immune activity-based adjustment
- Simplify gallbladder control using intestinal nutrient energy
- Refine heart autonomic tone using brain/spinal outputs
- Re-export BladderPhase, SleepStage, EsophagealStage

No breaking API changes.

.gitea/workflows/multi-platform.yml

@@ -87,20 +87,23 @@ jobs:
         env:
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
         run: |
-          # Get git log since last release
+          # Get git log with actual changes since last release
           if [ -n "${{ steps.last_tag.outputs.last_tag }}" ]; then
-            GIT_LOG=$(git log --pretty=format:"- %s (%an)" ${{ steps.last_tag.outputs.last_tag }}..HEAD)
+            GIT_LOG=$(git log --pretty=format:"**%s** (%an)" --stat ${{ steps.last_tag.outputs.last_tag }}..HEAD)
           else
-            GIT_LOG=$(git log --pretty=format:"- %s (%an)" HEAD~10..HEAD)
+            GIT_LOG=$(git log --pretty=format:"**%s** (%an)" --stat HEAD~10..HEAD)
           fi
 
+          echo "Git changes for release notes:"
+          echo "$GIT_LOG"
+
           # Try to generate AI-powered release notes
           if [ -n "$OPENAI_API_KEY" ]; then
             echo "Generating AI release notes..."
 
-            PROMPT="Generate professional release notes for version ${{ steps.version.outputs.version }} based on these git commits. Focus on user-facing changes and improvements. Use markdown formatting with sections like ## What's New, ## Improvements, ## Bug Fixes. Keep it concise and under 500 words.
+            PROMPT="Generate professional release notes for version ${{ steps.version.outputs.version }} based on these git commits and file changes. Focus on user-facing changes and improvements. Use markdown formatting with sections like ## What's New, ## Improvements, ## Bug Fixes. Keep it concise and under 500 words.
 
-          Commits:
+          Commits and Changes:
           $GIT_LOG"
 
             RESPONSE=$(curl -s -X POST "https://api.openai.com/v1/responses" \

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "medicallib_rust"
-version = "0.1.1"
+version = "0.2.0"
 edition = "2021"
 description = "MedicalSim core library rewrite in Rust: basic clinical calculations and types."
 authors = ["MedicalSim Team"]

build.rs

@@ -10,7 +10,8 @@ fn main() {
     println!("cargo:rerun-if-changed=src/ffi.rs");
     println!("cargo:rerun-if-changed=cbindgen.toml");
 
-    let crate_dir = PathBuf::from(env::var("CARGO_MANIFEST_DIR").expect("CARGO_MANIFEST_DIR not set"));
+    let crate_dir =
+        PathBuf::from(env::var("CARGO_MANIFEST_DIR").expect("CARGO_MANIFEST_DIR not set"));
     let crate_dir_string = crate_dir
         .to_str()
         .expect("crate directory must be valid UTF-8")
@@ -36,7 +37,8 @@ fn main() {
     let mut generated = Vec::new();
     bindings.write(&mut generated);
 
-    let header_contents = String::from_utf8(generated).expect("generated header was not valid UTF-8");
+    let header_contents =
+        String::from_utf8(generated).expect("generated header was not valid UTF-8");
 
     let header_path = header_dir.join("medicallib.h");
     let needs_write = fs::read_to_string(&header_path)

src/organs/bladder.rs

@@ -1,21 +1,183 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum BladderPhase {
+    Filling,
+    Voiding,
+    PostVoidRefractory,
+}
+
 #[derive(Debug, Clone)]
 pub struct Bladder {
     info: OrganInfo,
-    /// Urine volume ml
+    /// Urine volume stored in the bladder (ml).
     pub volume_ml: f32,
-    /// Pressure proxy (cmH2O)
+    /// Intraluminal/detrusor pressure (cmH2O).
     pub pressure: f32,
+    /// Normalized afferent firing (0..=1) representing stretch receptor activity.
+    pub afferent_signal: f32,
+    /// Normalized urgency perception (0..=1).
+    pub urgency: f32,
+    /// Current phase of the bladder state machine.
+    pub phase: BladderPhase,
+    /// Functional capacity where continence is expected (ml).
+    pub capacity_ml: f32,
+    /// Residual volume expected after a complete void (ml).
+    pub residual_volume_ml: f32,
+    /// Compliance relating volume change to pressure (ml per cmH2O).
+    pub compliance_ml_per_cm_h2o: f32,
+    /// Baseline pressure generated by abdominal cavity (cmH2O).
+    pub baseline_pressure_cm_h2o: f32,
+    /// Volume threshold at which a full micturition reflex is triggered (ml).
+    pub micturition_threshold_ml: f32,
+    /// Volume threshold where urge perception begins (ml).
+    pub urge_threshold_ml: f32,
+    /// Average renal inflow into the bladder (ml/min).
+    pub filling_rate_ml_per_min: f32,
+    /// Peak voluntary/automatic outflow during voiding (ml/s).
+    pub voiding_flow_ml_per_s: f32,
+    /// Tone of the internal urethral sphincter (0..=1, higher means more closed).
+    pub internal_sphincter_tone: f32,
+    /// Tone of the external urethral sphincter/pelvic floor (0..=1).
+    pub external_sphincter_tone: f32,
+    /// Parasympathetic drive to the detrusor (0..=1).
+    pub parasympathetic_drive: f32,
+    /// Sympathetic drive maintaining storage (0..=1).
+    pub sympathetic_drive: f32,
+    /// Somatic drive through the pudendal nerve to the external sphincter (0..=1).
+    pub somatic_drive: f32,
+    time_since_last_void_s: f32,
+    refractory_seconds: f32,
 }
 
 impl Bladder {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Bladder),
-            volume_ml: 100.0,
+            volume_ml: 120.0,
             pressure: 5.0,
+            afferent_signal: 0.1,
+            urgency: 0.1,
+            phase: BladderPhase::Filling,
+            capacity_ml: 500.0,
+            residual_volume_ml: 30.0,
+            compliance_ml_per_cm_h2o: 18.0,
+            baseline_pressure_cm_h2o: 5.0,
+            micturition_threshold_ml: 350.0,
+            urge_threshold_ml: 200.0,
+            filling_rate_ml_per_min: 60.0,
+            voiding_flow_ml_per_s: 15.0,
+            internal_sphincter_tone: 0.85,
+            external_sphincter_tone: 0.9,
+            parasympathetic_drive: 0.05,
+            sympathetic_drive: 0.8,
+            somatic_drive: 0.8,
+            time_since_last_void_s: 0.0,
+            refractory_seconds: 15.0,
+        }
+    }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_drives(&mut self, dt_seconds: f32) {
+        let urgency = self.urgency;
+        let (parasym_target, sym_target, somatic_target) = match self.phase {
+            BladderPhase::Filling => {
+                let parasym = urgency.powf(1.2).clamp(0.0, 0.85);
+                let sym = (1.0 - 0.6 * urgency).clamp(0.2, 1.0);
+                let somatic = (0.95 - 0.5 * urgency).clamp(0.3, 0.95);
+                (parasym, sym, somatic)
+            }
+            BladderPhase::Voiding => (1.0, 0.1, 0.2),
+            BladderPhase::PostVoidRefractory => (0.2, 0.6, 0.7),
+        };
+
+        self.parasympathetic_drive =
+            Self::approach(self.parasympathetic_drive, parasym_target, 0.8, dt_seconds);
+        self.sympathetic_drive =
+            Self::approach(self.sympathetic_drive, sym_target, 0.6, dt_seconds);
+        self.somatic_drive = Self::approach(self.somatic_drive, somatic_target, 0.9, dt_seconds);
+
+        self.parasympathetic_drive = self.parasympathetic_drive.clamp(0.0, 1.0);
+        self.sympathetic_drive = self.sympathetic_drive.clamp(0.0, 1.0);
+        self.somatic_drive = self.somatic_drive.clamp(0.0, 1.0);
+    }
+
+    fn update_sphincters(&mut self) {
+        let internal = 0.3 + 0.7 * self.sympathetic_drive;
+        let external = 0.2 + 0.8 * self.somatic_drive;
+        self.internal_sphincter_tone = internal.clamp(0.0, 1.0);
+        self.external_sphincter_tone = external.clamp(0.0, 1.0);
+    }
+
+    fn update_afferents(&mut self) {
+        let low_volume_component = (self.volume_ml / 50.0).clamp(0.0, 1.0) * 0.15;
+        let fullness_component = if self.capacity_ml > self.urge_threshold_ml {
+            let denom = (self.capacity_ml - self.urge_threshold_ml).max(1.0);
+            ((self.volume_ml - self.urge_threshold_ml) / denom).clamp(0.0, 1.0)
+        } else {
+            (self.volume_ml / self.capacity_ml.max(1.0)).clamp(0.0, 1.0)
+        };
+        self.afferent_signal = (low_volume_component + fullness_component).clamp(0.0, 1.0);
+        self.urgency = self.afferent_signal.powf(1.35).clamp(0.0, 1.0);
+    }
+
+    fn update_pressure(&mut self) {
+        let passive_volume_ml = (self.volume_ml - 30.0).max(0.0);
+        let normalized_volume = (self.volume_ml / self.capacity_ml).clamp(0.0, 1.5);
+        let compliance_factor = 1.0 + 4.0 * normalized_volume.powf(4.0);
+        let passive_pressure = if self.compliance_ml_per_cm_h2o > 0.0 {
+            passive_volume_ml / self.compliance_ml_per_cm_h2o * compliance_factor
+        } else {
+            0.0
+        };
+        let active_pressure = 40.0 * self.parasympathetic_drive;
+        let abdominal = self.baseline_pressure_cm_h2o;
+        self.pressure = (abdominal + passive_pressure + active_pressure).clamp(0.0, 90.0);
+    }
+
+    fn handle_filling_phase(&mut self, _dt_seconds: f32) {
+        if self.volume_ml >= self.micturition_threshold_ml || self.pressure > 45.0 {
+            if self.external_sphincter_tone < 0.4 || self.urgency > 0.95 {
+                self.phase = BladderPhase::Voiding;
+            }
+        }
+        let overdistention_limit = self.capacity_ml * 1.4;
+        if self.volume_ml > overdistention_limit {
+            self.volume_ml = overdistention_limit;
+        }
+    }
+
+    fn handle_voiding_phase(&mut self, dt_seconds: f32) {
+        let relaxation_factor = 1.0 - 0.5 * self.external_sphincter_tone;
+        let drive = (self.parasympathetic_drive * relaxation_factor).clamp(0.0, 1.0);
+        let pressure_factor = (self.pressure / 40.0).clamp(0.0, 2.5);
+        let outflow = self.voiding_flow_ml_per_s.max(0.0) * pressure_factor * drive * dt_seconds;
+        self.volume_ml = (self.volume_ml - outflow).max(self.residual_volume_ml);
+        if self.volume_ml <= self.residual_volume_ml + 1.0 {
+            self.phase = BladderPhase::PostVoidRefractory;
+            self.time_since_last_void_s = 0.0;
+        }
+    }
+
+    fn handle_post_void_phase(&mut self) {
+        if self.time_since_last_void_s >= self.refractory_seconds {
+            self.phase = BladderPhase::Filling;
         }
     }
 }
@@ -27,16 +189,42 @@ impl Organ for Bladder {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        // simplistic pressure-volume relation
-        self.pressure = (self.volume_ml / 50.0).clamp(0.0, 30.0);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_since_last_void_s += dt_seconds;
+        let inflow = (self.filling_rate_ml_per_min / 60.0).max(0.0) * dt_seconds;
+        self.volume_ml += inflow;
+
+        self.update_afferents();
+        self.update_drives(dt_seconds);
+        self.update_sphincters();
+        self.update_pressure();
+
+        match self.phase {
+            BladderPhase::Filling => self.handle_filling_phase(dt_seconds),
+            BladderPhase::Voiding => self.handle_voiding_phase(dt_seconds),
+            BladderPhase::PostVoidRefractory => self.handle_post_void_phase(),
+        }
+
+        if matches!(self.phase, BladderPhase::Voiding)
+            && self.volume_ml <= self.residual_volume_ml + 1.0
+        {
+            self.phase = BladderPhase::PostVoidRefractory;
+            self.time_since_last_void_s = 0.0;
+        }
     }
     fn summary(&self) -> String {
         format!(
-            "Bladder[id={}, vol={:.0} ml, P={:.1}]",
+            "Bladder[id={}, phase={:?}, vol={:.0}/{:.0} ml, P={:.1} cmH2O, urge={:.0}%]",
             self.id(),
+            self.phase,
             self.volume_ml,
-            self.pressure
+            self.capacity_ml,
+            self.pressure,
+            self.urgency * 100.0
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/brain.rs

@@ -1,21 +1,173 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
+use core::f32::consts::TAU;
+
+const CIRCADIAN_PERIOD_SECONDS: f32 = 24.0 * 3600.0;
+const HOMEOSTATIC_WAKE_ACCUMULATION_S: f32 = 16.0 * 3600.0;
+const HOMEOSTATIC_DISCHARGE_S: f32 = 6.0 * 3600.0;
+
+/// Sleep architecture stages used for brain state transitions.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum SleepStage {
+    Wake,
+    N1,
+    N2,
+    N3,
+    Rem,
+}
 
 #[derive(Debug, Clone)]
 pub struct Brain {
     info: OrganInfo,
-    /// 0..=100 scale of consciousness.
+    /// 0..=100 index approximating global cortical consciousness/alertness.
     pub consciousness: u8,
-    /// Simplified neural activity index.
+    /// Composite neural activity index blending frequency and metabolic power.
     pub activity_index: f32,
+    /// Normalized cortical arousal (0..=1).
+    pub cortical_arousal: f32,
+    /// Brainstem autonomic output regulating MAP and respiratory drive (0..=1).
+    pub brainstem_autonomic_drive: f32,
+    /// Intracranial pressure (mmHg).
+    pub intracranial_pressure_mm_hg: f32,
+    /// Cerebral perfusion pressure (mmHg).
+    pub cerebral_perfusion_pressure_mm_hg: f32,
+    /// Cerebral blood flow (ml/100g/min).
+    pub cerebral_blood_flow_ml_per_100g_min: f32,
+    /// Fractional metabolic demand relative to resting wakefulness.
+    pub metabolic_demand_fraction: f32,
+    /// Cortical oxygen saturation (fraction 0..=1).
+    pub oxygenation_saturation: f32,
+    /// Excitatory glutamatergic tone (relative units 0.3..=1.4).
+    pub glutamate_level: f32,
+    /// Inhibitory GABAergic tone (relative units 0.4..=1.2).
+    pub gaba_level: f32,
+    /// Mesolimbic/striatal dopamine tone (0..=1).
+    pub dopamine_tone: f32,
+    /// Sleep homeostatic pressure (0..≈1.1).
+    pub sleep_pressure: f32,
+    /// Circadian phase in radians (0..TAU, midnight ≈ 0).
+    pub circadian_phase_radians: f32,
+    /// Current polysomnographic sleep stage.
+    pub sleep_stage: SleepStage,
+    /// Dominant EEG frequency (Hz).
+    pub eeg_dominant_frequency_hz: f32,
+    /// Instantaneous seizure risk (0..=1).
+    pub seizure_risk: f32,
+    /// Autonomic variability (0..=1, higher reflects sympathetic swings).
+    pub autonomic_variability: f32,
+    /// Cognitive/task load (0..=1) influencing metabolic demand.
+    pub cognitive_load: f32,
+    time_in_stage_s: f32,
 }
 
 impl Brain {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Brain),
-            consciousness: 100,
+            consciousness: 95,
             activity_index: 1.0,
+            cortical_arousal: 0.82,
+            brainstem_autonomic_drive: 0.9,
+            intracranial_pressure_mm_hg: 10.0,
+            cerebral_perfusion_pressure_mm_hg: 75.0,
+            cerebral_blood_flow_ml_per_100g_min: 52.0,
+            metabolic_demand_fraction: 1.05,
+            oxygenation_saturation: 0.98,
+            glutamate_level: 0.65,
+            gaba_level: 0.55,
+            dopamine_tone: 0.6,
+            sleep_pressure: 0.4,
+            circadian_phase_radians: TAU * 0.25,
+            sleep_stage: SleepStage::Wake,
+            eeg_dominant_frequency_hz: 18.0,
+            seizure_risk: 0.05,
+            autonomic_variability: 0.35,
+            cognitive_load: 0.35,
+            time_in_stage_s: 0.0,
+        }
+    }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn wrap_phase(phase: f32) -> f32 {
+        if phase >= 0.0 && phase < TAU {
+            return phase;
+        }
+        let mut wrapped = phase % TAU;
+        if wrapped < 0.0 {
+            wrapped += TAU;
+        }
+        wrapped
+    }
+
+    fn transition_stage(&mut self, stage: SleepStage) {
+        if self.sleep_stage != stage {
+            self.sleep_stage = stage;
+            self.time_in_stage_s = 0.0;
+        }
+    }
+
+    fn evaluate_sleep_stage(&mut self, base_arousal: f32) {
+        match self.sleep_stage {
+            SleepStage::Wake => {
+                if base_arousal < 0.35 && self.sleep_pressure > 0.55 {
+                    self.transition_stage(SleepStage::N1);
+                }
+            }
+            SleepStage::N1 => {
+                if base_arousal > 0.5 {
+                    self.transition_stage(SleepStage::Wake);
+                } else if self.time_in_stage_s > 180.0 && self.sleep_pressure > 0.6 {
+                    self.transition_stage(SleepStage::N2);
+                }
+            }
+            SleepStage::N2 => {
+                if base_arousal > 0.52 {
+                    self.transition_stage(SleepStage::Wake);
+                } else if self.time_in_stage_s > 900.0 && self.sleep_pressure > 0.65 {
+                    self.transition_stage(SleepStage::N3);
+                } else if self.time_in_stage_s > 2400.0 {
+                    self.transition_stage(SleepStage::Rem);
+                }
+            }
+            SleepStage::N3 => {
+                if self.time_in_stage_s > 1800.0 {
+                    self.transition_stage(SleepStage::Rem);
+                } else if base_arousal > 0.45 {
+                    self.transition_stage(SleepStage::N2);
+                }
+            }
+            SleepStage::Rem => {
+                if self.time_in_stage_s > 1500.0 {
+                    self.transition_stage(SleepStage::N2);
+                } else if base_arousal > 0.65 {
+                    self.transition_stage(SleepStage::Wake);
+                }
+            }
+        }
+    }
+
+    fn stage_arousal_target(&self, base_arousal: f32) -> f32 {
+        match self.sleep_stage {
+            SleepStage::Wake => base_arousal.max(0.6),
+            SleepStage::N1 => base_arousal.clamp(0.3, 0.55),
+            SleepStage::N2 => base_arousal.clamp(0.2, 0.45),
+            SleepStage::N3 => base_arousal.min(0.25),
+            SleepStage::Rem => base_arousal.clamp(0.45, 0.7),
         }
     }
 }
@@ -27,15 +179,195 @@ impl Organ for Brain {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        self.activity_index = self.activity_index.clamp(0.0, 2.0);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_in_stage_s += dt_seconds;
+        let circadian_increment = TAU * (dt_seconds / CIRCADIAN_PERIOD_SECONDS);
+        self.circadian_phase_radians =
+            Self::wrap_phase(self.circadian_phase_radians + circadian_increment);
+
+        let circadian_arousal = 0.55 + 0.45 * (self.circadian_phase_radians - TAU * 0.25).sin();
+
+        let asleep = !matches!(self.sleep_stage, SleepStage::Wake);
+        let sleep_pressure_delta = if asleep {
+            -dt_seconds / HOMEOSTATIC_DISCHARGE_S
+        } else {
+            dt_seconds / HOMEOSTATIC_WAKE_ACCUMULATION_S
+        };
+        self.sleep_pressure = (self.sleep_pressure + sleep_pressure_delta).clamp(0.0, 1.1);
+
+        let base_arousal = (circadian_arousal - 0.55 * self.sleep_pressure).clamp(0.05, 1.0);
+        self.evaluate_sleep_stage(base_arousal);
+
+        let arousal_target = self.stage_arousal_target(base_arousal);
+        self.cortical_arousal =
+            Self::approach(self.cortical_arousal, arousal_target, 0.8, dt_seconds).clamp(0.05, 1.0);
+
+        let (autonomic_target, variability_target) = match self.sleep_stage {
+            SleepStage::Wake => (0.9, 0.35),
+            SleepStage::N1 => (0.82, 0.4),
+            SleepStage::N2 => (0.78, 0.45),
+            SleepStage::N3 => (0.72, 0.3),
+            SleepStage::Rem => (0.86, 0.6),
+        };
+        self.brainstem_autonomic_drive = Self::approach(
+            self.brainstem_autonomic_drive,
+            autonomic_target,
+            0.6,
+            dt_seconds,
+        )
+        .clamp(0.3, 1.1);
+        self.autonomic_variability = Self::approach(
+            self.autonomic_variability,
+            variability_target,
+            0.4,
+            dt_seconds,
+        )
+        .clamp(0.05, 0.95);
+
+        let cognitive_target = if matches!(self.sleep_stage, SleepStage::Wake) {
+            (0.3 + 0.45 * self.cortical_arousal).clamp(0.15, 1.0)
+        } else {
+            0.12
+        };
+        self.cognitive_load =
+            Self::approach(self.cognitive_load, cognitive_target, 0.25, dt_seconds)
+                .clamp(0.05, 1.0);
+
+        let base_metabolic = match self.sleep_stage {
+            SleepStage::Wake => 1.05,
+            SleepStage::N1 => 0.95,
+            SleepStage::N2 => 0.85,
+            SleepStage::N3 => 0.7,
+            SleepStage::Rem => 1.0,
+        };
+        let metabolic_target = (base_metabolic
+            + 0.25 * (self.cognitive_load - 0.2)
+            + 0.1 * (self.glutamate_level - self.gaba_level))
+            .clamp(0.6, 1.4);
+        self.metabolic_demand_fraction = Self::approach(
+            self.metabolic_demand_fraction,
+            metabolic_target,
+            0.35,
+            dt_seconds,
+        )
+        .clamp(0.6, 1.5);
+
+        let (glu_base, gaba_base, dopamine_base, eeg_target_base) = match self.sleep_stage {
+            SleepStage::Wake => (0.65, 0.55, 0.6, 18.0),
+            SleepStage::N1 => (0.55, 0.62, 0.5, 9.0),
+            SleepStage::N2 => (0.5, 0.68, 0.45, 6.0),
+            SleepStage::N3 => (0.45, 0.75, 0.4, 2.0),
+            SleepStage::Rem => (0.68, 0.6, 0.65, 10.5),
+        };
+        let arousal_offset = self.cortical_arousal - 0.5;
+        let glutamate_target = (glu_base + 0.15 * arousal_offset).clamp(0.3, 1.3);
+        let gaba_target = (gaba_base - 0.1 * arousal_offset).clamp(0.4, 1.2);
+        let dopamine_target = (dopamine_base + 0.05 * circadian_arousal
+            - 0.03 * self.sleep_pressure)
+            .clamp(0.35, 0.85);
+        let eeg_target = match self.sleep_stage {
+            SleepStage::Wake => eeg_target_base + 4.0 * (self.cortical_arousal - 0.7).max(0.0),
+            SleepStage::Rem => eeg_target_base + 2.0 * (self.cortical_arousal - 0.6).max(0.0),
+            _ => eeg_target_base,
+        };
+
+        self.glutamate_level =
+            Self::approach(self.glutamate_level, glutamate_target, 0.5, dt_seconds).clamp(0.3, 1.4);
+        self.gaba_level =
+            Self::approach(self.gaba_level, gaba_target, 0.45, dt_seconds).clamp(0.4, 1.2);
+        self.dopamine_tone =
+            Self::approach(self.dopamine_tone, dopamine_target, 0.3, dt_seconds).clamp(0.3, 0.9);
+        self.eeg_dominant_frequency_hz =
+            Self::approach(self.eeg_dominant_frequency_hz, eeg_target, 0.8, dt_seconds)
+                .clamp(0.5, 35.0);
+
+        let oxygen_target = (0.95 + 0.03 * self.brainstem_autonomic_drive
+            - 0.04 * (self.metabolic_demand_fraction - 1.0))
+            .clamp(0.88, 0.99);
+        self.oxygenation_saturation =
+            Self::approach(self.oxygenation_saturation, oxygen_target, 0.4, dt_seconds)
+                .clamp(0.8, 1.0);
+
+        let cbf_target = (50.0 * self.metabolic_demand_fraction
+            + 0.25 * (self.cerebral_perfusion_pressure_mm_hg - 70.0))
+            .clamp(30.0, 90.0);
+        self.cerebral_blood_flow_ml_per_100g_min = Self::approach(
+            self.cerebral_blood_flow_ml_per_100g_min,
+            cbf_target,
+            1.6,
+            dt_seconds,
+        )
+        .clamp(25.0, 95.0);
+
+        let stage_icp_term = match self.sleep_stage {
+            SleepStage::Wake => 0.0,
+            SleepStage::N1 => 0.5,
+            SleepStage::N2 => 1.0,
+            SleepStage::N3 => 1.8,
+            SleepStage::Rem => 1.2,
+        };
+        let icp_target = (10.0
+            + stage_icp_term
+            + 0.12 * (self.cerebral_blood_flow_ml_per_100g_min - 50.0)
+            + 4.0 * (self.metabolic_demand_fraction - 1.0))
+            .clamp(5.0, 30.0);
+        self.intracranial_pressure_mm_hg = Self::approach(
+            self.intracranial_pressure_mm_hg,
+            icp_target,
+            0.4,
+            dt_seconds,
+        )
+        .clamp(4.0, 35.0);
+
+        let map_proxy = 90.0 + 15.0 * (self.brainstem_autonomic_drive - 0.8)
+            - 8.0 * (self.autonomic_variability - 0.4);
+        let cpp_target = (map_proxy - self.intracranial_pressure_mm_hg).clamp(40.0, 110.0);
+        self.cerebral_perfusion_pressure_mm_hg = Self::approach(
+            self.cerebral_perfusion_pressure_mm_hg,
+            cpp_target,
+            1.2,
+            dt_seconds,
+        );
+
+        let activity = (self.cortical_arousal * 0.6
+            + self.metabolic_demand_fraction * 0.25
+            + (self.glutamate_level - self.gaba_level + 0.7) * 0.1
+            + self.dopamine_tone * 0.05)
+            .clamp(0.1, 2.3);
+        self.activity_index = activity;
+
+        let perfusion_factor = (self.cerebral_perfusion_pressure_mm_hg / 70.0).clamp(0.4, 1.3);
+        let oxygen_factor = (self.oxygenation_saturation / 0.96).clamp(0.5, 1.1);
+        let stage_bonus = match self.sleep_stage {
+            SleepStage::Wake => 18.0,
+            SleepStage::Rem => 8.0,
+            _ => 3.0,
+        };
+        let target_consciousness =
+            ((self.cortical_arousal * 70.0 * perfusion_factor * oxygen_factor) + stage_bonus)
+                .clamp(0.0, 100.0);
+        self.consciousness = target_consciousness.round() as u8;
+
+        let excitability =
+            (self.glutamate_level - self.gaba_level + self.cortical_arousal - 0.5).max(0.0);
+        let hypoxia = (0.94 - self.oxygenation_saturation).max(0.0) * 4.0;
+        let perfusion_deficit = (55.0 - self.cerebral_perfusion_pressure_mm_hg).max(0.0) / 40.0;
+        self.seizure_risk = (0.25 * excitability + hypoxia + perfusion_deficit).clamp(0.0, 1.0);
     }
     fn summary(&self) -> String {
         format!(
-            "Brain[id={}, GCS~{}, activity={:.2}]",
+            "Brain[id={}, stage={:?}, arousal={:.2}, ICP={:.1} mmHg, CPP={:.0} mmHg, O2={:.0}%, szrisk={:.0}%]",
             self.id(),
-            self.consciousness,
-            self.activity_index
+            self.sleep_stage,
+            self.cortical_arousal,
+            self.intracranial_pressure_mm_hg,
+            self.cerebral_perfusion_pressure_mm_hg,
+            self.oxygenation_saturation * 100.0,
+            self.seizure_risk * 100.0
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/esophagus.rs

@@ -1,20 +1,253 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+const ESOPHAGEAL_LENGTH_CM: f32 = 25.0;
+const PRIMARY_WAVE_SPEED_CM_S: f32 = 4.5;
+const SECONDARY_WAVE_SPEED_CM_S: f32 = 3.2;
+const BASE_HIATAL_PRESSURE_CM_H2O: f32 = 6.0;
+
+/// Functional sequence of the esophagus during swallowing and reflux handling.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum EsophagealStage {
+    Idle,
+    SwallowInitiation,
+    PrimaryPeristalsis,
+    SecondaryPeristalsis,
+    Clearing,
+    RefluxExposure,
+}
+
 #[derive(Debug, Clone)]
 pub struct Esophagus {
     info: OrganInfo,
-    /// Reflux severity 0..=100
-    pub reflux: u8,
+    /// Luminal pH along the distal esophagus.
+    pub luminal_ph: f32,
+    /// Lower esophageal sphincter tone (0..=1).
+    pub lower_sphincter_tone: f32,
+    /// Upper esophageal sphincter tone (0..=1).
+    pub upper_sphincter_tone: f32,
+    /// Distance traversed by the current peristaltic wave (cm).
+    pub peristaltic_progress_cm: f32,
+    /// Bolus volume currently descending (ml).
+    pub bolus_volume_ml: f32,
+    /// Salivary buffer content available to neutralize acid (ml).
+    pub saliva_buffer_ml: f32,
+    /// Estimated reflux episodes per hour.
+    pub reflux_events_per_hour: f32,
+    /// Fractional acid exposure burden (0..≈1.2).
+    pub acid_exposure_fraction: f32,
+    /// Mucosal integrity (0..≈1; <0.7 suggests erosive disease).
+    pub mucosal_integrity: f32,
+    /// Current functional state.
+    pub stage: EsophagealStage,
+    /// Swallow drive (0..=1) influenced by salivary demand and mucosal irritation.
+    pub swallow_drive: f32,
+    /// Peristaltic contractile strength scaling factor.
+    pub peristaltic_strength: f32,
+    /// Vagal tone modulating motility (0..=1).
+    pub vagal_tone: f32,
+    /// Time since the last initiated swallow (s).
+    pub time_since_last_swallow_s: f32,
+    time_in_stage_s: f32,
+    /// Target interval between swallows based on drive (s).
+    pub swallow_interval_target_s: f32,
+    /// Pressure gradient promoting reflux (cmH2O).
+    pub hiatal_pressure_gradient_cm_h2o: f32,
 }
 
 impl Esophagus {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Esophagus),
-            reflux: 0,
+            luminal_ph: 6.4,
+            lower_sphincter_tone: 0.78,
+            upper_sphincter_tone: 0.9,
+            peristaltic_progress_cm: 0.0,
+            bolus_volume_ml: 0.0,
+            saliva_buffer_ml: 1.2,
+            reflux_events_per_hour: 1.5,
+            acid_exposure_fraction: 0.08,
+            mucosal_integrity: 0.95,
+            stage: EsophagealStage::Idle,
+            swallow_drive: 0.35,
+            peristaltic_strength: 0.9,
+            vagal_tone: 0.65,
+            time_since_last_swallow_s: 0.0,
+            time_in_stage_s: 0.0,
+            swallow_interval_target_s: 22.0,
+            hiatal_pressure_gradient_cm_h2o: BASE_HIATAL_PRESSURE_CM_H2O,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn transition_stage(&mut self, stage: EsophagealStage) {
+        if self.stage != stage {
+            self.stage = stage;
+            self.time_in_stage_s = 0.0;
+        }
+    }
+
+    fn start_primary_swallow(&mut self) {
+        self.transition_stage(EsophagealStage::SwallowInitiation);
+        self.peristaltic_progress_cm = 0.0;
+        self.bolus_volume_ml = 4.0 + 3.0 * self.swallow_drive;
+        self.saliva_buffer_ml += 1.5 + 1.2 * self.swallow_drive;
+        self.time_since_last_swallow_s = 0.0;
+    }
+
+    fn update_swallow_drive(&mut self, dt_seconds: f32) {
+        let dryness = (self.time_since_last_swallow_s / 45.0).clamp(0.0, 1.4);
+        let irritation = (self.acid_exposure_fraction * 0.7) + (1.0 - self.mucosal_integrity) * 0.8;
+        let target_drive = (0.2 + dryness + irritation).clamp(0.05, 1.0);
+        self.swallow_drive = Self::approach(self.swallow_drive, target_drive, 0.35, dt_seconds);
+        let interval_target = (35.0 - 18.0 * self.swallow_drive).clamp(4.5, 55.0);
+        self.swallow_interval_target_s = Self::approach(
+            self.swallow_interval_target_s,
+            interval_target,
+            0.5,
+            dt_seconds,
+        );
+        let vagal_target =
+            (0.6 + 0.25 * self.swallow_drive - 0.15 * self.acid_exposure_fraction).clamp(0.35, 0.9);
+        self.vagal_tone = Self::approach(self.vagal_tone, vagal_target, 0.3, dt_seconds);
+        let strength_target = (0.85 + 0.5 * (self.vagal_tone - 0.6)).clamp(0.5, 1.3);
+        self.peristaltic_strength =
+            Self::approach(self.peristaltic_strength, strength_target, 0.4, dt_seconds);
+    }
+
+    fn update_sphincter_tones(&mut self, dt_seconds: f32) {
+        let base_les =
+            (0.7 + 0.18 * self.vagal_tone - 0.25 * self.acid_exposure_fraction).clamp(0.25, 0.98);
+        let base_ues = (0.82 + 0.1 * self.vagal_tone - 0.1 * self.swallow_drive).clamp(0.4, 0.98);
+        let (les_modifier, ues_modifier) = match self.stage {
+            EsophagealStage::Idle => (0.0, 0.0),
+            EsophagealStage::SwallowInitiation => (-0.4, -0.5),
+            EsophagealStage::PrimaryPeristalsis => (-0.25, -0.4),
+            EsophagealStage::SecondaryPeristalsis => (-0.18, -0.2),
+            EsophagealStage::Clearing => (-0.1, -0.1),
+            EsophagealStage::RefluxExposure => (-0.35, 0.0),
+        };
+        let les_target = (base_les + les_modifier).clamp(0.1, 0.98);
+        let ues_target = (base_ues + ues_modifier).clamp(0.05, 0.98);
+        self.lower_sphincter_tone =
+            Self::approach(self.lower_sphincter_tone, les_target, 1.4, dt_seconds).clamp(0.05, 1.0);
+        self.upper_sphincter_tone =
+            Self::approach(self.upper_sphincter_tone, ues_target, 2.0, dt_seconds).clamp(0.05, 1.0);
+    }
+
+    fn update_hiatal_gradient(&mut self, dt_seconds: f32) {
+        let target = (BASE_HIATAL_PRESSURE_CM_H2O
+            + 2.0 * (self.swallow_drive - 0.3)
+            + if matches!(self.stage, EsophagealStage::RefluxExposure) {
+                1.0
+            } else {
+                0.0
+            })
+        .clamp(3.0, 18.0);
+        self.hiatal_pressure_gradient_cm_h2o = Self::approach(
+            self.hiatal_pressure_gradient_cm_h2o,
+            target,
+            0.25,
+            dt_seconds,
+        );
+    }
+
+    fn handle_stage(&mut self, dt_seconds: f32) {
+        match self.stage {
+            EsophagealStage::Idle => {
+                self.peristaltic_progress_cm =
+                    Self::approach(self.peristaltic_progress_cm, 0.0, 10.0, dt_seconds);
+                self.bolus_volume_ml = Self::approach(self.bolus_volume_ml, 0.0, 6.0, dt_seconds);
+                if self.acid_exposure_fraction > 0.35 {
+                    self.transition_stage(EsophagealStage::RefluxExposure);
+                }
+            }
+            EsophagealStage::SwallowInitiation => {
+                if self.time_in_stage_s > 0.28 {
+                    self.transition_stage(EsophagealStage::PrimaryPeristalsis);
+                }
+            }
+            EsophagealStage::PrimaryPeristalsis => {
+                let speed = PRIMARY_WAVE_SPEED_CM_S * self.peristaltic_strength.clamp(0.4, 1.5);
+                self.peristaltic_progress_cm += speed * dt_seconds;
+                self.bolus_volume_ml = (self.bolus_volume_ml - dt_seconds * (speed * 0.8)).max(0.6);
+                if self.peristaltic_progress_cm >= ESOPHAGEAL_LENGTH_CM {
+                    if self.bolus_volume_ml > 1.2 {
+                        self.transition_stage(EsophagealStage::SecondaryPeristalsis);
+                    } else {
+                        self.transition_stage(EsophagealStage::Clearing);
+                    }
+                }
+            }
+            EsophagealStage::SecondaryPeristalsis => {
+                let speed = SECONDARY_WAVE_SPEED_CM_S * self.peristaltic_strength.clamp(0.4, 1.4);
+                self.peristaltic_progress_cm += speed * dt_seconds;
+                self.bolus_volume_ml = (self.bolus_volume_ml - dt_seconds * (speed * 0.7)).max(0.3);
+                if self.time_in_stage_s > 6.0 || self.bolus_volume_ml <= 0.4 {
+                    self.transition_stage(EsophagealStage::Clearing);
+                }
+            }
+            EsophagealStage::Clearing => {
+                self.bolus_volume_ml = Self::approach(self.bolus_volume_ml, 0.0, 4.0, dt_seconds);
+                if self.time_in_stage_s > 2.0 {
+                    self.transition_stage(EsophagealStage::Idle);
+                }
+            }
+            EsophagealStage::RefluxExposure => {
+                self.peristaltic_progress_cm =
+                    Self::approach(self.peristaltic_progress_cm, 0.0, 5.0, dt_seconds);
+                if self.acid_exposure_fraction < 0.12 {
+                    self.transition_stage(EsophagealStage::Idle);
+                }
+            }
+        }
+    }
+
+    fn update_acid_balance(&mut self, dt_seconds: f32) {
+        let reflux_propensity = (self.hiatal_pressure_gradient_cm_h2o - 4.0).max(0.0)
+            * (1.0 - self.lower_sphincter_tone);
+        let reflux_influx = reflux_propensity * 0.012 * dt_seconds;
+        if reflux_influx > 0.0 {
+            self.acid_exposure_fraction =
+                (self.acid_exposure_fraction + reflux_influx).clamp(0.0, 1.2);
+            if self.acid_exposure_fraction > 0.25 {
+                self.transition_stage(EsophagealStage::RefluxExposure);
+            }
+        }
+        let saliva_clearance =
+            (self.saliva_buffer_ml * 0.015 + self.peristaltic_strength * 0.01) * dt_seconds;
+        self.acid_exposure_fraction = (self.acid_exposure_fraction - saliva_clearance).max(0.0);
+        let mucosal_damage = (self.acid_exposure_fraction - 0.18).max(0.0) * 0.006 * dt_seconds;
+        let mucosal_healing = (self.saliva_buffer_ml * 0.003 + 0.0025) * dt_seconds;
+        self.mucosal_integrity =
+            (self.mucosal_integrity - mucosal_damage + mucosal_healing).clamp(0.55, 1.02);
+        let target_reflux_rate = (reflux_propensity * 11.0).clamp(0.0, 30.0);
+        self.reflux_events_per_hour = Self::approach(
+            self.reflux_events_per_hour,
+            target_reflux_rate,
+            0.12,
+            dt_seconds,
+        );
+        let acid_drop = (self.acid_exposure_fraction * 4.5).clamp(0.0, 6.5);
+        let base_recovery = (self.saliva_buffer_ml * 0.18).clamp(0.0, 3.0);
+        self.luminal_ph = (6.5 - acid_drop + base_recovery).clamp(1.0, 7.2);
+        self.saliva_buffer_ml = (self.saliva_buffer_ml - dt_seconds * 1.0).max(0.0);
+    }
 }
 
 impl Organ for Esophagus {
@@ -24,11 +257,39 @@ impl Organ for Esophagus {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        self.reflux = self.reflux.min(100);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_since_last_swallow_s += dt_seconds;
+        self.time_in_stage_s += dt_seconds;
+
+        self.update_swallow_drive(dt_seconds);
+        self.update_hiatal_gradient(dt_seconds);
+        self.update_sphincter_tones(dt_seconds);
+
+        if self.time_since_last_swallow_s >= self.swallow_interval_target_s
+            && matches!(
+                self.stage,
+                EsophagealStage::Idle | EsophagealStage::RefluxExposure
+            )
+        {
+            self.start_primary_swallow();
+        }
+
+        self.handle_stage(dt_seconds);
+        self.update_acid_balance(dt_seconds);
     }
     fn summary(&self) -> String {
-        format!("Esophagus[id={}, reflux={}]", self.id(), self.reflux)
+        format!(
+            "Esophagus[id={}, stage={:?}, pH={:.1}, LES={:.0}%, reflux≈{:.1}/h]",
+            self.id(),
+            self.stage,
+            self.luminal_ph,
+            self.lower_sphincter_tone * 100.0,
+            self.reflux_events_per_hour
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/organs/gallbladder.rs

@@ -1,20 +1,224 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+const DEFAULT_CAPACITY_ML: f32 = 50.0;
+const RESIDUAL_VOLUME_ML: f32 = 8.0;
+
+/// Functional state of the gallbladder during the interdigestive and post-prandial cycle.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum GallbladderPhase {
+    Filling,
+    Primed,
+    Contraction,
+    Expulsion,
+    Recovery,
+}
+
 #[derive(Debug, Clone)]
 pub struct Gallbladder {
     info: OrganInfo,
-    /// Bile volume ml
-    pub bile_ml: f32,
+    /// Stored bile volume (ml).
+    pub bile_volume_ml: f32,
+    /// Bile acid concentration (mmol/L).
+    pub bile_acid_concentration_mmol_l: f32,
+    /// Cholesterol saturation index (dimensionless; >1 predisposes to stones).
+    pub cholesterol_saturation_index: f32,
+    /// Flow of bile exiting via the cystic duct/common bile duct (ml/min).
+    pub bile_outflow_ml_per_min: f32,
+    /// Tone of the sphincter of Oddi (0..=1, higher = more closed).
+    pub sphincter_of_oddi_tone: f32,
+    /// Circulating cholecystokinin level (ng/mL proxy).
+    pub cck_level_ng_ml: f32,
+    /// Hepatic bile inflow (ml/min) delivered to the gallbladder when filling.
+    pub hepatic_bile_flow_ml_per_min: f32,
+    /// Total bile-acid pool currently stored in the gallbladder (mmol).
+    pub bile_acid_pool_mmol: f32,
+    /// Efficiency of enterohepatic recycling (0..=1).
+    pub bile_salt_recycling_efficiency: f32,
+    /// Vagal tone supporting coordinated contraction (0..=1).
+    pub vagal_tone: f32,
+    /// Fractional mucosal absorption rate.
+    pub mucosal_absorption_fraction: f32,
+    /// Current state in the contraction cycle.
+    pub phase: GallbladderPhase,
+    /// External or simulated meal stimulus (0..=1).
+    pub meal_signal: f32,
+    /// Internal fasting-driven feed-forward signal (0..=1).
+    pub internal_meal_drive: f32,
+    time_in_phase_s: f32,
+    fasting_clock_s: f32,
+    target_meal_interval_s: f32,
+    /// Stone-forming propensity index (0..≈2).
+    pub gallstone_nucleation_index: f32,
 }
 
 impl Gallbladder {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Gallbladder),
-            bile_ml: 30.0,
+            bile_volume_ml: 35.0,
+            bile_acid_concentration_mmol_l: 65.0,
+            cholesterol_saturation_index: 0.9,
+            bile_outflow_ml_per_min: 0.05,
+            sphincter_of_oddi_tone: 0.85,
+            cck_level_ng_ml: 0.2,
+            hepatic_bile_flow_ml_per_min: 0.55,
+            bile_acid_pool_mmol: 2.6,
+            bile_salt_recycling_efficiency: 0.92,
+            vagal_tone: 0.58,
+            mucosal_absorption_fraction: 0.03,
+            phase: GallbladderPhase::Filling,
+            meal_signal: 0.1,
+            internal_meal_drive: 0.12,
+            time_in_phase_s: 0.0,
+            fasting_clock_s: 0.0,
+            target_meal_interval_s: 4.8 * 3600.0,
+            gallstone_nucleation_index: 0.2,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn transition_phase(&mut self, phase: GallbladderPhase) {
+        if self.phase != phase {
+            self.phase = phase;
+            self.time_in_phase_s = 0.0;
+        }
+    }
+
+    fn update_meal_drives(&mut self, dt_seconds: f32) {
+        self.fasting_clock_s += dt_seconds;
+        if self.fasting_clock_s >= self.target_meal_interval_s {
+            self.internal_meal_drive = 1.0;
+            self.fasting_clock_s = 0.0;
+            self.target_meal_interval_s = (4.0 + 1.5 * self.vagal_tone) * 3600.0;
+        }
+        self.internal_meal_drive = (self.internal_meal_drive - dt_seconds / 900.0).clamp(0.0, 1.0);
+        // Allow external stimuli to decay gently if not continuously refreshed.
+        self.meal_signal = Self::approach(self.meal_signal, 0.1, 0.05, dt_seconds);
+        let stimulus = self.meal_signal.max(self.internal_meal_drive);
+        let cck_target = (0.15 + 1.6 * stimulus).clamp(0.1, 2.5);
+        self.cck_level_ng_ml =
+            Self::approach(self.cck_level_ng_ml, cck_target, 0.8, dt_seconds).clamp(0.05, 3.0);
+        let vagal_target = (0.55 + 0.35 * stimulus).clamp(0.4, 0.92);
+        self.vagal_tone = Self::approach(self.vagal_tone, vagal_target, 0.35, dt_seconds);
+    }
+
+    fn update_sphincter_tone(&mut self, dt_seconds: f32) {
+        let tone_target = match self.phase {
+            GallbladderPhase::Filling => 0.88,
+            GallbladderPhase::Primed => 0.75,
+            GallbladderPhase::Contraction => 0.45,
+            GallbladderPhase::Expulsion => 0.35,
+            GallbladderPhase::Recovery => 0.7,
+        } - 0.18 * (self.cck_level_ng_ml - 0.3).max(0.0);
+        self.sphincter_of_oddi_tone = Self::approach(
+            self.sphincter_of_oddi_tone,
+            tone_target.clamp(0.2, 0.95),
+            0.9,
+            dt_seconds,
+        );
+    }
+
+    fn hepatic_inflow(&self) -> f32 {
+        match self.phase {
+            GallbladderPhase::Contraction | GallbladderPhase::Expulsion => {
+                self.hepatic_bile_flow_ml_per_min * 0.4
+            }
+            _ => self.hepatic_bile_flow_ml_per_min,
+        }
+    }
+
+    fn update_bile_pool(&mut self, dt_seconds: f32, outflow_ml: f32) {
+        let inflow_ml = self.hepatic_inflow() * dt_seconds / 60.0;
+        let inflow_bile_acids = inflow_ml * 0.075 * self.bile_salt_recycling_efficiency;
+        let absorption_loss =
+            self.bile_acid_pool_mmol * self.mucosal_absorption_fraction * dt_seconds / 3600.0;
+        let pool_after = (self.bile_acid_pool_mmol + inflow_bile_acids - absorption_loss).max(0.5);
+        let volume_after = (self.bile_volume_ml + inflow_ml - outflow_ml)
+            .clamp(RESIDUAL_VOLUME_ML, DEFAULT_CAPACITY_ML);
+        let volume_ratio = if self.bile_volume_ml > 0.0 {
+            outflow_ml / self.bile_volume_ml
+        } else {
+            0.0
+        }
+        .clamp(0.0, 0.95);
+        let pool_after = (pool_after * (1.0 - volume_ratio)).max(0.5);
+        self.bile_volume_ml = volume_after;
+        self.bile_acid_pool_mmol = pool_after;
+        let volume_l = (self.bile_volume_ml / 1000.0).max(0.005);
+        self.bile_acid_concentration_mmol_l =
+            (self.bile_acid_pool_mmol / volume_l).clamp(20.0, 140.0);
+        let saturation = (1.0 + 0.32 * (self.bile_volume_ml / DEFAULT_CAPACITY_ML - 0.5)
+            - 0.45 * (self.bile_acid_concentration_mmol_l / 60.0 - 1.0))
+            .clamp(0.6, 1.6);
+        self.cholesterol_saturation_index = saturation;
+    }
+
+    fn handle_phase(&mut self, _dt_seconds: f32) {
+        match self.phase {
+            GallbladderPhase::Filling => {
+                self.bile_outflow_ml_per_min = 0.05 * (1.0 - self.sphincter_of_oddi_tone);
+                if (self.cck_level_ng_ml > 0.35 && self.bile_volume_ml > DEFAULT_CAPACITY_ML * 0.55)
+                    || self.mucosal_absorption_fraction < 0.02
+                {
+                    self.transition_phase(GallbladderPhase::Primed);
+                }
+            }
+            GallbladderPhase::Primed => {
+                self.bile_outflow_ml_per_min = 0.2 + 1.5 * (self.cck_level_ng_ml - 0.3).max(0.0);
+                if self.time_in_phase_s > 60.0 || self.cck_level_ng_ml > 0.6 {
+                    self.transition_phase(GallbladderPhase::Contraction);
+                }
+            }
+            GallbladderPhase::Contraction => {
+                self.bile_outflow_ml_per_min = (2.5
+                    + 8.0 * (self.cck_level_ng_ml - 0.3).max(0.0)
+                    + 4.5 * (self.vagal_tone - 0.5).max(0.0))
+                    * (1.0 - self.sphincter_of_oddi_tone);
+                if self.bile_volume_ml < DEFAULT_CAPACITY_ML * 0.3 {
+                    self.transition_phase(GallbladderPhase::Expulsion);
+                }
+            }
+            GallbladderPhase::Expulsion => {
+                self.bile_outflow_ml_per_min =
+                    (1.2 + 6.0 * (1.0 - self.sphincter_of_oddi_tone)).clamp(0.6, 12.0);
+                if self.bile_volume_ml <= RESIDUAL_VOLUME_ML + 1.0 || self.time_in_phase_s > 180.0 {
+                    self.transition_phase(GallbladderPhase::Recovery);
+                }
+            }
+            GallbladderPhase::Recovery => {
+                self.bile_outflow_ml_per_min = 0.1 * (1.0 - self.sphincter_of_oddi_tone);
+                if self.cck_level_ng_ml < 0.25 && self.time_in_phase_s > 120.0 {
+                    self.transition_phase(GallbladderPhase::Filling);
+                }
+            }
+        }
+    }
+
+    fn update_gallstone_index(&mut self, dt_seconds: f32) {
+        let stasis = (1.0 - (self.bile_outflow_ml_per_min / 8.0).clamp(0.0, 1.0)).max(0.0);
+        let supersaturation = (self.cholesterol_saturation_index - 1.0).max(0.0);
+        let volume_factor = (self.bile_volume_ml / DEFAULT_CAPACITY_ML - 0.6).max(0.0);
+        let target =
+            (0.3 + 1.8 * supersaturation * (0.6 + stasis) + 0.5 * volume_factor).clamp(0.0, 2.2);
+        self.gallstone_nucleation_index =
+            Self::approach(self.gallstone_nucleation_index, target, 0.15, dt_seconds);
+    }
 }
 
 impl Organ for Gallbladder {
@@ -24,9 +228,48 @@ impl Organ for Gallbladder {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {}
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_in_phase_s += dt_seconds;
+
+        self.update_meal_drives(dt_seconds);
+        self.update_sphincter_tone(dt_seconds);
+        self.handle_phase(dt_seconds);
+
+        let outflow_ml = (self.bile_outflow_ml_per_min * dt_seconds / 60.0).clamp(0.0, 25.0);
+        self.update_bile_pool(dt_seconds, outflow_ml);
+
+        // Adjust mucosal absorption with concentration and phase.
+        let absorption_target = match self.phase {
+            GallbladderPhase::Filling => 0.035,
+            GallbladderPhase::Primed => 0.03,
+            GallbladderPhase::Contraction => 0.02,
+            GallbladderPhase::Expulsion => 0.015,
+            GallbladderPhase::Recovery => 0.028,
+        } * (self.bile_acid_concentration_mmol_l / 60.0).clamp(0.7, 1.4);
+        self.mucosal_absorption_fraction = Self::approach(
+            self.mucosal_absorption_fraction,
+            absorption_target,
+            0.2,
+            dt_seconds,
+        )
+        .clamp(0.01, 0.05);
+
+        self.update_gallstone_index(dt_seconds);
+    }
     fn summary(&self) -> String {
-        format!("Gallbladder[id={}, bile={:.0} ml]", self.id(), self.bile_ml)
+        format!(
+            "Gallbladder[id={}, phase={:?}, vol={:.0}/{:.0} ml, bileAcid={:.0} mmol/L, CSI={:.2}]",
+            self.id(),
+            self.phase,
+            self.bile_volume_ml,
+            DEFAULT_CAPACITY_ML,
+            self.bile_acid_concentration_mmol_l,
+            self.cholesterol_saturation_index
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/organs/heart.rs

@@ -1,18 +1,71 @@
 use super::{Organ, OrganInfo};
 use crate::types::{BloodPressure, OrganType};
 
-/// Cardiac model with simple rate and arterial pressure coupling.
+const BASE_SV_ML: f32 = 70.0;
+const BASE_SVR_MMHG_MIN_PER_L: f32 = 17.0;
+const BAROREFLEX_SET_POINT_MMHG: f32 = 93.0;
+
+/// Rhythm archetypes representing dominant autonomic/conduction control of the heart.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum CardiacRhythmState {
+    Sinus,
+    SympatheticDrive,
+    ParasympatheticDominance,
+    CompensatoryTachycardia,
+    Arrhythmic,
+}
+
+/// Cardiac pump model featuring autonomic reflexes and hemodynamic coupling.
 #[derive(Debug, Clone)]
 pub struct Heart {
     info: OrganInfo,
-    /// Heart rate in beats per minute.
+    /// Heart rate (beats per minute).
     pub heart_rate_bpm: f32,
     /// Arterial blood pressure snapshot.
     pub arterial_bp: BloodPressure,
-    /// ECG lead count configured for this heart.
+    /// Number of ECG leads configured for monitoring.
     pub leads: u8,
-    /// Simplified arrhythmia flag; increases HR variability.
+    /// Allow external systems to force arrhythmic behavior.
     pub arrhythmia: bool,
+    /// Stroke volume (ml/beat).
+    pub stroke_volume_ml: f32,
+    /// Cardiac output (L/min).
+    pub cardiac_output_l_min: f32,
+    /// End-diastolic volume (ml).
+    pub end_diastolic_volume_ml: f32,
+    /// End-systolic volume (ml).
+    pub end_systolic_volume_ml: f32,
+    /// Ejection fraction (0..=1).
+    pub ejection_fraction: f32,
+    /// Contractility index (dimensionless relative to baseline 1.0).
+    pub contractility_index: f32,
+    /// Preload expressed as estimated left-ventricular end-diastolic pressure (mmHg).
+    pub preload_mm_hg: f32,
+    /// Afterload (mmHg) approximated from systemic vascular resistance.
+    pub afterload_mm_hg: f32,
+    /// Systemic vascular resistance (mmHg·min/L).
+    pub systemic_vascular_resistance: f32,
+    /// Venous return (L/min).
+    pub venous_return_l_min: f32,
+    /// Sinoatrial node intrinsic rate (bpm).
+    pub sa_node_rate_bpm: f32,
+    /// Atrioventricular conduction delay (ms).
+    pub av_delay_ms: f32,
+    /// Autonomic tone (-1 parasympathetic, +1 sympathetic).
+    pub autonomic_tone: f32,
+    /// Current rhythm classification.
+    pub rhythm_state: CardiacRhythmState,
+    /// Arrhythmia burden (0..=1).
+    pub arrhythmia_burden: f32,
+    /// Myocardial oxygen demand (mL O2/beat scaled).
+    pub myocardial_oxygen_demand: f32,
+    /// Myocardial oxygen supply proxy (mL O2/beat scaled).
+    pub myocardial_oxygen_supply: f32,
+    /// Coronary perfusion pressure (mmHg).
+    pub coronary_perfusion_mm_hg: f32,
+    /// Stroke work (J per beat).
+    pub stroke_work_joule: f32,
+    time_in_state_s: f32,
 }
 
 impl Heart {
@@ -20,12 +73,189 @@ impl Heart {
     pub fn new(id: impl Into<String>, leads: u8) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Heart),
-            heart_rate_bpm: 70.0,
+            heart_rate_bpm: 72.0,
             arterial_bp: BloodPressure::default(),
             leads,
             arrhythmia: false,
+            stroke_volume_ml: BASE_SV_ML,
+            cardiac_output_l_min: 5.0,
+            end_diastolic_volume_ml: 120.0,
+            end_systolic_volume_ml: 50.0,
+            ejection_fraction: 0.58,
+            contractility_index: 1.0,
+            preload_mm_hg: 8.0,
+            afterload_mm_hg: 85.0,
+            systemic_vascular_resistance: BASE_SVR_MMHG_MIN_PER_L,
+            venous_return_l_min: 5.0,
+            sa_node_rate_bpm: 72.0,
+            av_delay_ms: 160.0,
+            autonomic_tone: 0.0,
+            rhythm_state: CardiacRhythmState::Sinus,
+            arrhythmia_burden: 0.05,
+            myocardial_oxygen_demand: 9.0,
+            myocardial_oxygen_supply: 9.5,
+            coronary_perfusion_mm_hg: 70.0,
+            stroke_work_joule: 1.1,
+            time_in_state_s: 0.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn mean_arterial_pressure(&self) -> f32 {
+        let sys = self.arterial_bp.systolic as f32;
+        let dia = self.arterial_bp.diastolic as f32;
+        dia + (sys - dia) / 3.0
+    }
+
+    fn update_autonomic_state(&mut self, dt_seconds: f32) {
+        let map_error = self.mean_arterial_pressure() - BAROREFLEX_SET_POINT_MMHG;
+        let autonomic_target = (-map_error / 30.0).clamp(-1.0, 1.0);
+        self.autonomic_tone =
+            Self::approach(self.autonomic_tone, autonomic_target, 0.8, dt_seconds);
+        self.sa_node_rate_bpm = Self::approach(
+            self.sa_node_rate_bpm,
+            (70.0 + 45.0 * self.autonomic_tone).clamp(45.0, 150.0),
+            1.5,
+            dt_seconds,
+        );
+        self.av_delay_ms = Self::approach(
+            self.av_delay_ms,
+            (170.0 - 40.0 * self.autonomic_tone).clamp(110.0, 240.0),
+            5.0,
+            dt_seconds,
+        );
+        let svr_target = (BASE_SVR_MMHG_MIN_PER_L - 5.5 * self.autonomic_tone).clamp(10.0, 26.0);
+        self.systemic_vascular_resistance = Self::approach(
+            self.systemic_vascular_resistance,
+            svr_target,
+            0.3,
+            dt_seconds,
+        );
+    }
+
+    fn determine_rhythm_state(&mut self) {
+        let arrhythmic = self.arrhythmia || self.arrhythmia_burden > 0.45;
+        self.rhythm_state = if arrhythmic {
+            CardiacRhythmState::Arrhythmic
+        } else if self.autonomic_tone > 0.5 {
+            CardiacRhythmState::SympatheticDrive
+        } else if self.autonomic_tone < -0.4 {
+            CardiacRhythmState::ParasympatheticDominance
+        } else if self.venous_return_l_min < 4.2 && self.mean_arterial_pressure() < 75.0 {
+            CardiacRhythmState::CompensatoryTachycardia
+        } else {
+            CardiacRhythmState::Sinus
+        };
+    }
+
+    fn update_rate_and_contractility(&mut self, dt_seconds: f32) {
+        let mut rate_target = self.sa_node_rate_bpm;
+        match self.rhythm_state {
+            CardiacRhythmState::SympatheticDrive => rate_target += 18.0,
+            CardiacRhythmState::ParasympatheticDominance => rate_target -= 12.0,
+            CardiacRhythmState::CompensatoryTachycardia => rate_target += 22.0,
+            CardiacRhythmState::Arrhythmic => rate_target += 8.0,
+            CardiacRhythmState::Sinus => {}
+        }
+        rate_target += 8.0 * (self.arrhythmia_burden - 0.2).max(0.0);
+        self.heart_rate_bpm = Self::approach(
+            self.heart_rate_bpm,
+            rate_target.clamp(38.0, 190.0),
+            1.2,
+            dt_seconds,
+        );
+        let demand_scale = (self.heart_rate_bpm / 70.0).clamp(0.6, 2.0);
+        let afterload_penalty = (self.afterload_mm_hg - 90.0).max(0.0) / 120.0;
+        let contractility_target = (1.05 + 0.35 * self.autonomic_tone
+            - afterload_penalty
+            - (self.arrhythmia_burden * 0.2))
+            .clamp(0.5, 1.6);
+        self.contractility_index = Self::approach(
+            self.contractility_index,
+            contractility_target,
+            0.8,
+            dt_seconds,
+        );
+        self.myocardial_oxygen_demand = (8.5 * demand_scale
+            + 0.6 * self.contractility_index * (self.afterload_mm_hg / 80.0))
+            .clamp(4.0, 20.0);
+    }
+
+    fn update_volumes_and_output(&mut self, dt_seconds: f32) {
+        self.preload_mm_hg = Self::approach(
+            self.preload_mm_hg,
+            (6.5 + 1.2 * (self.venous_return_l_min - 4.5)).clamp(4.0, 18.0),
+            0.6,
+            dt_seconds,
+        );
+        let edv_target = (90.0 + 6.5 * self.preload_mm_hg).clamp(80.0, 210.0);
+        self.end_diastolic_volume_ml =
+            Self::approach(self.end_diastolic_volume_ml, edv_target, 1.1, dt_seconds);
+        let elastance = 0.22 + 0.25 * self.contractility_index;
+        let esv_target = (self.end_diastolic_volume_ml * (1.0 - elastance)).clamp(30.0, 120.0);
+        self.end_systolic_volume_ml =
+            Self::approach(self.end_systolic_volume_ml, esv_target, 1.6, dt_seconds);
+        self.stroke_volume_ml =
+            (self.end_diastolic_volume_ml - self.end_systolic_volume_ml).clamp(25.0, 130.0);
+        self.ejection_fraction =
+            (self.stroke_volume_ml / self.end_diastolic_volume_ml.max(1.0)).clamp(0.2, 0.85);
+        self.cardiac_output_l_min =
+            (self.stroke_volume_ml * self.heart_rate_bpm / 1000.0).clamp(2.0, 12.0);
+        self.venous_return_l_min = Self::approach(
+            self.venous_return_l_min,
+            self.cardiac_output_l_min,
+            0.4,
+            dt_seconds,
+        );
+        self.afterload_mm_hg = Self::approach(
+            self.afterload_mm_hg,
+            (self.systemic_vascular_resistance * self.cardiac_output_l_min).clamp(60.0, 160.0),
+            0.5,
+            dt_seconds,
+        );
+        let map_target = self.cardiac_output_l_min * self.systemic_vascular_resistance;
+        let pulse_pressure = (self.stroke_volume_ml / BASE_SV_ML).clamp(0.6, 2.0) * 40.0;
+        let systolic = (map_target + pulse_pressure / 2.0).clamp(80.0, 220.0);
+        let diastolic = (map_target - pulse_pressure / 2.5).clamp(40.0, systolic - 5.0);
+        self.arterial_bp.systolic = systolic.round() as u16;
+        self.arterial_bp.diastolic = diastolic.round() as u16;
+        self.coronary_perfusion_mm_hg =
+            (self.arterial_bp.diastolic as f32 - self.preload_mm_hg).clamp(20.0, 120.0);
+        self.myocardial_oxygen_supply = (9.5 + 0.08 * self.coronary_perfusion_mm_hg
+            - 0.5 * (self.heart_rate_bpm - 70.0) / 40.0)
+            .clamp(4.0, 20.0);
+        self.stroke_work_joule = (self.stroke_volume_ml / 1000.0)
+            * (self.mean_arterial_pressure() - 5.0).max(0.0)
+            * 0.133;
+    }
+
+    fn update_arrhythmia_burden(&mut self, dt_seconds: f32) {
+        let supply_demand_ratio =
+            (self.myocardial_oxygen_supply / self.myocardial_oxygen_demand).clamp(0.4, 1.6);
+        let mismatch = (1.0 - supply_demand_ratio).max(0.0);
+        let target = if self.arrhythmia {
+            0.7
+        } else {
+            0.2 + 0.6 * mismatch + 0.2 * (self.autonomic_tone - 0.5).max(0.0)
+        }
+        .clamp(0.05, 0.95);
+        self.arrhythmia_burden = Self::approach(self.arrhythmia_burden, target, 0.3, dt_seconds);
+    }
 }
 
 impl Organ for Heart {
@@ -36,26 +266,27 @@ impl Organ for Heart {
         self.info.kind()
     }
     fn update(&mut self, dt_seconds: f32) {
-        let dt = dt_seconds.clamp(0.0, 10.0);
-        let target = 70.0f32;
-        let mut diff = target - self.heart_rate_bpm;
-        if self.arrhythmia {
-            // add variability
-            diff += self.heart_rate_bpm.sin() * 5.0;
+        if dt_seconds <= 0.0 {
+            return;
         }
-        self.heart_rate_bpm += 0.1 * diff * (dt / 1.0);
-        // crude BP coupling to HR
-        let sys = (90.0 + 0.5 * self.heart_rate_bpm).clamp(80.0, 220.0) as u16;
-        let dia = (60.0 + 0.3 * self.heart_rate_bpm).clamp(40.0, 140.0) as u16;
-        self.arterial_bp.systolic = sys;
-        self.arterial_bp.diastolic = dia.min(sys.saturating_sub(10));
+
+        self.time_in_state_s += dt_seconds;
+
+        self.update_autonomic_state(dt_seconds);
+        self.determine_rhythm_state();
+        self.update_rate_and_contractility(dt_seconds);
+        self.update_volumes_and_output(dt_seconds);
+        self.update_arrhythmia_burden(dt_seconds);
     }
     fn summary(&self) -> String {
         format!(
-            "Heart[id={}, leads={}, HR={:.1} bpm, BP={}/{} mmHg]",
+            "Heart[id={}, leads={}, rhythm={:?}, HR={:.0} bpm, CO={:.1} L/min, EF={:.0}%, BP={}/{}]",
             self.id(),
             self.leads,
+            self.rhythm_state,
             self.heart_rate_bpm,
+            self.cardiac_output_l_min,
+            self.ejection_fraction * 100.0,
             self.arterial_bp.systolic,
             self.arterial_bp.diastolic
         )

src/organs/intestines.rs

@@ -1,22 +1,293 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Predominant motility/functional state of the small and large intestine.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum IntestinalPhase {
+    Interdigestive,
+    FedProcessing,
+    MigratingMotorComplex,
+    IlealBrake,
+    Dysmotility,
+}
+
 #[derive(Debug, Clone)]
 pub struct Intestines {
     info: OrganInfo,
-    /// Nutrient absorption rate 0..=100
-    pub absorption: u8,
-    pub peristalsis: bool,
+    /// Carbohydrate absorption (g/hour).
+    pub carbohydrate_absorption_g_per_h: f32,
+    /// Fat absorption (g/hour).
+    pub fat_absorption_g_per_h: f32,
+    /// Protein absorption (g/hour).
+    pub protein_absorption_g_per_h: f32,
+    /// Electrolyte reclamation (mmol/min).
+    pub electrolyte_absorption_mmol_min: f32,
+    /// Water reabsorption rate (ml/min).
+    pub water_reabsorption_ml_min: f32,
+    /// Integrated motility index (0..=1) dominated by peristaltic waves.
+    pub motility_index: f32,
+    /// Segmentation/segmental contractions index (0..=1).
+    pub segmentation_index: f32,
+    /// Migrating motor complex activity (0..=1).
+    pub mmc_activity: f32,
+    /// Current functional phase.
+    pub phase: IntestinalPhase,
+    /// Luminal volume of chyme (ml).
+    pub lumen_volume_ml: f32,
+    /// Luminal pH.
+    pub chyme_ph: f32,
+    /// Fraction of bile acids reclaimed in the terminal ileum (0..=1).
+    pub bile_acid_recirculation_fraction: f32,
+    /// Microbiome balance (0..=1, >0.5 reflects eubiosis).
+    pub microbiome_balance: f32,
+    /// Short-chain fatty acids produced (mmol).
+    pub short_chain_fatty_acids_mmol: f32,
+    /// Mucosal integrity (0..=1).
+    pub mucosal_integrity: f32,
+    /// Inflammatory index (0..=1).
+    pub inflammation_index: f32,
+    /// Motilin level (pg/mL proxy) driving MMC.
+    pub hormone_motilin: f32,
+    /// GLP-1 level influencing ileal brake (pmol/L proxy).
+    pub hormone_glp1: f32,
+    /// Enteric nervous system tone (0..=1).
+    pub enteric_tone: f32,
+    /// Pending nutrient energy load within the lumen (kcal).
+    pub nutrient_energy_kcal: f32,
+    /// Fermentable fiber load (g).
+    pub fiber_load_g: f32,
+    time_in_phase_s: f32,
+    feeding_clock_s: f32,
+    target_feed_interval_s: f32,
 }
 
 impl Intestines {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Intestines),
-            absorption: 80,
-            peristalsis: true,
+            carbohydrate_absorption_g_per_h: 45.0,
+            fat_absorption_g_per_h: 12.0,
+            protein_absorption_g_per_h: 18.0,
+            electrolyte_absorption_mmol_min: 2.5,
+            water_reabsorption_ml_min: 12.0,
+            motility_index: 0.55,
+            segmentation_index: 0.45,
+            mmc_activity: 0.3,
+            phase: IntestinalPhase::Interdigestive,
+            lumen_volume_ml: 350.0,
+            chyme_ph: 6.6,
+            bile_acid_recirculation_fraction: 0.92,
+            microbiome_balance: 0.62,
+            short_chain_fatty_acids_mmol: 22.0,
+            mucosal_integrity: 0.93,
+            inflammation_index: 0.12,
+            hormone_motilin: 110.0,
+            hormone_glp1: 8.0,
+            enteric_tone: 0.55,
+            nutrient_energy_kcal: 40.0,
+            fiber_load_g: 6.0,
+            time_in_phase_s: 0.0,
+            feeding_clock_s: 0.0,
+            target_feed_interval_s: 3.8 * 3600.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_internal_feeding(&mut self, dt_seconds: f32) {
+        self.feeding_clock_s += dt_seconds;
+        if self.feeding_clock_s >= self.target_feed_interval_s {
+            self.nutrient_energy_kcal += 410.0;
+            self.fiber_load_g += 4.0;
+            self.lumen_volume_ml = (self.lumen_volume_ml + 200.0).clamp(150.0, 800.0);
+            self.phase = IntestinalPhase::FedProcessing;
+            self.time_in_phase_s = 0.0;
+            self.feeding_clock_s = 0.0;
+            self.target_feed_interval_s = (3.0 + 1.5 * (1.0 - self.microbiome_balance)) * 3600.0;
+        }
+    }
+
+    fn update_enteric_tone(&mut self, dt_seconds: f32) {
+        let load_factor = (self.nutrient_energy_kcal / 400.0).clamp(0.0, 2.0);
+        let irritation = (1.0 - self.mucosal_integrity) * 1.2 + self.inflammation_index * 0.8;
+        let tone_target = (0.5 + 0.35 * load_factor - 0.2 * irritation).clamp(0.2, 0.95);
+        self.enteric_tone = Self::approach(self.enteric_tone, tone_target, 0.4, dt_seconds);
+    }
+
+    fn transition_phase(&mut self, phase: IntestinalPhase) {
+        if self.phase != phase {
+            self.phase = phase;
+            self.time_in_phase_s = 0.0;
+        }
+    }
+
+    fn update_phase(&mut self) {
+        match self.phase {
+            IntestinalPhase::Interdigestive => {
+                if self.nutrient_energy_kcal > 80.0 {
+                    self.transition_phase(IntestinalPhase::FedProcessing);
+                } else if self.time_in_phase_s > 90.0 * 60.0 {
+                    self.transition_phase(IntestinalPhase::MigratingMotorComplex);
+                }
+            }
+            IntestinalPhase::FedProcessing => {
+                if self.nutrient_energy_kcal < 100.0 {
+                    self.transition_phase(IntestinalPhase::IlealBrake);
+                }
+            }
+            IntestinalPhase::MigratingMotorComplex => {
+                if self.nutrient_energy_kcal > 40.0 {
+                    self.transition_phase(IntestinalPhase::FedProcessing);
+                } else if self.time_in_phase_s > 120.0 * 60.0 {
+                    self.transition_phase(IntestinalPhase::Interdigestive);
+                }
+            }
+            IntestinalPhase::IlealBrake => {
+                if self.hormone_glp1 < 6.0 && self.fiber_load_g < 8.0 {
+                    self.transition_phase(IntestinalPhase::Interdigestive);
+                } else if self.mucosal_integrity < 0.6 {
+                    self.transition_phase(IntestinalPhase::Dysmotility);
+                }
+            }
+            IntestinalPhase::Dysmotility => {
+                if self.mucosal_integrity > 0.75 && self.inflammation_index < 0.3 {
+                    self.transition_phase(IntestinalPhase::Interdigestive);
+                }
+            }
+        }
+    }
+
+    fn update_motility(&mut self, dt_seconds: f32) {
+        let (motility_target, segmentation_target, mmc_target, glp1_target, motilin_target) =
+            match self.phase {
+                IntestinalPhase::Interdigestive => (0.45, 0.4, 0.65, 6.0, 150.0),
+                IntestinalPhase::FedProcessing => (0.72, 0.55, 0.25, 18.0, 80.0),
+                IntestinalPhase::MigratingMotorComplex => (0.6, 0.35, 0.9, 8.0, 210.0),
+                IntestinalPhase::IlealBrake => (0.38, 0.6, 0.2, 28.0, 70.0),
+                IntestinalPhase::Dysmotility => (0.28, 0.35, 0.1, 22.0, 60.0),
+            };
+        self.motility_index = Self::approach(self.motility_index, motility_target, 0.6, dt_seconds);
+        self.segmentation_index = Self::approach(
+            self.segmentation_index,
+            segmentation_target,
+            0.5,
+            dt_seconds,
+        );
+        self.mmc_activity = Self::approach(self.mmc_activity, mmc_target, 0.4, dt_seconds);
+        self.hormone_glp1 =
+            Self::approach(self.hormone_glp1, glp1_target, 0.2, dt_seconds).clamp(2.0, 35.0);
+        self.hormone_motilin =
+            Self::approach(self.hormone_motilin, motilin_target, 0.8, dt_seconds)
+                .clamp(40.0, 280.0);
+    }
+
+    fn update_absorption(&mut self, dt_seconds: f32) {
+        let motility_effect =
+            (self.motility_index * 1.1 + self.segmentation_index * 0.6).clamp(0.3, 1.6);
+        let available = self.nutrient_energy_kcal.max(0.0);
+        let carbs_available = available * 0.55;
+        let fat_available = available * 0.28;
+        let protein_available = available * 0.17;
+        let carbs_abs_target = (carbs_available / 4.0).clamp(0.0, 90.0) * motility_effect;
+        let fat_abs_target = (fat_available / 9.0).clamp(0.0, 35.0) * motility_effect;
+        let protein_abs_target = (protein_available / 4.0).clamp(0.0, 50.0) * motility_effect;
+        self.carbohydrate_absorption_g_per_h = Self::approach(
+            self.carbohydrate_absorption_g_per_h,
+            carbs_abs_target,
+            0.3,
+            dt_seconds,
+        );
+        self.fat_absorption_g_per_h =
+            Self::approach(self.fat_absorption_g_per_h, fat_abs_target, 0.3, dt_seconds);
+        self.protein_absorption_g_per_h = Self::approach(
+            self.protein_absorption_g_per_h,
+            protein_abs_target,
+            0.3,
+            dt_seconds,
+        );
+        let absorbed_kcal = (self.carbohydrate_absorption_g_per_h * 4.0
+            + self.protein_absorption_g_per_h * 4.0
+            + self.fat_absorption_g_per_h * 9.0)
+            * dt_seconds
+            / 3600.0;
+        self.nutrient_energy_kcal = (self.nutrient_energy_kcal - absorbed_kcal).max(0.0);
+        self.electrolyte_absorption_mmol_min = Self::approach(
+            self.electrolyte_absorption_mmol_min,
+            (2.0 + 0.8 * self.motility_index + 1.2 * self.segmentation_index).clamp(1.0, 6.0),
+            0.2,
+            dt_seconds,
+        );
+        self.water_reabsorption_ml_min = Self::approach(
+            self.water_reabsorption_ml_min,
+            (10.0 + 8.0 * self.electrolyte_absorption_mmol_min / 3.0).clamp(5.0, 30.0),
+            0.2,
+            dt_seconds,
+        );
+        let water_removed = self.water_reabsorption_ml_min * dt_seconds / 60.0;
+        self.lumen_volume_ml =
+            (self.lumen_volume_ml + absorbed_kcal * 0.2 - water_removed).clamp(120.0, 800.0);
+    }
+
+    fn update_microbiome(&mut self, dt_seconds: f32) {
+        let scfa_generation =
+            (self.fiber_load_g * 0.12 * self.microbiome_balance) * dt_seconds / 60.0;
+        self.short_chain_fatty_acids_mmol =
+            (self.short_chain_fatty_acids_mmol + scfa_generation).clamp(5.0, 80.0);
+        self.fiber_load_g = (self.fiber_load_g - scfa_generation * 0.45).max(0.0);
+        let ph_target = (6.6 - 0.015 * self.short_chain_fatty_acids_mmol
+            + 0.2 * (1.0 - self.bile_acid_recirculation_fraction))
+            .clamp(5.8, 7.2);
+        self.chyme_ph = Self::approach(self.chyme_ph, ph_target, 0.1, dt_seconds);
+        let microbiome_target = (0.6 + 0.15 * (self.short_chain_fatty_acids_mmol / 30.0)
+            - 0.25 * self.inflammation_index)
+            .clamp(0.3, 0.95);
+        self.microbiome_balance =
+            Self::approach(self.microbiome_balance, microbiome_target, 0.05, dt_seconds);
+    }
+
+    fn update_mucosa(&mut self, dt_seconds: f32) {
+        let irritation = (1.0 - self.chyme_ph / 7.0).max(0.0)
+            + (self.short_chain_fatty_acids_mmol / 50.0).max(0.0) * 0.2;
+        let mucosal_target =
+            (0.95 - 0.25 * irritation + 0.1 * self.microbiome_balance).clamp(0.5, 0.99);
+        self.mucosal_integrity =
+            Self::approach(self.mucosal_integrity, mucosal_target, 0.02, dt_seconds);
+        let inflammation_target =
+            (0.1 + 0.3 * (1.0 - self.mucosal_integrity) + 0.2 * (1.0 - self.microbiome_balance))
+                .clamp(0.05, 0.9);
+        self.inflammation_index = Self::approach(
+            self.inflammation_index,
+            inflammation_target,
+            0.03,
+            dt_seconds,
+        );
+        let bile_target =
+            (0.9 + 0.15 * self.motility_index - 0.1 * self.glp1_effect()).clamp(0.6, 0.98);
+        self.bile_acid_recirculation_fraction = Self::approach(
+            self.bile_acid_recirculation_fraction,
+            bile_target,
+            0.03,
+            dt_seconds,
+        );
+    }
+
+    fn glp1_effect(&self) -> f32 {
+        (self.hormone_glp1 / 20.0).clamp(0.0, 1.2)
+    }
 }
 
 impl Organ for Intestines {
@@ -27,18 +298,28 @@ impl Organ for Intestines {
         self.info.kind()
     }
     fn update(&mut self, dt_seconds: f32) {
-        if self.peristalsis {
-            // minor oscillation around 80
-            let delta = (dt_seconds * 0.1).sin();
-            let val = (self.absorption as f32 + delta).clamp(0.0, 100.0);
-            self.absorption = val as u8;
+        if dt_seconds <= 0.0 {
+            return;
         }
+
+        self.time_in_phase_s += dt_seconds;
+
+        self.update_internal_feeding(dt_seconds);
+        self.update_enteric_tone(dt_seconds);
+        self.update_phase();
+        self.update_motility(dt_seconds);
+        self.update_absorption(dt_seconds);
+        self.update_microbiome(dt_seconds);
+        self.update_mucosa(dt_seconds);
     }
     fn summary(&self) -> String {
         format!(
-            "Intestines[id={}, absorption={}]",
+            "Intestines[id={}, phase={:?}, motility={:.2}, lumen={:.0} ml, pH={:.1}]",
             self.id(),
-            self.absorption
+            self.phase,
+            self.motility_index,
+            self.lumen_volume_ml,
+            self.chyme_ph
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/kidneys.rs

@@ -1,23 +1,233 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Renal perfusion/autoregulation status.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum RenalAutoregulationState {
+    Autoregulated,
+    Hypoperfused,
+    Hyperperfused,
+    Obstructed,
+}
+
 #[derive(Debug, Clone)]
 pub struct Kidneys {
     info: OrganInfo,
-    /// Filtration rate ml/min
+    /// Glomerular filtration rate (ml/min).
     pub gfr: f32,
-    /// Electrolyte balance index -1..=1
+    /// Electrolyte balance index -1..=1 (positive = hypernatremia tendency).
     pub electrolyte_balance: f32,
+    /// Renal plasma flow (ml/min).
+    pub renal_plasma_flow_ml_min: f32,
+    /// Filtration fraction (GFR/RPF).
+    pub filtration_fraction: f32,
+    /// Urine osmolality (mOsm/kg).
+    pub urine_osmolality_mosm: f32,
+    /// Urine flow (ml/min).
+    pub urine_flow_ml_min: f32,
+    /// Renin release proxy (ng/mL/h relative).
+    pub renin_release: f32,
+    /// Aldosterone drive (0..=1).
+    pub aldosterone_drive: f32,
+    /// Antidiuretic hormone sensitivity (0..=1).
+    pub adh_sensitivity: f32,
+    /// Acid-base compensation index (-1 acidotic .. +1 alkalotic).
+    pub acid_base_balance: f32,
+    /// Erythropoietin secretion (IU/day equivalent).
+    pub erythropoietin_iu_per_day: f32,
+    /// Sympathetic tone to the juxtaglomerular apparatus (0..=1).
+    pub sympathetic_tone: f32,
+    /// Tubular sodium reabsorption fraction (0..=1).
+    pub tubular_na_reabsorption: f32,
+    /// Potassium excretion (mmol/min).
+    pub potassium_excretion_mmol_min: f32,
+    /// Urea excretion (mg/min).
+    pub urea_excretion_mg_min: f32,
+    /// Medullary tonicity (mOsm/kg).
+    pub medullary_tonicity_mosm: f32,
+    /// Serum osmolality (mOsm/kg).
+    pub serum_osmolality_mosm: f32,
+    /// Estimated plasma volume (L).
+    pub plasma_volume_l: f32,
+    /// Current autoregulation state.
+    pub state: RenalAutoregulationState,
+    time_in_state_s: f32,
 }
 
 impl Kidneys {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Kidneys),
-            gfr: 100.0,
+            gfr: 110.0,
             electrolyte_balance: 0.0,
+            renal_plasma_flow_ml_min: 600.0,
+            filtration_fraction: 0.18,
+            urine_osmolality_mosm: 550.0,
+            urine_flow_ml_min: 1.2,
+            renin_release: 0.35,
+            aldosterone_drive: 0.45,
+            adh_sensitivity: 0.65,
+            acid_base_balance: 0.0,
+            erythropoietin_iu_per_day: 18.0,
+            sympathetic_tone: 0.35,
+            tubular_na_reabsorption: 0.99,
+            potassium_excretion_mmol_min: 0.11,
+            urea_excretion_mg_min: 550.0,
+            medullary_tonicity_mosm: 750.0,
+            serum_osmolality_mosm: 290.0,
+            plasma_volume_l: 3.1,
+            state: RenalAutoregulationState::Autoregulated,
+            time_in_state_s: 0.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_state(&mut self) {
+        let perfusion_ratio = self.renal_plasma_flow_ml_min / 600.0;
+        let obstruction = (1.0 - self.urine_flow_ml_min / 1.2).max(0.0)
+            + (self.medullary_tonicity_mosm - 1000.0).max(0.0) / 800.0;
+        self.state = if obstruction > 0.6 {
+            RenalAutoregulationState::Obstructed
+        } else if perfusion_ratio < 0.75 {
+            RenalAutoregulationState::Hypoperfused
+        } else if perfusion_ratio > 1.3 {
+            RenalAutoregulationState::Hyperperfused
+        } else {
+            RenalAutoregulationState::Autoregulated
+        };
+    }
+
+    fn update_perfusion(&mut self, dt_seconds: f32) {
+        let sympathetic_target =
+            (0.3 + 0.6 * (1.0 - self.plasma_volume_l / 3.0).max(0.0)).clamp(0.1, 0.95);
+        self.sympathetic_tone =
+            Self::approach(self.sympathetic_tone, sympathetic_target, 0.2, dt_seconds);
+        let rpf_target = (600.0 - 220.0 * self.sympathetic_tone
+            + 120.0 * (self.serum_osmolality_mosm - 285.0) / 20.0)
+            .clamp(300.0, 950.0);
+        self.renal_plasma_flow_ml_min =
+            Self::approach(self.renal_plasma_flow_ml_min, rpf_target, 3.0, dt_seconds);
+        let filtration_target = match self.state {
+            RenalAutoregulationState::Autoregulated => 0.18,
+            RenalAutoregulationState::Hypoperfused => 0.23,
+            RenalAutoregulationState::Hyperperfused => 0.16,
+            RenalAutoregulationState::Obstructed => 0.12,
+        };
+        self.filtration_fraction =
+            Self::approach(self.filtration_fraction, filtration_target, 0.1, dt_seconds)
+                .clamp(0.08, 0.3);
+        self.gfr = (self.renal_plasma_flow_ml_min * self.filtration_fraction).clamp(20.0, 180.0);
+    }
+
+    fn update_hormonal_axes(&mut self, dt_seconds: f32) {
+        let pressure_error = (105.0 - self.gfr).max(-40.0);
+        let osmo_error = (self.serum_osmolality_mosm - 285.0) / 15.0;
+        let renin_target =
+            (0.25 + 0.015 * pressure_error + 0.4 * self.sympathetic_tone).clamp(0.05, 1.6);
+        self.renin_release = Self::approach(self.renin_release, renin_target, 0.3, dt_seconds);
+        let aldosterone_target =
+            (0.4 + 0.5 * self.renin_release - 0.3 * self.electrolyte_balance).clamp(0.1, 1.0);
+        self.aldosterone_drive =
+            Self::approach(self.aldosterone_drive, aldosterone_target, 0.2, dt_seconds);
+        let adh_target =
+            (0.55 + 0.35 * osmo_error + 0.25 * (self.aldosterone_drive - 0.4)).clamp(0.1, 1.1);
+        self.adh_sensitivity = Self::approach(self.adh_sensitivity, adh_target, 0.25, dt_seconds);
+    }
+
+    fn update_tubular_handling(&mut self, dt_seconds: f32) {
+        let sodium_target = match self.state {
+            RenalAutoregulationState::Hypoperfused => 0.995,
+            RenalAutoregulationState::Autoregulated => 0.99,
+            RenalAutoregulationState::Hyperperfused => 0.985,
+            RenalAutoregulationState::Obstructed => 0.975,
+        } + 0.01 * (self.aldosterone_drive - 0.5);
+        self.tubular_na_reabsorption = Self::approach(
+            self.tubular_na_reabsorption,
+            sodium_target.clamp(0.94, 0.998),
+            0.05,
+            dt_seconds,
+        );
+        let filtered_nacl = self.gfr * 140.0 / 1000.0; // mmol/min approximated
+        let na_excreted = filtered_nacl * (1.0 - self.tubular_na_reabsorption);
+        self.electrolyte_balance = (0.5 - na_excreted / 8.0).clamp(-1.2, 1.2);
+        self.potassium_excretion_mmol_min = Self::approach(
+            self.potassium_excretion_mmol_min,
+            (0.08 + 0.12 * self.aldosterone_drive + 0.04 * self.electrolyte_balance)
+                .clamp(0.02, 0.3),
+            0.1,
+            dt_seconds,
+        );
+        let osmotic_load = 2.1 * na_excreted + self.potassium_excretion_mmol_min * 1.5;
+        let adh_effect = (1.3 - self.adh_sensitivity).clamp(0.2, 1.3);
+        self.urine_flow_ml_min = Self::approach(
+            self.urine_flow_ml_min,
+            (osmotic_load / 4.0 * adh_effect).clamp(0.2, 10.0),
+            0.4,
+            dt_seconds,
+        );
+        self.urine_osmolality_mosm = Self::approach(
+            self.urine_osmolality_mosm,
+            (550.0 + 220.0 * (self.adh_sensitivity - 0.5)
+                - 120.0 * (self.urine_flow_ml_min - 1.0) / 4.0)
+                .clamp(120.0, 1200.0),
+            0.6,
+            dt_seconds,
+        );
+        self.medullary_tonicity_mosm = Self::approach(
+            self.medullary_tonicity_mosm,
+            (750.0 + 200.0 * (self.adh_sensitivity - 0.6)).clamp(400.0, 1200.0),
+            0.1,
+            dt_seconds,
+        );
+    }
+
+    fn update_acid_base(&mut self, dt_seconds: f32) {
+        let acid_target = (0.1 * (self.potassium_excretion_mmol_min - 0.12)
+            + 0.3 * (self.urine_osmolality_mosm - 600.0) / 400.0)
+            .clamp(-1.0, 1.0);
+        self.acid_base_balance =
+            Self::approach(self.acid_base_balance, -acid_target, 0.1, dt_seconds);
+        let urea_target = (500.0 + 1.5 * (self.gfr - 110.0)).clamp(200.0, 900.0);
+        self.urea_excretion_mg_min =
+            Self::approach(self.urea_excretion_mg_min, urea_target, 0.3, dt_seconds);
+        self.serum_osmolality_mosm = Self::approach(
+            self.serum_osmolality_mosm,
+            (285.0 + 5.0 * self.acid_base_balance - 4.0 * self.urine_flow_ml_min / 5.0)
+                .clamp(270.0, 310.0),
+            0.05,
+            dt_seconds,
+        );
+        let plasma_target = (3.1 + 0.2 * (self.urine_flow_ml_min - 1.2)
+            - 0.25 * self.acid_base_balance)
+            .clamp(2.2, 3.8);
+        self.plasma_volume_l =
+            Self::approach(self.plasma_volume_l, plasma_target, 0.04, dt_seconds);
+    }
+
+    fn update_erythropoietin(&mut self, dt_seconds: f32) {
+        let epo_target = (18.0 + 40.0 * (0.95 - self.median_oxygenation())).clamp(8.0, 45.0);
+        self.erythropoietin_iu_per_day =
+            Self::approach(self.erythropoietin_iu_per_day, epo_target, 0.05, dt_seconds);
+    }
+
+    fn median_oxygenation(&self) -> f32 {
+        (self.renal_plasma_flow_ml_min / 600.0).clamp(0.5, 1.3)
+    }
 }
 
 impl Organ for Kidneys {
@@ -27,12 +237,29 @@ impl Organ for Kidneys {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        self.gfr = self.gfr.clamp(0.0, 200.0);
-        self.electrolyte_balance = self.electrolyte_balance.clamp(-1.0, 1.0);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_in_state_s += dt_seconds;
+        self.update_state();
+        self.update_perfusion(dt_seconds);
+        self.update_state();
+        self.update_hormonal_axes(dt_seconds);
+        self.update_tubular_handling(dt_seconds);
+        self.update_acid_base(dt_seconds);
+        self.update_erythropoietin(dt_seconds);
     }
     fn summary(&self) -> String {
-        format!("Kidneys[id={}, GFR={:.0} ml/min]", self.id(), self.gfr)
+        format!(
+            "Kidneys[id={}, state={:?}, GFR={:.0} ml/min, urine={:.1} ml/min @ {:.0} mOsm]",
+            self.id(),
+            self.state,
+            self.gfr,
+            self.urine_flow_ml_min,
+            self.urine_osmolality_mosm
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/organs/liver.rs

@@ -1,15 +1,68 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// High-level metabolic mode of the liver.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum HepaticState {
+    Postabsorptive,
+    FedAnabolic,
+    FastingCatabolic,
+    AcutePhaseResponse,
+    Regenerating,
+}
+
 #[derive(Debug, Clone)]
 pub struct Liver {
     info: OrganInfo,
-    /// Detox capacity 0..=100
+    /// Detox capacity 0..=100.
     pub detox: u8,
-    /// Metabolism index
+    /// Composite metabolic activity index.
     pub metabolism: f32,
-    /// Enzyme production index
+    /// Microsomal enzyme (CYP) activity index.
     pub enzymes: f32,
+    /// Hepatic glycogen store (g).
+    pub glycogen_store_g: f32,
+    /// Gluconeogenesis rate (mg/kg/min proxy for 70kg adult).
+    pub gluconeogenesis_rate: f32,
+    /// Glycogenolysis rate (g/hour).
+    pub glycogenolysis_rate_g_per_h: f32,
+    /// De novo lipogenesis rate (g/hour).
+    pub lipogenesis_rate_g_per_h: f32,
+    /// Beta-oxidation rate (g/hour).
+    pub beta_oxidation_rate_g_per_h: f32,
+    /// Ammonia clearance (µmol/min).
+    pub ammonia_clearance_umol_min: f32,
+    /// Plasma albumin concentration (g/dL).
+    pub albumin_g_dl: f32,
+    /// Clotting factor synthesis (% of normal).
+    pub clotting_factor_synthesis_pct: f32,
+    /// Bile acid synthesis (mg/min).
+    pub bile_acid_synthesis_mg_min: f32,
+    /// Bile secretion (ml/min).
+    pub bile_secretion_ml_min: f32,
+    /// Kupffer cell activation (0..=1).
+    pub kupffer_activation: f32,
+    /// Acute phase response magnitude (0..=1).
+    pub acute_phase_response: f32,
+    /// Hepatic blood flow (L/min).
+    pub hepatic_blood_flow_l_min: f32,
+    /// Portal venous pressure (mmHg).
+    pub portal_pressure_mm_hg: f32,
+    /// Hepatic fat fraction (%).
+    pub hepatic_fat_fraction_pct: f32,
+    /// Insulin signaling intensity (0..=1).
+    pub insulin_signal: f32,
+    /// Glucagon signaling intensity (0..=1).
+    pub glucagon_signal: f32,
+    /// Cortisol signaling (0..=1).
+    pub cortisol_signal: f32,
+    /// Oxidative stress metric (0..=1).
+    pub oxidative_stress_index: f32,
+    /// Current metabolic state.
+    pub state: HepaticState,
+    time_in_state_s: f32,
+    feeding_clock_s: f32,
+    target_meal_interval_s: f32,
 }
 
 impl Liver {
@@ -19,8 +72,269 @@ impl Liver {
             detox: 100,
             metabolism: 1.0,
             enzymes: 1.0,
+            glycogen_store_g: 85.0,
+            gluconeogenesis_rate: 1.8,
+            glycogenolysis_rate_g_per_h: 6.0,
+            lipogenesis_rate_g_per_h: 2.5,
+            beta_oxidation_rate_g_per_h: 4.5,
+            ammonia_clearance_umol_min: 750.0,
+            albumin_g_dl: 4.1,
+            clotting_factor_synthesis_pct: 100.0,
+            bile_acid_synthesis_mg_min: 9.0,
+            bile_secretion_ml_min: 0.75,
+            kupffer_activation: 0.25,
+            acute_phase_response: 0.1,
+            hepatic_blood_flow_l_min: 1.35,
+            portal_pressure_mm_hg: 7.0,
+            hepatic_fat_fraction_pct: 8.0,
+            insulin_signal: 0.35,
+            glucagon_signal: 0.45,
+            cortisol_signal: 0.25,
+            oxidative_stress_index: 0.18,
+            state: HepaticState::Postabsorptive,
+            time_in_state_s: 0.0,
+            feeding_clock_s: 0.0,
+            target_meal_interval_s: 4.5 * 3600.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn simulate_hormone_inputs(&mut self, dt_seconds: f32) {
+        self.feeding_clock_s += dt_seconds;
+        if self.feeding_clock_s >= self.target_meal_interval_s {
+            self.insulin_signal = 0.95;
+            self.glucagon_signal = 0.2;
+            self.feeding_clock_s = 0.0;
+            self.target_meal_interval_s =
+                (4.0 + 1.5 * (self.hepatic_fat_fraction_pct / 20.0)) * 3600.0;
+            self.time_in_state_s = 0.0;
+            self.state = HepaticState::FedAnabolic;
+        } else {
+            self.insulin_signal = Self::approach(self.insulin_signal, 0.3, 0.1, dt_seconds);
+            self.glucagon_signal = Self::approach(self.glucagon_signal, 0.55, 0.08, dt_seconds);
+        }
+        self.cortisol_signal = Self::approach(
+            self.cortisol_signal,
+            (0.25
+                + 0.3 * (self.glucagon_signal - 0.5).max(0.0)
+                + 0.2 * self.oxidative_stress_index)
+                .clamp(0.1, 0.9),
+            0.05,
+            dt_seconds,
+        );
+    }
+
+    fn transition_state(&mut self, new_state: HepaticState) {
+        if self.state != new_state {
+            self.state = new_state;
+            self.time_in_state_s = 0.0;
+        }
+    }
+
+    fn update_state(&mut self) {
+        match self.state {
+            HepaticState::Postabsorptive => {
+                if self.oxidative_stress_index > 0.6 && self.glycogen_store_g < 40.0 {
+                    self.transition_state(HepaticState::Regenerating);
+                } else if self.insulin_signal > 0.6 {
+                    self.transition_state(HepaticState::FedAnabolic);
+                } else if self.glucagon_signal > 0.7 {
+                    self.transition_state(HepaticState::FastingCatabolic);
+                } else if self.acute_phase_response > 0.4 {
+                    self.transition_state(HepaticState::AcutePhaseResponse);
+                }
+            }
+            HepaticState::FedAnabolic => {
+                if self.time_in_state_s > 2.0 * 3600.0 && self.glycogen_store_g > 70.0 {
+                    self.transition_state(HepaticState::Postabsorptive);
+                }
+            }
+            HepaticState::FastingCatabolic => {
+                if self.oxidative_stress_index > 0.7 && self.glycogen_store_g < 30.0 {
+                    self.transition_state(HepaticState::Regenerating);
+                } else if self.insulin_signal > 0.55 {
+                    self.transition_state(HepaticState::FedAnabolic);
+                } else if self.time_in_state_s > 12.0 * 3600.0 {
+                    self.transition_state(HepaticState::Postabsorptive);
+                }
+            }
+            HepaticState::AcutePhaseResponse => {
+                if self.acute_phase_response < 0.2 {
+                    self.transition_state(HepaticState::Postabsorptive);
+                } else if self.oxidative_stress_index > 0.65 {
+                    self.transition_state(HepaticState::Regenerating);
+                }
+            }
+            HepaticState::Regenerating => {
+                if self.oxidative_stress_index < 0.3 && self.glycogen_store_g > 60.0 {
+                    self.transition_state(HepaticState::Postabsorptive);
+                }
+            }
+        }
+    }
+    fn update_metabolic_fluxes(&mut self, dt_seconds: f32) {
+        let (
+            gluconeogenesis_target,
+            glycogenolysis_target,
+            lipogenesis_target,
+            beta_oxidation_target,
+        ) = match self.state {
+            HepaticState::FedAnabolic => (0.8, 2.0, 6.0, 2.0),
+            HepaticState::Postabsorptive => (1.8, 6.0, 2.5, 4.5),
+            HepaticState::FastingCatabolic => (2.6, 9.0, 1.2, 6.5),
+            HepaticState::AcutePhaseResponse => (2.1, 5.0, 1.8, 4.0),
+            HepaticState::Regenerating => (1.5, 4.0, 3.5, 3.5),
+        };
+        self.gluconeogenesis_rate = Self::approach(
+            self.gluconeogenesis_rate,
+            (gluconeogenesis_target + 0.6 * (self.cortisol_signal - 0.3)).clamp(0.4, 3.5),
+            0.05,
+            dt_seconds,
+        );
+        self.glycogenolysis_rate_g_per_h = Self::approach(
+            self.glycogenolysis_rate_g_per_h,
+            (glycogenolysis_target + 4.0 * (self.glucagon_signal - self.insulin_signal))
+                .clamp(0.0, 14.0),
+            0.1,
+            dt_seconds,
+        );
+        self.lipogenesis_rate_g_per_h = Self::approach(
+            self.lipogenesis_rate_g_per_h,
+            (lipogenesis_target + 5.0 * (self.insulin_signal - 0.4).max(0.0)).clamp(0.5, 12.0),
+            0.06,
+            dt_seconds,
+        );
+        self.beta_oxidation_rate_g_per_h = Self::approach(
+            self.beta_oxidation_rate_g_per_h,
+            (beta_oxidation_target + 3.5 * (self.glucagon_signal - 0.5).max(0.0)).clamp(1.0, 10.0),
+            0.08,
+            dt_seconds,
+        );
+        let glycogen_change = (self.lipogenesis_rate_g_per_h * 0.2
+            - self.glycogenolysis_rate_g_per_h
+            - self.gluconeogenesis_rate * 0.6)
+            * dt_seconds
+            / 3600.0;
+        self.glycogen_store_g = (self.glycogen_store_g + glycogen_change).clamp(10.0, 140.0);
+        self.oxidative_stress_index = Self::approach(
+            self.oxidative_stress_index,
+            (0.15
+                + 0.25 * (self.beta_oxidation_rate_g_per_h - 3.0) / 7.0
+                + 0.2 * self.kupffer_activation)
+                .clamp(0.05, 0.9),
+            0.02,
+            dt_seconds,
+        );
+        self.metabolism = (self.gluconeogenesis_rate / 1.8
+            + self.lipogenesis_rate_g_per_h / 3.0
+            + self.beta_oxidation_rate_g_per_h / 4.5)
+            / 3.0;
+    }
+
+    fn update_bile_and_detox(&mut self, dt_seconds: f32) {
+        let bile_target = (0.75
+            + 0.3 * (self.lipogenesis_rate_g_per_h / 6.0)
+            + 0.2 * (self.kupffer_activation - 0.3))
+            .clamp(0.3, 1.5);
+        self.bile_secretion_ml_min =
+            Self::approach(self.bile_secretion_ml_min, bile_target, 0.04, dt_seconds);
+        self.bile_acid_synthesis_mg_min = Self::approach(
+            self.bile_acid_synthesis_mg_min,
+            (9.0 + 4.0 * (self.glucagon_signal - 0.4)).clamp(3.0, 20.0),
+            0.05,
+            dt_seconds,
+        );
+        let detox_target = (100.0 - 15.0 * self.oxidative_stress_index
+            + 10.0 * (self.insulin_signal - 0.4))
+            .clamp(40.0, 110.0);
+        self.detox = detox_target.round() as u8;
+        self.enzymes = Self::approach(
+            self.enzymes,
+            (1.0 + 0.4 * (self.cortisol_signal - 0.3) + 0.5 * (self.oxidative_stress_index - 0.2))
+                .clamp(0.4, 1.8),
+            0.03,
+            dt_seconds,
+        );
+        self.ammonia_clearance_umol_min = Self::approach(
+            self.ammonia_clearance_umol_min,
+            (750.0 + 120.0 * (self.metabolism - 1.0) - 200.0 * self.oxidative_stress_index)
+                .clamp(200.0, 900.0),
+            0.2,
+            dt_seconds,
+        );
+    }
+
+    fn update_hemodynamics(&mut self, dt_seconds: f32) {
+        let flow_target = (1.35
+            + 0.3 * (self.portal_pressure_mm_hg - 7.0) / 4.0
+            + 0.25 * (self.metabolism - 1.0))
+            .clamp(0.8, 2.0);
+        self.hepatic_blood_flow_l_min =
+            Self::approach(self.hepatic_blood_flow_l_min, flow_target, 0.05, dt_seconds);
+        self.portal_pressure_mm_hg = Self::approach(
+            self.portal_pressure_mm_hg,
+            (7.0 + 1.5 * (self.hepatic_fat_fraction_pct / 10.0 - 0.8)
+                + 0.8 * (self.kupffer_activation - 0.3))
+                .clamp(4.0, 16.0),
+            0.05,
+            dt_seconds,
+        );
+        self.kupffer_activation = Self::approach(
+            self.kupffer_activation,
+            (0.25 + 0.4 * self.acute_phase_response + 0.2 * self.portal_pressure_mm_hg / 15.0)
+                .clamp(0.1, 0.95),
+            0.04,
+            dt_seconds,
+        );
+        self.acute_phase_response = Self::approach(
+            self.acute_phase_response,
+            (0.1 + 0.6 * (self.oxidative_stress_index - 0.2).max(0.0)).clamp(0.05, 0.9),
+            0.03,
+            dt_seconds,
+        );
+    }
+
+    fn update_proteins(&mut self, dt_seconds: f32) {
+        self.albumin_g_dl = Self::approach(
+            self.albumin_g_dl,
+            (4.2 - 0.4 * self.acute_phase_response + 0.2 * (self.insulin_signal - 0.4))
+                .clamp(2.5, 4.8),
+            0.01,
+            dt_seconds,
+        );
+        self.clotting_factor_synthesis_pct = Self::approach(
+            self.clotting_factor_synthesis_pct,
+            (100.0
+                - 20.0 * self.oxidative_stress_index
+                - 15.0 * (0.5 - self.albumin_g_dl / 4.0).max(0.0))
+            .clamp(40.0, 120.0),
+            0.05,
+            dt_seconds,
+        );
+    }
+
+    fn update_fat_fraction(&mut self, dt_seconds: f32) {
+        let fat_delta = (self.lipogenesis_rate_g_per_h - self.beta_oxidation_rate_g_per_h)
+            * dt_seconds
+            / (24.0 * 3600.0);
+        self.hepatic_fat_fraction_pct =
+            (self.hepatic_fat_fraction_pct + fat_delta * 100.0).clamp(2.0, 25.0);
+    }
 }
 
 impl Organ for Liver {
@@ -30,16 +344,29 @@ impl Organ for Liver {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        self.enzymes = self.enzymes.clamp(0.0, 2.0);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_in_state_s += dt_seconds;
+
+        self.simulate_hormone_inputs(dt_seconds);
+        self.update_state();
+        self.update_metabolic_fluxes(dt_seconds);
+        self.update_bile_and_detox(dt_seconds);
+        self.update_hemodynamics(dt_seconds);
+        self.update_proteins(dt_seconds);
+        self.update_fat_fraction(dt_seconds);
     }
     fn summary(&self) -> String {
         format!(
-            "Liver[id={}, detox={}, k={:.2}, enz={:.2}]",
+            "Liver[id={}, state={:?}, glycogen={:.0} g, albumin={:.1} g/dL, bile={:.2} ml/min]",
             self.id(),
-            self.detox,
-            self.metabolism,
-            self.enzymes
+            self.state,
+            self.glycogen_store_g,
+            self.albumin_g_dl,
+            self.bile_secretion_ml_min
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/lungs.rs

@@ -1,7 +1,17 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
-/// Pulmonary model tracking respiratory rate and oxygen saturation.
+/// Ventilatory operating mode reflecting dominant chemoreceptor drive.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum VentilatoryState {
+    Resting,
+    HypercapnicResponse,
+    HypoxicResponse,
+    ExerciseAugmented,
+    MechanicalDistress,
+}
+
+/// Pulmonary model tracking ventilation mechanics and gas exchange.
 #[derive(Debug, Clone)]
 pub struct Lungs {
     info: OrganInfo,
@@ -9,8 +19,45 @@ pub struct Lungs {
     pub respiratory_rate_bpm: f32,
     /// Peripheral oxygen saturation percent.
     pub spo2_pct: f32,
-    /// Respiratory distress flag reduces SpO2.
+    /// Flag indicating external distress/vq mismatch triggers.
     pub distress: bool,
+    /// Tidal volume (ml).
+    pub tidal_volume_ml: f32,
+    /// Minute ventilation (L/min).
+    pub minute_ventilation_l_min: f32,
+    /// Dead-space fraction of each breath (0..=0.5).
+    pub dead_space_fraction: f32,
+    /// Alveolar oxygen partial pressure (mmHg).
+    pub alveolar_po2_mm_hg: f32,
+    /// Alveolar carbon dioxide partial pressure (mmHg).
+    pub alveolar_pco2_mm_hg: f32,
+    /// End tidal CO2 (mmHg).
+    pub end_tidal_co2_mm_hg: f32,
+    /// Lung compliance (ml/cmH2O).
+    pub compliance_ml_cm_h2o: f32,
+    /// Airway resistance (cmH2O·s/L).
+    pub airway_resistance_cm_h2o_l_s: f32,
+    /// Respiratory muscle drive (0..=1).
+    pub muscle_drive: f32,
+    /// Chemoreceptor drive (0..=1).
+    pub chemoreceptor_drive: f32,
+    /// Ventilation/perfusion ratio.
+    pub ventilation_perfusion_ratio: f32,
+    /// Shunt fraction (0..=0.4).
+    pub shunt_fraction: f32,
+    /// Pulmonary artery pressure (mmHg).
+    pub pulmonary_artery_pressure_mm_hg: f32,
+    /// Pulmonary capillary wedge pressure (mmHg).
+    pub pcwp_mm_hg: f32,
+    /// Oxygen delivery (ml O2/min).
+    pub oxygen_delivery_ml_min: f32,
+    /// CO2 elimination (ml/min).
+    pub co2_elimination_ml_min: f32,
+    /// Functional state.
+    pub state: VentilatoryState,
+    time_in_state_s: f32,
+    metabolic_o2_consumption_ml_min: f32,
+    metabolic_co2_production_ml_min: f32,
 }
 
 impl Lungs {
@@ -21,8 +68,233 @@ impl Lungs {
             respiratory_rate_bpm: 14.0,
             spo2_pct: 98.0,
             distress: false,
+            tidal_volume_ml: 500.0,
+            minute_ventilation_l_min: 6.5,
+            dead_space_fraction: 0.28,
+            alveolar_po2_mm_hg: 100.0,
+            alveolar_pco2_mm_hg: 38.0,
+            end_tidal_co2_mm_hg: 36.0,
+            compliance_ml_cm_h2o: 110.0,
+            airway_resistance_cm_h2o_l_s: 2.0,
+            muscle_drive: 0.45,
+            chemoreceptor_drive: 0.4,
+            ventilation_perfusion_ratio: 0.96,
+            shunt_fraction: 0.03,
+            pulmonary_artery_pressure_mm_hg: 18.0,
+            pcwp_mm_hg: 9.0,
+            oxygen_delivery_ml_min: 960.0,
+            co2_elimination_ml_min: 180.0,
+            state: VentilatoryState::Resting,
+            time_in_state_s: 0.0,
+            metabolic_o2_consumption_ml_min: 250.0,
+            metabolic_co2_production_ml_min: 200.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_metabolic_demand(&mut self, dt_seconds: f32) {
+        let exercise_factor =
+            matches!(self.state, VentilatoryState::ExerciseAugmented) as u8 as f32;
+        let distress_factor = if self.distress { 0.2 } else { 0.0 };
+        let o2_target = 250.0 * (1.0 + 0.8 * exercise_factor + distress_factor);
+        let co2_target = 200.0 * (1.0 + 0.9 * exercise_factor + distress_factor);
+        self.metabolic_o2_consumption_ml_min = Self::approach(
+            self.metabolic_o2_consumption_ml_min,
+            o2_target,
+            0.4,
+            dt_seconds,
+        );
+        self.metabolic_co2_production_ml_min = Self::approach(
+            self.metabolic_co2_production_ml_min,
+            co2_target,
+            0.4,
+            dt_seconds,
+        );
+    }
+
+    fn update_state(&mut self) {
+        self.state = if self.distress {
+            VentilatoryState::MechanicalDistress
+        } else if self.alveolar_pco2_mm_hg > 45.0 {
+            VentilatoryState::HypercapnicResponse
+        } else if self.alveolar_po2_mm_hg < 70.0 {
+            VentilatoryState::HypoxicResponse
+        } else if self.metabolic_o2_consumption_ml_min > 300.0 {
+            VentilatoryState::ExerciseAugmented
+        } else {
+            VentilatoryState::Resting
+        };
+    }
+
+    fn chemoreceptor_targets(&self) -> (f32, f32) {
+        match self.state {
+            VentilatoryState::Resting => (0.45, 0.48),
+            VentilatoryState::HypercapnicResponse => (0.8, 0.75),
+            VentilatoryState::HypoxicResponse => (0.85, 0.82),
+            VentilatoryState::ExerciseAugmented => (0.9, 0.7),
+            VentilatoryState::MechanicalDistress => (0.95, 0.65),
+        }
+    }
+
+    fn update_drives(&mut self, dt_seconds: f32) {
+        let (chemo_target, muscle_target) = self.chemoreceptor_targets();
+        let hypoxia_error = (90.0 - self.alveolar_po2_mm_hg).max(0.0) / 40.0;
+        let hypercapnia_error = (self.alveolar_pco2_mm_hg - 40.0).max(0.0) / 20.0;
+        let drive_boost = (hypoxia_error + hypercapnia_error).clamp(0.0, 1.0);
+        self.chemoreceptor_drive = Self::approach(
+            self.chemoreceptor_drive,
+            (chemo_target + 0.6 * drive_boost).clamp(0.2, 1.0),
+            0.8,
+            dt_seconds,
+        );
+        self.muscle_drive = Self::approach(
+            self.muscle_drive,
+            (muscle_target + 0.5 * drive_boost).clamp(0.2, 1.0),
+            0.6,
+            dt_seconds,
+        );
+    }
+
+    fn update_mechanics(&mut self, dt_seconds: f32) {
+        let rate_target = (12.0
+            + 18.0 * self.muscle_drive
+            + 6.0 * (self.chemoreceptor_drive - 0.5).max(0.0)
+            + 8.0 * matches!(self.state, VentilatoryState::MechanicalDistress) as i32 as f32)
+            .clamp(8.0, 40.0);
+        self.respiratory_rate_bpm =
+            Self::approach(self.respiratory_rate_bpm, rate_target, 1.5, dt_seconds);
+        let compliance_target = if self.distress {
+            65.0
+        } else {
+            110.0 - 20.0 * (self.muscle_drive - 0.5).max(0.0)
+        }
+        .clamp(40.0, 140.0);
+        self.compliance_ml_cm_h2o = Self::approach(
+            self.compliance_ml_cm_h2o,
+            compliance_target,
+            0.2,
+            dt_seconds,
+        );
+        let resistance_target = if self.distress {
+            4.5
+        } else {
+            2.0 + 1.5 * (0.4 - self.compliance_ml_cm_h2o / 150.0).max(0.0)
+        }
+        .clamp(1.2, 6.0);
+        self.airway_resistance_cm_h2o_l_s = Self::approach(
+            self.airway_resistance_cm_h2o_l_s,
+            resistance_target,
+            0.3,
+            dt_seconds,
+        );
+        let tidal_target = (450.0 + 160.0 * (self.muscle_drive - 0.4)
+            - 50.0 * self.airway_resistance_cm_h2o_l_s)
+            .clamp(250.0, 900.0);
+        self.tidal_volume_ml = Self::approach(self.tidal_volume_ml, tidal_target, 30.0, dt_seconds);
+        self.dead_space_fraction = Self::approach(
+            self.dead_space_fraction,
+            (0.28
+                + 0.15 * (self.airway_resistance_cm_h2o_l_s - 2.0).max(0.0)
+                + 0.1 * self.shunt_fraction)
+                .clamp(0.15, 0.5),
+            0.2,
+            dt_seconds,
+        );
+        let alveolar_ventilation = (self.tidal_volume_ml * (1.0 - self.dead_space_fraction)
+            / 1000.0)
+            * self.respiratory_rate_bpm;
+        self.minute_ventilation_l_min =
+            (self.tidal_volume_ml / 1000.0 * self.respiratory_rate_bpm).clamp(3.0, 25.0);
+        self.ventilation_perfusion_ratio = Self::approach(
+            self.ventilation_perfusion_ratio,
+            (alveolar_ventilation / 5.0).clamp(0.4, 1.4),
+            0.3,
+            dt_seconds,
+        );
+    }
+
+    fn update_gas_exchange(&mut self, dt_seconds: f32) {
+        let effective_ventilation =
+            self.minute_ventilation_l_min * (1.0 - self.dead_space_fraction);
+        let po2_target = (100.0 + 12.0 * (effective_ventilation - 5.5)
+            - 30.0 * self.shunt_fraction
+            - 15.0 * (1.0 - self.ventilation_perfusion_ratio))
+            .clamp(40.0, 120.0);
+        let pco2_target = (40.0 - 5.0 * (effective_ventilation - 6.0) + 10.0 * self.shunt_fraction)
+            .clamp(25.0, 60.0);
+        self.alveolar_po2_mm_hg =
+            Self::approach(self.alveolar_po2_mm_hg, po2_target, 0.5, dt_seconds);
+        self.alveolar_pco2_mm_hg =
+            Self::approach(self.alveolar_pco2_mm_hg, pco2_target, 0.5, dt_seconds);
+        self.end_tidal_co2_mm_hg = Self::approach(
+            self.end_tidal_co2_mm_hg,
+            self.alveolar_pco2_mm_hg,
+            1.2,
+            dt_seconds,
+        );
+        let spo2_target = (97.0 + 8.0 * (self.alveolar_po2_mm_hg - 90.0) / 40.0
+            - 12.0 * self.shunt_fraction
+            - 5.0 * (self.metabolic_o2_consumption_ml_min - 250.0) / 200.0)
+            .clamp(70.0, 100.0);
+        self.spo2_pct = Self::approach(self.spo2_pct, spo2_target, 0.6, dt_seconds);
+        self.shunt_fraction = Self::approach(
+            self.shunt_fraction,
+            (0.03
+                + 0.2 * (1.0 - self.ventilation_perfusion_ratio).max(0.0)
+                + if self.distress { 0.12 } else { 0.0 })
+            .clamp(0.0, 0.35),
+            0.4,
+            dt_seconds,
+        );
+        self.oxygen_delivery_ml_min = Self::approach(
+            self.oxygen_delivery_ml_min,
+            self.spo2_pct * 10.0,
+            2.0,
+            dt_seconds,
+        );
+        self.co2_elimination_ml_min = Self::approach(
+            self.co2_elimination_ml_min,
+            (self.metabolic_co2_production_ml_min
+                * (self.minute_ventilation_l_min / 6.0).clamp(0.5, 2.0))
+            .clamp(80.0, 600.0),
+            1.5,
+            dt_seconds,
+        );
+    }
+
+    fn update_pressures(&mut self, dt_seconds: f32) {
+        let pap_target = (18.0
+            + 8.0 * (self.shunt_fraction - 0.05).max(0.0)
+            + 4.0 * (self.minute_ventilation_l_min - 6.0) / 6.0)
+            .clamp(12.0, 35.0);
+        self.pulmonary_artery_pressure_mm_hg = Self::approach(
+            self.pulmonary_artery_pressure_mm_hg,
+            pap_target,
+            0.2,
+            dt_seconds,
+        );
+        self.pcwp_mm_hg = Self::approach(
+            self.pcwp_mm_hg,
+            (8.0 + 0.5 * (self.pulmonary_artery_pressure_mm_hg - 18.0)).clamp(5.0, 18.0),
+            0.2,
+            dt_seconds,
+        );
+    }
 }
 
 impl Organ for Lungs {
@@ -33,22 +305,26 @@ impl Organ for Lungs {
         self.info.kind()
     }
     fn update(&mut self, dt_seconds: f32) {
-        let dt = dt_seconds.clamp(0.0, 10.0);
-        let target_rr = 14.0;
-        self.respiratory_rate_bpm += 0.1 * (target_rr - self.respiratory_rate_bpm) * (dt / 1.0);
-        // distress drifts SpO2 downward
-        if self.distress {
-            self.spo2_pct -= 0.5 * (dt / 1.0);
+        if dt_seconds <= 0.0 {
+            return;
         }
-        // keep spo2 in [70, 100]
-        self.spo2_pct = self.spo2_pct.clamp(70.0, 100.0);
+        self.time_in_state_s += dt_seconds;
+        self.update_metabolic_demand(dt_seconds);
+        self.update_state();
+        self.update_drives(dt_seconds);
+        self.update_mechanics(dt_seconds);
+        self.update_gas_exchange(dt_seconds);
+        self.update_pressures(dt_seconds);
     }
     fn summary(&self) -> String {
         format!(
-            "Lungs[id={}, RR={:.1} bpm, SpO2={:.0}%]",
+            "Lungs[id={}, state={:?}, RR={:.0}, VT={:.0} ml, SpO2={:.0}%, PaO2~{:.0}]",
             self.id(),
+            self.state,
             self.respiratory_rate_bpm,
-            self.spo2_pct
+            self.tidal_volume_ml,
+            self.spo2_pct,
+            self.alveolar_po2_mm_hg
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/mod.rs

@@ -55,9 +55,9 @@ mod spinal_cord;
 mod spleen;
 mod stomach;
 
-pub use bladder::Bladder;
-pub use brain::Brain;
-pub use esophagus::Esophagus;
+pub use bladder::{Bladder, BladderPhase};
+pub use brain::{Brain, SleepStage};
+pub use esophagus::{EsophagealStage, Esophagus};
 pub use gallbladder::Gallbladder;
 pub use heart::Heart;
 pub use intestines::Intestines;

src/organs/pancreas.rs

@@ -1,20 +1,206 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Dominant endocrine/exocrine activity mode of the pancreas.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum PancreaticState {
+    Basal,
+    PostprandialAnabolic,
+    HypoglycemicCounterregulation,
+    BetaCellExhaustion,
+}
+
 #[derive(Debug, Clone)]
 pub struct Pancreas {
     info: OrganInfo,
-    /// Insulin secretion index
+    /// Insulin secretion index (µU/mL proxy).
     pub insulin: f32,
+    /// Glucagon secretion index (pg/mL proxy).
+    pub glucagon: f32,
+    /// Somatostatin output (pg/mL proxy).
+    pub somatostatin: f32,
+    /// Pancreatic polypeptide level.
+    pub pancreatic_polypeptide: f32,
+    /// Enzyme output (kIU/min).
+    pub digestive_enzyme_output: f32,
+    /// Bicarbonate secretion (mmol/min).
+    pub bicarbonate_output_mmol_min: f32,
+    /// Estimated beta-cell functional mass fraction (0..=1).
+    pub beta_cell_mass_fraction: f32,
+    /// Islet stress index (0..=1).
+    pub islet_stress_index: f32,
+    /// Acinar secretion flow (ml/min).
+    pub acinar_flow_ml_min: f32,
+    /// Ductal pressure (cmH2O).
+    pub duct_pressure_cm_h2o: f32,
+    /// Blood glucose sensed by islets (mg/dL).
+    pub blood_glucose_mg_dl: f32,
+    /// Incretin stimulus (0..=1).
+    pub incretin_signal: f32,
+    /// Autonomic tone (-1 vagal, +1 sympathetic).
+    pub autonomic_tone: f32,
+    /// Current pancreas state.
+    pub state: PancreaticState,
+    time_in_state_s: f32,
+    feeding_clock_s: f32,
+    target_meal_interval_s: f32,
 }
 
 impl Pancreas {
     pub fn new(id: impl Into<String>) -> Self {
         Self {
             info: OrganInfo::new(id, OrganType::Pancreas),
-            insulin: 1.0,
+            insulin: 12.0,
+            glucagon: 60.0,
+            somatostatin: 20.0,
+            pancreatic_polypeptide: 120.0,
+            digestive_enzyme_output: 18.0,
+            bicarbonate_output_mmol_min: 1.8,
+            beta_cell_mass_fraction: 0.92,
+            islet_stress_index: 0.25,
+            acinar_flow_ml_min: 0.7,
+            duct_pressure_cm_h2o: 6.0,
+            blood_glucose_mg_dl: 95.0,
+            incretin_signal: 0.2,
+            autonomic_tone: 0.0,
+            state: PancreaticState::Basal,
+            time_in_state_s: 0.0,
+            feeding_clock_s: 0.0,
+            target_meal_interval_s: 4.2 * 3600.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn simulate_meals(&mut self, dt_seconds: f32) {
+        self.feeding_clock_s += dt_seconds;
+        if self.feeding_clock_s >= self.target_meal_interval_s {
+            self.blood_glucose_mg_dl = 155.0;
+            self.incretin_signal = 0.85;
+            self.autonomic_tone = -0.4; // vagal dominance
+            self.feeding_clock_s = 0.0;
+            self.state = PancreaticState::PostprandialAnabolic;
+            self.time_in_state_s = 0.0;
+            self.target_meal_interval_s = (3.5 + 1.2 * self.islet_stress_index) * 3600.0;
+        } else {
+            self.incretin_signal = Self::approach(self.incretin_signal, 0.15, 0.06, dt_seconds);
+            self.autonomic_tone = Self::approach(self.autonomic_tone, 0.1, 0.08, dt_seconds);
+        }
+        self.blood_glucose_mg_dl = Self::approach(
+            self.blood_glucose_mg_dl,
+            90.0 + 12.0 * (-self.autonomic_tone).max(0.0),
+            0.1,
+            dt_seconds,
+        );
+    }
+
+    fn update_state(&mut self) {
+        self.state = if self.beta_cell_mass_fraction < 0.6 || self.islet_stress_index > 0.75 {
+            PancreaticState::BetaCellExhaustion
+        } else if self.blood_glucose_mg_dl < 70.0 {
+            PancreaticState::HypoglycemicCounterregulation
+        } else if self.blood_glucose_mg_dl > 130.0 || self.incretin_signal > 0.5 {
+            PancreaticState::PostprandialAnabolic
+        } else {
+            PancreaticState::Basal
+        };
+    }
+
+    fn update_endocrine(&mut self, dt_seconds: f32) {
+        let insulin_target = match self.state {
+            PancreaticState::PostprandialAnabolic => {
+                8.0 + 0.6 * (self.blood_glucose_mg_dl - 90.0).max(0.0) + 25.0 * self.incretin_signal
+            }
+            PancreaticState::Basal => 10.0 + 0.2 * (self.blood_glucose_mg_dl - 90.0),
+            PancreaticState::HypoglycemicCounterregulation => 4.0,
+            PancreaticState::BetaCellExhaustion => 6.0,
+        };
+        self.insulin = Self::approach(
+            self.insulin,
+            (insulin_target * self.beta_cell_mass_fraction).clamp(2.0, 80.0),
+            0.5,
+            dt_seconds,
+        );
+        let glucagon_target = match self.state {
+            PancreaticState::HypoglycemicCounterregulation => 150.0,
+            PancreaticState::Basal => 70.0,
+            PancreaticState::PostprandialAnabolic => 40.0,
+            PancreaticState::BetaCellExhaustion => 110.0,
+        };
+        self.glucagon = Self::approach(
+            self.glucagon,
+            (glucagon_target + 20.0 * self.autonomic_tone.max(0.0)).clamp(20.0, 200.0),
+            0.4,
+            dt_seconds,
+        );
+        let somatostatin_target = (20.0
+            + 15.0 * (self.incretin_signal - 0.3).max(0.0)
+            + 0.3 * (self.blood_glucose_mg_dl - 90.0))
+            .clamp(10.0, 80.0);
+        self.somatostatin = Self::approach(self.somatostatin, somatostatin_target, 0.5, dt_seconds);
+        self.pancreatic_polypeptide = Self::approach(
+            self.pancreatic_polypeptide,
+            (100.0 + 80.0 * (-self.autonomic_tone).max(0.0) + 40.0 * self.incretin_signal)
+                .clamp(60.0, 260.0),
+            0.3,
+            dt_seconds,
+        );
+        self.islet_stress_index = Self::approach(
+            self.islet_stress_index,
+            (0.2 + 0.4 * (self.blood_glucose_mg_dl - 100.0).max(0.0) / 80.0
+                + 0.3 * (self.autonomic_tone).max(0.0))
+            .clamp(0.05, 0.95),
+            0.04,
+            dt_seconds,
+        );
+        self.beta_cell_mass_fraction = (self.beta_cell_mass_fraction
+            - 0.00002 * dt_seconds * (self.islet_stress_index - 0.3).max(0.0)
+            + 0.000015 * dt_seconds * (0.5 - self.islet_stress_index).max(0.0))
+        .clamp(0.4, 1.05);
+    }
+
+    fn update_exocrine(&mut self, dt_seconds: f32) {
+        let enzyme_target =
+            (15.0 + 25.0 * self.incretin_signal + 10.0 * (-self.autonomic_tone).max(0.0))
+                .clamp(5.0, 60.0);
+        self.digestive_enzyme_output =
+            Self::approach(self.digestive_enzyme_output, enzyme_target, 0.5, dt_seconds);
+        let bicarb_target =
+            (1.5 + 2.5 * self.incretin_signal - 0.5 * self.islet_stress_index).clamp(0.5, 5.0);
+        self.bicarbonate_output_mmol_min = Self::approach(
+            self.bicarbonate_output_mmol_min,
+            bicarb_target,
+            0.4,
+            dt_seconds,
+        );
+        self.acinar_flow_ml_min = Self::approach(
+            self.acinar_flow_ml_min,
+            (0.6 + 0.5 * self.incretin_signal + 0.3 * (-self.autonomic_tone).max(0.0))
+                .clamp(0.3, 2.0),
+            0.4,
+            dt_seconds,
+        );
+        self.duct_pressure_cm_h2o = Self::approach(
+            self.duct_pressure_cm_h2o,
+            (6.0 + 4.0 * (self.acinar_flow_ml_min - 0.7)).clamp(4.0, 18.0),
+            0.3,
+            dt_seconds,
+        );
+    }
 }
 
 impl Organ for Pancreas {
@@ -24,9 +210,26 @@ impl Organ for Pancreas {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {}
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        self.time_in_state_s += dt_seconds;
+        self.simulate_meals(dt_seconds);
+        self.update_state();
+        self.update_endocrine(dt_seconds);
+        self.update_exocrine(dt_seconds);
+    }
     fn summary(&self) -> String {
-        format!("Pancreas[id={}, insulin={:.2}]", self.id(), self.insulin)
+        format!(
+            "Pancreas[id={}, state={:?}, insulin={:.1}, glucagon={:.0}, enzymes={:.1} kIU/min]",
+            self.id(),
+            self.state,
+            self.insulin,
+            self.glucagon,
+            self.digestive_enzyme_output
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/organs/spinal_cord.rs

@@ -1,12 +1,45 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Functional state of spinal cord circuitry.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum SpinalCordState {
+    Intact,
+    Concussed,
+    Inflammatory,
+    Ischemic,
+    NeurogenicShock,
+}
+
 #[derive(Debug, Clone)]
 pub struct SpinalCord {
     info: OrganInfo,
     /// 0..=100 nerve signal integrity.
     pub signal_integrity: u8,
     pub injury: bool,
+    /// Ascending conduction velocity (m/s).
+    pub ascending_conduction_velocity: f32,
+    /// Descending motor conduction (m/s).
+    pub descending_conduction_velocity: f32,
+    /// Segmental reflex gain (dimensionless 0..=2).
+    pub reflex_gain: f32,
+    /// Sympathetic preganglionic output (0..=1).
+    pub sympathetic_outflow: f32,
+    /// Parasympathetic sacral outflow (0..=1).
+    pub parasympathetic_outflow: f32,
+    /// Central pattern generator tone (0..=1).
+    pub locomotor_cpg_tone: f32,
+    /// Nociceptive facilitation (0..=1).
+    pub nociceptive_facilitation: f32,
+    /// Glial scar formation index (0..=1).
+    pub glial_scar_index: f32,
+    /// Cord perfusion pressure (mmHg).
+    pub cord_perfusion_pressure_mm_hg: f32,
+    /// Inflammation marker (0..=1).
+    pub inflammation_index: f32,
+    /// State of spinal cord.
+    pub state: SpinalCordState,
+    time_in_state_s: f32,
 }
 
 impl SpinalCord {
@@ -15,8 +48,131 @@ impl SpinalCord {
             info: OrganInfo::new(id, OrganType::SpinalCord),
             signal_integrity: 100,
             injury: false,
+            ascending_conduction_velocity: 54.0,
+            descending_conduction_velocity: 60.0,
+            reflex_gain: 1.0,
+            sympathetic_outflow: 0.6,
+            parasympathetic_outflow: 0.55,
+            locomotor_cpg_tone: 0.65,
+            nociceptive_facilitation: 0.2,
+            glial_scar_index: 0.05,
+            cord_perfusion_pressure_mm_hg: 75.0,
+            inflammation_index: 0.1,
+            state: SpinalCordState::Intact,
+            time_in_state_s: 0.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_state(&mut self) {
+        self.state = if self.cord_perfusion_pressure_mm_hg < 60.0 {
+            SpinalCordState::Ischemic
+        } else if self.injury && self.time_in_state_s < 6.0 * 3600.0 {
+            SpinalCordState::NeurogenicShock
+        } else if self.inflammation_index > 0.5 {
+            SpinalCordState::Inflammatory
+        } else if self.glial_scar_index > 0.4 {
+            SpinalCordState::Concussed
+        } else {
+            SpinalCordState::Intact
+        };
+    }
+
+    fn update_integrity(&mut self, dt_seconds: f32) {
+        if self.injury {
+            let drop = (0.03 * dt_seconds).min(self.signal_integrity as f32);
+            self.signal_integrity = self.signal_integrity.saturating_sub(drop as u8);
+            self.glial_scar_index = (self.glial_scar_index + 0.00005 * dt_seconds).clamp(0.0, 1.0);
+        } else {
+            self.signal_integrity = (self.signal_integrity + 1).min(100);
+            self.glial_scar_index = Self::approach(self.glial_scar_index, 0.05, 0.0002, dt_seconds);
+        }
+    }
+
+    fn update_conduction(&mut self, dt_seconds: f32) {
+        let integrity_factor = self.signal_integrity as f32 / 100.0;
+        let scar_penalty = self.glial_scar_index * 20.0;
+        self.ascending_conduction_velocity = Self::approach(
+            self.ascending_conduction_velocity,
+            (54.0 * integrity_factor - scar_penalty).clamp(10.0, 60.0),
+            0.2,
+            dt_seconds,
+        );
+        self.descending_conduction_velocity = Self::approach(
+            self.descending_conduction_velocity,
+            (60.0 * integrity_factor - scar_penalty * 1.2).clamp(15.0, 70.0),
+            0.2,
+            dt_seconds,
+        );
+    }
+
+    fn update_autonomic_outflow(&mut self, dt_seconds: f32) {
+        let (sym_target, parasym_target, reflex_target, nocice_target) = match self.state {
+            SpinalCordState::Intact => (0.6, 0.55, 1.0, 0.2),
+            SpinalCordState::Concussed => (0.5, 0.45, 0.8, 0.35),
+            SpinalCordState::Inflammatory => (0.65, 0.4, 1.1, 0.6),
+            SpinalCordState::Ischemic => (0.45, 0.35, 0.6, 0.7),
+            SpinalCordState::NeurogenicShock => (0.3, 0.25, 0.4, 0.5),
+        };
+        self.sympathetic_outflow =
+            Self::approach(self.sympathetic_outflow, sym_target, 0.4, dt_seconds);
+        self.parasympathetic_outflow = Self::approach(
+            self.parasympathetic_outflow,
+            parasym_target,
+            0.4,
+            dt_seconds,
+        );
+        self.reflex_gain = Self::approach(self.reflex_gain, reflex_target, 0.3, dt_seconds);
+        self.nociceptive_facilitation = Self::approach(
+            self.nociceptive_facilitation,
+            nocice_target,
+            0.3,
+            dt_seconds,
+        );
+        self.locomotor_cpg_tone = Self::approach(
+            self.locomotor_cpg_tone,
+            (0.65 * (self.reflex_gain / 1.0) * (self.descending_conduction_velocity / 60.0))
+                .clamp(0.2, 0.9),
+            0.2,
+            dt_seconds,
+        );
+    }
+
+    fn update_perfusion(&mut self, dt_seconds: f32) {
+        let perfusion_target = (75.0 - 10.0 * (self.sympathetic_outflow - 0.6)
+            + 6.0 * (self.parasympathetic_outflow - 0.5)
+            - 15.0 * (1.0 - self.signal_integrity as f32 / 100.0))
+            .clamp(40.0, 90.0);
+        self.cord_perfusion_pressure_mm_hg = Self::approach(
+            self.cord_perfusion_pressure_mm_hg,
+            perfusion_target,
+            0.2,
+            dt_seconds,
+        );
+        self.inflammation_index = Self::approach(
+            self.inflammation_index,
+            (0.1 + 0.8 * (1.0 - self.cord_perfusion_pressure_mm_hg / 80.0).max(0.0)
+                + 0.5 * self.glial_scar_index)
+                .clamp(0.05, 1.0),
+            0.02,
+            dt_seconds,
+        );
+    }
 }
 
 impl Organ for SpinalCord {
@@ -26,16 +182,25 @@ impl Organ for SpinalCord {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {
-        if self.injury {
-            self.signal_integrity = self.signal_integrity.saturating_sub(1);
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
         }
+        self.time_in_state_s += dt_seconds;
+        self.update_integrity(dt_seconds);
+        self.update_perfusion(dt_seconds);
+        self.update_state();
+        self.update_conduction(dt_seconds);
+        self.update_autonomic_outflow(dt_seconds);
     }
     fn summary(&self) -> String {
         format!(
-            "SpinalCord[id={}, integrity={}]",
+            "SpinalCord[id={}, state={:?}, integrity={}, sym={:.2}, reflex={:.2}]",
             self.id(),
-            self.signal_integrity
+            self.state,
+            self.signal_integrity,
+            self.sympathetic_outflow,
+            self.reflex_gain
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {

src/organs/spleen.rs

@@ -1,11 +1,40 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Functional status of the spleen.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum SplenicState {
+    Homeostatic,
+    SympatheticContraction,
+    HyperimmuneActivation,
+    Sequestration,
+    Hypofunction,
+}
+
 #[derive(Debug, Clone)]
 pub struct Spleen {
     info: OrganInfo,
-    /// Immune activity 0..=100
+    /// Immune activity 0..=100.
     pub immune_activity: u8,
+    /// Red pulp blood volume (ml).
+    pub red_pulp_volume_ml: f32,
+    /// White pulp lymphocyte activation (0..=1).
+    pub white_pulp_activation: f32,
+    /// Platelet reservoir (10^9 cells/L contribution).
+    pub platelet_reservoir: f32,
+    /// Sympathetic tone (0..=1).
+    pub sympathetic_tone: f32,
+    /// Cytokine output (relative units).
+    pub cytokine_output: f32,
+    /// Filtered aged erythrocytes (10^6 cells/min).
+    pub erythrocyte_culling_rate: f32,
+    /// IgM production (mg/dL).
+    pub igm_production_mg_dl: f32,
+    /// Splenic contraction level (0..=1).
+    pub contraction_fraction: f32,
+    /// Current spleen state.
+    pub state: SplenicState,
+    time_in_state_s: f32,
 }
 
 impl Spleen {
@@ -13,8 +42,121 @@ impl Spleen {
         Self {
             info: OrganInfo::new(id, OrganType::Spleen),
             immune_activity: 80,
+            red_pulp_volume_ml: 180.0,
+            white_pulp_activation: 0.45,
+            platelet_reservoir: 70.0,
+            sympathetic_tone: 0.35,
+            cytokine_output: 0.2,
+            erythrocyte_culling_rate: 2.5,
+            igm_production_mg_dl: 95.0,
+            contraction_fraction: 0.1,
+            state: SplenicState::Homeostatic,
+            time_in_state_s: 0.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn update_state(&mut self) {
+        self.state = if self.sympathetic_tone > 0.7 {
+            SplenicState::SympatheticContraction
+        } else if self.white_pulp_activation > 0.75 || self.cytokine_output > 0.6 {
+            SplenicState::HyperimmuneActivation
+        } else if self.red_pulp_volume_ml > 260.0 {
+            SplenicState::Sequestration
+        } else if self.white_pulp_activation < 0.2 {
+            SplenicState::Hypofunction
+        } else {
+            SplenicState::Homeostatic
+        };
+    }
+
+    fn update_sympathetic_tone(&mut self, dt_seconds: f32) {
+        self.sympathetic_tone = Self::approach(
+            self.sympathetic_tone,
+            (0.3 + 0.5 * (self.contraction_fraction - 0.3).max(0.0)).clamp(0.2, 0.95),
+            0.3,
+            dt_seconds,
+        );
+    }
+
+    fn update_contraction(&mut self, dt_seconds: f32) {
+        let contraction_target = match self.state {
+            SplenicState::SympatheticContraction => 0.85,
+            SplenicState::HyperimmuneActivation => 0.45,
+            SplenicState::Sequestration => 0.15,
+            SplenicState::Hypofunction => 0.1,
+            SplenicState::Homeostatic => 0.3,
+        };
+        self.contraction_fraction = Self::approach(
+            self.contraction_fraction,
+            contraction_target,
+            0.4,
+            dt_seconds,
+        );
+        let volume_target = (180.0 + 120.0 * (0.4 - self.contraction_fraction)).clamp(80.0, 320.0);
+        self.red_pulp_volume_ml =
+            Self::approach(self.red_pulp_volume_ml, volume_target, 0.8, dt_seconds);
+        self.platelet_reservoir = Self::approach(
+            self.platelet_reservoir,
+            (70.0 + 40.0 * (self.red_pulp_volume_ml - 180.0) / 120.0).clamp(20.0, 160.0),
+            0.6,
+            dt_seconds,
+        );
+    }
+
+    fn update_immune_activity(&mut self, dt_seconds: f32) {
+        let activation_target = match self.state {
+            SplenicState::HyperimmuneActivation => 0.85,
+            SplenicState::Sequestration => 0.55,
+            SplenicState::Hypofunction => 0.18,
+            SplenicState::SympatheticContraction => 0.4,
+            SplenicState::Homeostatic => 0.45,
+        };
+        self.white_pulp_activation = Self::approach(
+            self.white_pulp_activation,
+            activation_target,
+            0.3,
+            dt_seconds,
+        );
+        self.immune_activity = ((self.white_pulp_activation * 120.0)
+            + (self.cytokine_output * 40.0))
+            .clamp(10.0, 160.0) as u8;
+        self.cytokine_output = Self::approach(
+            self.cytokine_output,
+            (0.2 + 0.8 * (self.white_pulp_activation - 0.3).max(0.0)).clamp(0.05, 1.2),
+            0.1,
+            dt_seconds,
+        );
+        self.erythrocyte_culling_rate = Self::approach(
+            self.erythrocyte_culling_rate,
+            (2.0 + 1.5 * (self.red_pulp_volume_ml - 180.0) / 100.0 + 1.2 * self.cytokine_output)
+                .clamp(0.5, 8.0),
+            0.2,
+            dt_seconds,
+        );
+        self.igm_production_mg_dl = Self::approach(
+            self.igm_production_mg_dl,
+            (90.0 + 60.0 * self.white_pulp_activation - 20.0 * self.sympathetic_tone)
+                .clamp(30.0, 220.0),
+            0.4,
+            dt_seconds,
+        );
+    }
 }
 
 impl Organ for Spleen {
@@ -24,9 +166,25 @@ impl Organ for Spleen {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {}
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        self.time_in_state_s += dt_seconds;
+        self.update_state();
+        self.update_contraction(dt_seconds);
+        self.update_sympathetic_tone(dt_seconds);
+        self.update_immune_activity(dt_seconds);
+    }
     fn summary(&self) -> String {
-        format!("Spleen[id={}, immune={}]", self.id(), self.immune_activity)
+        format!(
+            "Spleen[id={}, state={:?}, immune={}, redpulp={:.0} ml, platelets={:.0}]",
+            self.id(),
+            self.state,
+            self.immune_activity,
+            self.red_pulp_volume_ml,
+            self.platelet_reservoir
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/organs/stomach.rs

@@ -1,11 +1,52 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+/// Gastric functional phase.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum GastricPhase {
+    Fasting,
+    Cephalic,
+    Gastric,
+    Intestinal,
+    DelayedEmptying,
+}
+
 #[derive(Debug, Clone)]
 pub struct Stomach {
     info: OrganInfo,
-    /// Acid level 0..=100
+    /// Acid level 0..=100 (higher = more secretion).
     pub acid_level: u8,
+    /// Gastric lumen pH.
+    pub ph: f32,
+    /// Current gastric volume (ml).
+    pub volume_ml: f32,
+    /// Gastric motility index (0..=1).
+    pub motility_index: f32,
+    /// Antral pump strength (0..=1).
+    pub antral_pump_strength: f32,
+    /// Gastric emptying rate (ml/min).
+    pub emptying_rate_ml_min: f32,
+    /// Ghrelin level (pg/mL proxy).
+    pub ghrelin: f32,
+    /// Gastrin level (pg/mL proxy).
+    pub gastrin: f32,
+    /// Histamine release (relative units).
+    pub histamine: f32,
+    /// Somatostatin brake (relative units).
+    pub somatostatin: f32,
+    /// Protective mucus production (g/hour).
+    pub mucus_production_g_per_h: f32,
+    /// Intrinsic factor secretion (relative units).
+    pub intrinsic_factor: f32,
+    /// Vagal tone (0..=1).
+    pub vagal_tone: f32,
+    /// Gastric phase.
+    pub phase: GastricPhase,
+    /// Pending meal caloric load (kcal).
+    pub nutrient_load_kcal: f32,
+    time_in_phase_s: f32,
+    fasting_clock_s: f32,
+    target_meal_interval_s: f32,
 }
 
 impl Stomach {
@@ -13,8 +54,197 @@ impl Stomach {
         Self {
             info: OrganInfo::new(id, OrganType::Stomach),
             acid_level: 50,
+            ph: 2.2,
+            volume_ml: 120.0,
+            motility_index: 0.35,
+            antral_pump_strength: 0.3,
+            emptying_rate_ml_min: 1.5,
+            ghrelin: 950.0,
+            gastrin: 80.0,
+            histamine: 0.4,
+            somatostatin: 0.3,
+            mucus_production_g_per_h: 15.0,
+            intrinsic_factor: 0.6,
+            vagal_tone: 0.4,
+            phase: GastricPhase::Fasting,
+            nutrient_load_kcal: 60.0,
+            time_in_phase_s: 0.0,
+            fasting_clock_s: 0.0,
+            target_meal_interval_s: 4.5 * 3600.0,
         }
     }
+
+    fn approach(current: f32, target: f32, rate_per_second: f32, dt_seconds: f32) -> f32 {
+        let rate = rate_per_second.max(0.0);
+        if rate == 0.0 || dt_seconds <= 0.0 {
+            return current;
+        }
+        let delta = target - current;
+        let max_step = rate * dt_seconds;
+        if delta > max_step {
+            current + max_step
+        } else if delta < -max_step {
+            current - max_step
+        } else {
+            target
+        }
+    }
+
+    fn simulate_meals(&mut self, dt_seconds: f32) {
+        self.fasting_clock_s += dt_seconds;
+        if self.fasting_clock_s >= self.target_meal_interval_s {
+            self.phase = GastricPhase::Cephalic;
+            self.time_in_phase_s = 0.0;
+            self.vagal_tone = 0.85;
+            self.ghrelin = 600.0;
+            self.gastrin = 160.0;
+            self.nutrient_load_kcal = 650.0;
+            self.volume_ml = (self.volume_ml + 450.0).clamp(80.0, 1600.0);
+            self.target_meal_interval_s =
+                (4.0 + 1.0 * (self.mucus_production_g_per_h / 15.0)) * 3600.0;
+            self.fasting_clock_s = 0.0;
+        } else {
+            self.vagal_tone = Self::approach(self.vagal_tone, 0.35, 0.04, dt_seconds);
+            self.ghrelin = Self::approach(self.ghrelin, 1200.0, 1.0, dt_seconds);
+        }
+    }
+
+    fn update_phase(&mut self) {
+        self.phase = match self.phase {
+            GastricPhase::Cephalic => {
+                if self.time_in_phase_s > 300.0 {
+                    GastricPhase::Gastric
+                } else {
+                    GastricPhase::Cephalic
+                }
+            }
+            GastricPhase::Gastric => {
+                if self.volume_ml < 200.0 {
+                    GastricPhase::Intestinal
+                } else {
+                    GastricPhase::Gastric
+                }
+            }
+            GastricPhase::Intestinal => {
+                if self.nutrient_load_kcal < 80.0 {
+                    GastricPhase::Fasting
+                } else if self.emptying_rate_ml_min < 1.0 {
+                    GastricPhase::DelayedEmptying
+                } else {
+                    GastricPhase::Intestinal
+                }
+            }
+            GastricPhase::DelayedEmptying => {
+                if self.emptying_rate_ml_min > 1.5 {
+                    GastricPhase::Fasting
+                } else {
+                    GastricPhase::DelayedEmptying
+                }
+            }
+            GastricPhase::Fasting => {
+                if self.nutrient_load_kcal > 120.0 {
+                    GastricPhase::Cephalic
+                } else {
+                    GastricPhase::Fasting
+                }
+            }
+        };
+    }
+
+    fn update_secretions(&mut self, dt_seconds: f32) {
+        let gastrin_target = match self.phase {
+            GastricPhase::Cephalic => 180.0,
+            GastricPhase::Gastric => 220.0,
+            GastricPhase::Intestinal => 120.0,
+            GastricPhase::DelayedEmptying => 160.0,
+            GastricPhase::Fasting => 60.0,
+        };
+        self.gastrin = Self::approach(
+            self.gastrin,
+            (gastrin_target + 0.5 * (self.volume_ml - 250.0).max(0.0)).clamp(40.0, 320.0),
+            0.5,
+            dt_seconds,
+        );
+        self.histamine = Self::approach(
+            self.histamine,
+            (0.3 + 0.004 * self.gastrin + 0.2 * (self.vagal_tone - 0.4).max(0.0)).clamp(0.1, 2.0),
+            0.3,
+            dt_seconds,
+        );
+        self.somatostatin = Self::approach(
+            self.somatostatin,
+            (0.25
+                + 0.2 * (self.ph - 2.0).max(0.0)
+                + 0.3 * (self.phase == GastricPhase::Intestinal) as i32 as f32)
+                .clamp(0.1, 2.0),
+            0.4,
+            dt_seconds,
+        );
+        let acid_drive =
+            (self.gastrin / 200.0 + self.histamine - self.somatostatin).clamp(0.0, 2.0);
+        let acid_numeric = (50.0 + 35.0 * acid_drive).clamp(10.0, 100.0);
+        self.acid_level = acid_numeric.round() as u8;
+        self.ph = Self::approach(
+            self.ph,
+            (7.0 - 0.045 * self.acid_level as f32 + 0.4 * (self.volume_ml / 500.0)).clamp(1.2, 6.5),
+            0.6,
+            dt_seconds,
+        );
+        self.mucus_production_g_per_h = Self::approach(
+            self.mucus_production_g_per_h,
+            (15.0
+                + 6.0 * (self.acid_level as f32 / 60.0)
+                + 4.0 * (self.somatostatin - 0.3).max(0.0))
+            .clamp(8.0, 40.0),
+            0.2,
+            dt_seconds,
+        );
+        self.intrinsic_factor = Self::approach(
+            self.intrinsic_factor,
+            (0.6 + 0.4 * (self.acid_level as f32 / 80.0)).clamp(0.2, 1.2),
+            0.2,
+            dt_seconds,
+        );
+    }
+
+    fn update_motility(&mut self, dt_seconds: f32) {
+        let motility_target = match self.phase {
+            GastricPhase::Cephalic => 0.4,
+            GastricPhase::Gastric => 0.75,
+            GastricPhase::Intestinal => 0.6,
+            GastricPhase::DelayedEmptying => 0.35,
+            GastricPhase::Fasting => 0.3,
+        };
+        self.motility_index = Self::approach(self.motility_index, motility_target, 0.5, dt_seconds);
+        self.antral_pump_strength = Self::approach(
+            self.antral_pump_strength,
+            (0.3 + 0.5 * self.motility_index + 0.3 * self.vagal_tone).clamp(0.2, 0.95),
+            0.5,
+            dt_seconds,
+        );
+        self.emptying_rate_ml_min = Self::approach(
+            self.emptying_rate_ml_min,
+            (1.5 + 3.5 * self.antral_pump_strength
+                - 1.0 * (self.ph - 3.0).max(0.0)
+                - 0.5 * (self.nutrient_load_kcal / 300.0))
+                .clamp(0.2, 9.0),
+            0.4,
+            dt_seconds,
+        );
+    }
+
+    fn update_volume(&mut self, dt_seconds: f32) {
+        let emptied = self.emptying_rate_ml_min * dt_seconds / 60.0;
+        let metabolic_use = (self.nutrient_load_kcal * 0.3) * dt_seconds / 3600.0;
+        self.volume_ml = (self.volume_ml - emptied).clamp(30.0, 1800.0);
+        self.nutrient_load_kcal = (self.nutrient_load_kcal - metabolic_use).max(0.0);
+        self.ghrelin = Self::approach(
+            self.ghrelin,
+            (1200.0 - 0.8 * self.volume_ml).clamp(200.0, 1400.0),
+            0.4,
+            dt_seconds,
+        );
+    }
 }
 
 impl Organ for Stomach {
@@ -24,9 +254,26 @@ impl Organ for Stomach {
     fn organ_type(&self) -> OrganType {
         self.info.kind()
     }
-    fn update(&mut self, _dt_seconds: f32) {}
+    fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        self.time_in_phase_s += dt_seconds;
+        self.simulate_meals(dt_seconds);
+        self.update_phase();
+        self.update_secretions(dt_seconds);
+        self.update_motility(dt_seconds);
+        self.update_volume(dt_seconds);
+    }
     fn summary(&self) -> String {
-        format!("Stomach[id={}, acid={}]", self.id(), self.acid_level)
+        format!(
+            "Stomach[id={}, phase={:?}, vol={:.0} ml, pH={:.1}, acid={}]",
+            self.id(),
+            self.phase,
+            self.volume_ml,
+            self.ph,
+            self.acid_level
+        )
     }
     fn as_any(&self) -> &dyn core::any::Any {
         self

src/patient.rs

@@ -1,7 +1,10 @@
 //! Patient type holding organs and core physiology snapshots.
 
 use crate::error::MedicalError;
-use crate::organs::{Heart, Lungs, Organ};
+use crate::organs::{
+    Bladder, BladderPhase, Brain, EsophagealStage, Esophagus, Gallbladder, Heart, Intestines,
+    Kidneys, Liver, Lungs, Organ, Pancreas, SleepStage, SpinalCord, Spleen, Stomach,
+};
 use crate::types::{Blood, BloodPressure, OrganType};
 
 /// Patient container and simulation entry.
@@ -15,6 +18,94 @@ pub struct Patient {
     pub blood_pressure: BloodPressure,
 }
 
+#[derive(Clone, Copy)]
+struct HeartSignals {
+    map: f32,
+    cardiac_output: f32,
+}
+
+#[derive(Clone, Copy)]
+struct LungSignals {
+    spo2_pct: f32,
+    alveolar_pco2_mm_hg: f32,
+}
+
+#[derive(Clone, Copy)]
+struct BrainSignals {
+    brainstem_drive: f32,
+    autonomic_variability: f32,
+    consciousness: f32,
+    sleep_depth: f32,
+    rem_tone: f32,
+}
+
+#[derive(Clone, Copy)]
+struct EsophagusSignals {
+    stage: EsophagealStage,
+    bolus_volume_ml: f32,
+    peristaltic_progress_cm: f32,
+    lower_sphincter_tone: f32,
+    hiatal_pressure_cm_h2o: f32,
+}
+
+#[derive(Clone, Copy)]
+struct BladderSignals {
+    afferent_signal: f32,
+    urgency: f32,
+    phase: BladderPhase,
+}
+
+#[derive(Clone, Copy)]
+struct StomachSignals {
+    emptying_rate_ml_min: f32,
+    nutrient_load_kcal: f32,
+    volume_ml: f32,
+    acid_level: u8,
+    motility_index: f32,
+}
+
+#[derive(Clone, Copy)]
+struct LiverSignals {
+    bile_secretion_ml_min: f32,
+}
+
+#[derive(Clone, Copy)]
+struct PancreasSignals {
+    insulin: f32,
+    glucagon: f32,
+    incretin_signal: f32,
+    somatostatin: f32,
+}
+
+#[derive(Clone, Copy)]
+struct IntestineSignals {
+    nutrient_energy_kcal: f32,
+}
+
+#[derive(Clone, Copy)]
+struct GallbladderSignals {
+    bile_acid_concentration_mmol_l: f32,
+}
+
+#[derive(Clone, Copy)]
+struct SpinalSignals {
+    sympathetic_outflow: f32,
+    parasympathetic_outflow: f32,
+    reflex_gain: f32,
+}
+
+#[derive(Clone, Copy)]
+struct KidneySignals {
+    urine_flow_ml_min: f32,
+}
+
+#[derive(Clone, Copy)]
+struct SpleenSignals {
+    immune_activity: u8,
+    red_pulp_volume_ml: f32,
+    platelet_reservoir: f32,
+}
+
 impl Patient {
     /// Construct a new patient with validated id.
     pub fn new(id: impl Into<String>) -> crate::Result<Self> {
@@ -71,7 +162,7 @@ impl Patient {
         self.with_heart(12)
     }
 
-    /// Initialize a patient with a heart with `leads`.
+    /// Initialize a patient with a heart with leads.
     pub fn with_heart(mut self, leads: u8) -> Self {
         let id = format!("{}-heart", self.id);
         self.add_organ(Heart::new(id, leads));
@@ -98,74 +189,553 @@ impl Patient {
             }
             OrganType::Brain => {
                 let id = format!("{}-brain", self.id);
-                self.add_organ(crate::organs::Brain::new(id));
+                self.add_organ(Brain::new(id));
             }
             OrganType::SpinalCord => {
                 let id = format!("{}-sc", self.id);
-                self.add_organ(crate::organs::SpinalCord::new(id));
+                self.add_organ(SpinalCord::new(id));
             }
             OrganType::Stomach => {
                 let id = format!("{}-stomach", self.id);
-                self.add_organ(crate::organs::Stomach::new(id));
+                self.add_organ(Stomach::new(id));
             }
             OrganType::Liver => {
                 let id = format!("{}-liver", self.id);
-                self.add_organ(crate::organs::Liver::new(id));
+                self.add_organ(Liver::new(id));
             }
             OrganType::Gallbladder => {
                 let id = format!("{}-gb", self.id);
-                self.add_organ(crate::organs::Gallbladder::new(id));
+                self.add_organ(Gallbladder::new(id));
             }
             OrganType::Pancreas => {
                 let id = format!("{}-pancreas", self.id);
-                self.add_organ(crate::organs::Pancreas::new(id));
+                self.add_organ(Pancreas::new(id));
             }
             OrganType::Intestines => {
                 let id = format!("{}-intestines", self.id);
-                self.add_organ(crate::organs::Intestines::new(id));
+                self.add_organ(Intestines::new(id));
             }
             OrganType::Esophagus => {
                 let id = format!("{}-eso", self.id);
-                self.add_organ(crate::organs::Esophagus::new(id));
+                self.add_organ(Esophagus::new(id));
             }
             OrganType::Kidneys => {
                 let id = format!("{}-kidneys", self.id);
-                self.add_organ(crate::organs::Kidneys::new(id));
+                self.add_organ(Kidneys::new(id));
             }
             OrganType::Bladder => {
                 let id = format!("{}-bladder", self.id);
-                self.add_organ(crate::organs::Bladder::new(id));
+                self.add_organ(Bladder::new(id));
             }
             OrganType::Spleen => {
                 let id = format!("{}-spleen", self.id);
-                self.add_organ(crate::organs::Spleen::new(id));
+                self.add_organ(Spleen::new(id));
             }
         }
         self
     }
 
-    /// Advance simulation by `dt_seconds`.
+    /// Advance simulation by dt_seconds.
     pub fn update(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        let heart_signals = self.find_organ_typed::<Heart>().map(|h| {
+            let systolic = h.arterial_bp.systolic as f32;
+            let diastolic = h.arterial_bp.diastolic as f32;
+            HeartSignals {
+                map: diastolic + (systolic - diastolic) / 3.0,
+                cardiac_output: h.cardiac_output_l_min,
+            }
+        });
+
+        let lungs_signals = self.find_organ_typed::<Lungs>().map(|l| LungSignals {
+            spo2_pct: l.spo2_pct,
+            alveolar_pco2_mm_hg: l.alveolar_pco2_mm_hg,
+        });
+
+        let stomach_signals = self.find_organ_typed::<Stomach>().map(|s| StomachSignals {
+            emptying_rate_ml_min: s.emptying_rate_ml_min,
+            nutrient_load_kcal: s.nutrient_load_kcal,
+            volume_ml: s.volume_ml,
+            acid_level: s.acid_level,
+            motility_index: s.motility_index,
+        });
+
+        let liver_signals = self.find_organ_typed::<Liver>().map(|l| LiverSignals {
+            bile_secretion_ml_min: l.bile_secretion_ml_min,
+        });
+
+        let intestine_signals = self
+            .find_organ_typed::<Intestines>()
+            .map(|i| IntestineSignals {
+                nutrient_energy_kcal: i.nutrient_energy_kcal,
+            });
+
+        let gallbladder_signals =
+            self.find_organ_typed::<Gallbladder>()
+                .map(|g| GallbladderSignals {
+                    bile_acid_concentration_mmol_l: g.bile_acid_concentration_mmol_l,
+                });
+
+        let esophagus_before = self
+            .find_organ_typed::<Esophagus>()
+            .map(|e| EsophagusSignals {
+                stage: e.stage,
+                bolus_volume_ml: e.bolus_volume_ml,
+                peristaltic_progress_cm: e.peristaltic_progress_cm,
+                lower_sphincter_tone: e.lower_sphincter_tone,
+                hiatal_pressure_cm_h2o: e.hiatal_pressure_gradient_cm_h2o,
+            });
+
+        let kidney_signals = self.find_organ_typed::<Kidneys>().map(|k| KidneySignals {
+            urine_flow_ml_min: k.urine_flow_ml_min,
+        });
+
+        let spinal_signals = self
+            .find_organ_typed::<SpinalCord>()
+            .map(|s| SpinalSignals {
+                sympathetic_outflow: s.sympathetic_outflow,
+                parasympathetic_outflow: s.parasympathetic_outflow,
+                reflex_gain: s.reflex_gain,
+            });
+
+        let blood_glucose = self.blood.glucose_mg_dl;
+        if let Some(pancreas) = self.find_organ_typed_mut::<Pancreas>() {
+            pancreas.blood_glucose_mg_dl = blood_glucose;
+            if let Some(intestines) = intestine_signals {
+                let incretin_target = (intestines.nutrient_energy_kcal / 400.0).clamp(0.05, 1.0);
+                pancreas.incretin_signal =
+                    Self::relax_value(pancreas.incretin_signal, incretin_target, dt_seconds, 90.0);
+            }
+            if let Some(spinal) = spinal_signals {
+                let tone_target =
+                    (spinal.sympathetic_outflow - spinal.parasympathetic_outflow).clamp(-1.0, 1.0);
+                pancreas.autonomic_tone =
+                    Self::relax_value(pancreas.autonomic_tone, tone_target, dt_seconds, 120.0);
+            }
+        }
+
+        if let Some(brain) = self.find_organ_typed_mut::<Brain>() {
+            if let Some(lungs) = lungs_signals {
+                brain.oxygenation_saturation = (lungs.spo2_pct / 100.0).clamp(0.8, 1.0);
+                let drive_target =
+                    (0.55 + (lungs.alveolar_pco2_mm_hg - 38.0) / 40.0).clamp(0.2, 1.0);
+                brain.brainstem_autonomic_drive = Self::relax_value(
+                    brain.brainstem_autonomic_drive,
+                    drive_target,
+                    dt_seconds,
+                    20.0,
+                );
+            }
+            if let Some(heart) = heart_signals {
+                let cpp_target = (heart.map - brain.intracranial_pressure_mm_hg).clamp(40.0, 110.0);
+                brain.cerebral_perfusion_pressure_mm_hg = Self::relax_value(
+                    brain.cerebral_perfusion_pressure_mm_hg,
+                    cpp_target,
+                    dt_seconds,
+                    15.0,
+                );
+            }
+        }
+
+        let blood_glucose_for_kidneys = self.blood.glucose_mg_dl;
+        if let Some(kidneys) = self.find_organ_typed_mut::<Kidneys>() {
+            let osm_target = 285.0 + (blood_glucose_for_kidneys - 95.0) * 0.06;
+            kidneys.serum_osmolality_mosm =
+                Self::relax_value(kidneys.serum_osmolality_mosm, osm_target, dt_seconds, 120.0);
+            if let Some(heart) = heart_signals {
+                let plasma_target = (3.0 + 0.22 * (heart.cardiac_output - 5.0)).clamp(2.4, 3.6);
+                kidneys.plasma_volume_l =
+                    Self::relax_value(kidneys.plasma_volume_l, plasma_target, dt_seconds, 180.0);
+            }
+        }
+
+        if let Some(gallbladder) = self.find_organ_typed_mut::<Gallbladder>() {
+            if let Some(liver) = liver_signals {
+                let inflow_target = (liver.bile_secretion_ml_min * 0.8).clamp(0.05, 2.4);
+                gallbladder.hepatic_bile_flow_ml_per_min = Self::relax_value(
+                    gallbladder.hepatic_bile_flow_ml_per_min,
+                    inflow_target,
+                    dt_seconds,
+                    80.0,
+                );
+            }
+            if let Some(intestines) = intestine_signals {
+                if intestines.nutrient_energy_kcal < 80.0 {
+                    gallbladder.sphincter_of_oddi_tone = (gallbladder.sphincter_of_oddi_tone
+                        + 0.05 * dt_seconds / 60.0)
+                        .clamp(0.2, 0.95);
+                }
+            }
+        }
+
+        if let Some(intestines) = self.find_organ_typed_mut::<Intestines>() {
+            if let Some(gall) = gallbladder_signals {
+                let recirc_target =
+                    (0.82 + (gall.bile_acid_concentration_mmol_l - 60.0) / 320.0).clamp(0.5, 0.98);
+                intestines.bile_acid_recirculation_fraction = Self::relax_value(
+                    intestines.bile_acid_recirculation_fraction,
+                    recirc_target,
+                    dt_seconds,
+                    240.0,
+                );
+            }
+        }
+
+        if let Some(spinal) = self.find_organ_typed_mut::<SpinalCord>() {
+            if let Some(heart) = heart_signals {
+                let perfusion_target = (heart.map - 8.0).clamp(45.0, 90.0);
+                spinal.cord_perfusion_pressure_mm_hg = Self::relax_value(
+                    spinal.cord_perfusion_pressure_mm_hg,
+                    perfusion_target,
+                    dt_seconds,
+                    120.0,
+                );
+            }
+        }
+
+        if let Some(bladder) = self.find_organ_typed_mut::<Bladder>() {
+            if let Some(kidney) = kidney_signals {
+                let fill_target = (kidney.urine_flow_ml_min * 60.0).clamp(5.0, 180.0);
+                bladder.filling_rate_ml_per_min = Self::relax_value(
+                    bladder.filling_rate_ml_per_min,
+                    fill_target,
+                    dt_seconds,
+                    90.0,
+                );
+            }
+        }
+
+        if let Some(stomach) = stomach_signals {
+            let delivered_ml = stomach.emptying_rate_ml_min * dt_seconds / 60.0;
+            let delivered_kcal = (delivered_ml * 0.8).min(stomach.nutrient_load_kcal);
+            if delivered_kcal > 0.0 {
+                if let Some(intestines) = self.find_organ_typed_mut::<Intestines>() {
+                    intestines.nutrient_energy_kcal += delivered_kcal;
+                }
+            }
+        }
+
         for organ in &mut self.organs {
             organ.update(dt_seconds);
         }
-        // Simple inter-organ signaling: low SpO2 nudges heart rate higher.
-        if let Some(spo2) = self.find_organ_typed::<Lungs>().map(|l| l.spo2_pct) {
-            if let Some(heart) = self.find_organ_typed_mut::<Heart>() {
-                let target = if spo2 < 92.0 { 90.0 } else { 70.0 };
-                let diff = target - heart.heart_rate_bpm;
-                heart.heart_rate_bpm += 0.05 * diff;
+
+        if let Some(heart) = self.find_organ_typed::<Heart>() {
+            self.blood_pressure = heart.arterial_bp;
+        }
+        if let Some(lungs) = self.find_organ_typed::<Lungs>() {
+            self.blood.spo2_pct = lungs.spo2_pct;
+        }
+
+        let mut glucose = self.blood.glucose_mg_dl;
+        if let Some(liver) = self.find_organ_typed::<Liver>() {
+            let hepatic_balance = liver.gluconeogenesis_rate * 24.0
+                + liver.glycogenolysis_rate_g_per_h * 6.0
+                - liver.lipogenesis_rate_g_per_h * 4.0
+                - liver.beta_oxidation_rate_g_per_h * 2.5
+                - (liver.insulin_signal - liver.glucagon_signal) * 30.0;
+            glucose += hepatic_balance * (dt_seconds / 3600.0);
+        }
+        if let Some(pancreas) = self.find_organ_typed::<Pancreas>() {
+            let hormonal_balance = pancreas.glucagon * 0.05 - pancreas.insulin * 0.08;
+            glucose += hormonal_balance * (dt_seconds / 60.0);
+        }
+        glucose = glucose.clamp(60.0, 220.0);
+        self.blood.glucose_mg_dl = glucose;
+
+        let kidneys_after = self
+            .find_organ_typed::<Kidneys>()
+            .map(|k| (k.erythropoietin_iu_per_day, k.urine_flow_ml_min));
+
+        if let Some((epo, _)) = kidneys_after {
+            let hgb_target = 14.0 + (epo - 18.0) / 80.0;
+            self.blood.hemoglobin_g_dl = Self::relax_value(
+                self.blood.hemoglobin_g_dl,
+                hgb_target.clamp(9.0, 18.0),
+                dt_seconds,
+                600.0,
+            );
+        }
+
+        let spleen_after = self.find_organ_typed::<Spleen>().map(|s| SpleenSignals {
+            immune_activity: s.immune_activity,
+            red_pulp_volume_ml: s.red_pulp_volume_ml,
+            platelet_reservoir: s.platelet_reservoir,
+        });
+
+        if let Some(spleen) = spleen_after {
+            let immune_penalty = (spleen.immune_activity as f32 - 80.0) / 120.0;
+            let hematocrit_target = 42.0
+                - (spleen.red_pulp_volume_ml - 180.0) / 8.0
+                - (spleen.platelet_reservoir - 70.0) / 30.0
+                + immune_penalty * 2.0;
+            self.blood.hematocrit_pct = Self::relax_value(
+                self.blood.hematocrit_pct,
+                hematocrit_target.clamp(30.0, 55.0),
+                dt_seconds,
+                600.0,
+            );
+        }
+
+        let blood_glucose_for_pancreas = self.blood.glucose_mg_dl;
+        if let Some(pancreas) = self.find_organ_typed_mut::<Pancreas>() {
+            pancreas.blood_glucose_mg_dl = blood_glucose_for_pancreas;
+        }
+
+        let pancreas_after = self
+            .find_organ_typed::<Pancreas>()
+            .map(|p| PancreasSignals {
+                insulin: p.insulin,
+                glucagon: p.glucagon,
+                incretin_signal: p.incretin_signal,
+                somatostatin: p.somatostatin,
+            });
+
+        let brain_after = self.find_organ_typed::<Brain>().map(|b| BrainSignals {
+            brainstem_drive: b.brainstem_autonomic_drive,
+            autonomic_variability: b.autonomic_variability,
+            consciousness: b.consciousness as f32 / 100.0,
+            sleep_depth: match b.sleep_stage {
+                SleepStage::Wake => 0.0,
+                SleepStage::N1 => 0.25,
+                SleepStage::N2 => 0.55,
+                SleepStage::N3 => 0.9,
+                SleepStage::Rem => 0.4,
+            },
+            rem_tone: matches!(b.sleep_stage, SleepStage::Rem) as i32 as f32,
+        });
+        let spinal_after = self
+            .find_organ_typed::<SpinalCord>()
+            .map(|s| SpinalSignals {
+                sympathetic_outflow: s.sympathetic_outflow,
+                parasympathetic_outflow: s.parasympathetic_outflow,
+                reflex_gain: s.reflex_gain,
+            });
+        let bladder_after = self.find_organ_typed::<Bladder>().map(|b| BladderSignals {
+            afferent_signal: b.afferent_signal,
+            urgency: b.urgency,
+            phase: b.phase,
+        });
+        let esophagus_after = self
+            .find_organ_typed::<Esophagus>()
+            .map(|e| EsophagusSignals {
+                stage: e.stage,
+                bolus_volume_ml: e.bolus_volume_ml,
+                peristaltic_progress_cm: e.peristaltic_progress_cm,
+                lower_sphincter_tone: e.lower_sphincter_tone,
+                hiatal_pressure_cm_h2o: e.hiatal_pressure_gradient_cm_h2o,
+            });
+
+        if let (Some(before), Some(after)) = (esophagus_before, esophagus_after) {
+            let mut delivered_ml = 0.0;
+            if matches!(
+                after.stage,
+                EsophagealStage::Clearing | EsophagealStage::Idle
+            ) {
+                delivered_ml = (before.bolus_volume_ml - after.bolus_volume_ml).max(0.0);
+            } else if after.peristaltic_progress_cm > 22.0 && before.peristaltic_progress_cm <= 22.0
+            {
+                delivered_ml = before.bolus_volume_ml * 0.6;
+            }
+            let delivered_ml = delivered_ml.clamp(0.0, 40.0);
+            if delivered_ml > 0.0 {
+                if let Some(stomach) = self.find_organ_typed_mut::<Stomach>() {
+                    stomach.volume_ml = (stomach.volume_ml + delivered_ml).clamp(80.0, 1600.0);
+                    stomach.nutrient_load_kcal += delivered_ml * 0.8;
+                }
             }
         }
-        // Kidneys produce urine into bladder
-        let produced_opt = self
-            .find_organ_typed::<crate::organs::Kidneys>()
-            .map(|kidneys| (kidneys.gfr * (dt_seconds / 60.0)).max(0.0) * 0.5); // ml
-        if let (Some(produced), Some(bladder)) = (
-            produced_opt,
-            self.find_organ_typed_mut::<crate::organs::Bladder>(),
-        ) {
-            bladder.volume_ml += produced;
+
+        if let (Some(stomach), Some(esophagus_state)) = (stomach_signals, esophagus_after) {
+            if let Some(esophagus) = self.find_organ_typed_mut::<Esophagus>() {
+                let distension = ((stomach.volume_ml - 250.0) / 160.0).clamp(-0.3, 2.2);
+                let acid_factor = (stomach.acid_level as f32 / 100.0 - 0.65).max(0.0);
+                let motility_relief = (stomach.motility_index - 0.5).min(0.0).abs();
+                let gradient_target =
+                    (esophagus_state.hiatal_pressure_cm_h2o + distension * 6.0 + acid_factor * 3.0
+                        - motility_relief * 2.0)
+                        .clamp(4.0, 22.0);
+                esophagus.hiatal_pressure_gradient_cm_h2o = Self::relax_value(
+                    esophagus.hiatal_pressure_gradient_cm_h2o,
+                    gradient_target,
+                    dt_seconds,
+                    90.0,
+                );
+                let les_target = (esophagus_state.lower_sphincter_tone
+                    + 0.15 * (0.6 - distension).clamp(-0.4, 0.4)
+                    - 0.1 * acid_factor)
+                    .clamp(0.2, 0.95);
+                esophagus.lower_sphincter_tone = Self::relax_value(
+                    esophagus.lower_sphincter_tone,
+                    les_target,
+                    dt_seconds,
+                    120.0,
+                );
+            }
+        }
+
+        if let Some(bladder_state) = bladder_after {
+            if let Some(spinal) = self.find_organ_typed_mut::<SpinalCord>() {
+                let stretch = bladder_state.afferent_signal;
+                let urgency = bladder_state.urgency;
+                let voiding_signal =
+                    matches!(bladder_state.phase, BladderPhase::Voiding) as i32 as f32;
+                let sleep_bias = brain_after.map(|b| b.sleep_depth).unwrap_or(0.0);
+                let para_target = (0.42 + 0.5 * stretch + 0.25 * voiding_signal
+                    - 0.15 * sleep_bias)
+                    .clamp(0.2, 0.95);
+                let sym_target = (0.65 - 0.4 * stretch - 0.25 * voiding_signal + 0.2 * sleep_bias)
+                    .clamp(0.15, 0.9);
+                spinal.parasympathetic_outflow = Self::relax_value(
+                    spinal.parasympathetic_outflow,
+                    para_target,
+                    dt_seconds,
+                    90.0,
+                );
+                spinal.sympathetic_outflow =
+                    Self::relax_value(spinal.sympathetic_outflow, sym_target, dt_seconds, 90.0);
+                let sedation = brain_after.map(|b| 1.0 - b.consciousness).unwrap_or(0.0);
+                let reflex_target =
+                    (1.0 + 0.55 * stretch + 0.3 * voiding_signal - 0.3 * sedation).clamp(0.6, 1.6);
+                spinal.reflex_gain =
+                    Self::relax_value(spinal.reflex_gain, reflex_target, dt_seconds, 120.0);
+                spinal.nociceptive_facilitation = Self::relax_value(
+                    spinal.nociceptive_facilitation,
+                    (0.2 + 0.5 * urgency + 0.1 * voiding_signal).clamp(0.15, 1.0),
+                    dt_seconds,
+                    120.0,
+                );
+            }
+
+            if let Some(bladder) = self.find_organ_typed_mut::<Bladder>() {
+                if let Some(brain) = brain_after {
+                    let sedation = (1.0 - brain.consciousness).clamp(0.0, 1.0);
+                    let sleep_bonus = brain.sleep_depth * 0.25 + brain.rem_tone * 0.1;
+                    let capacity = bladder.capacity_ml.max(1.0);
+                    let micturition_target = (capacity
+                        * (0.65 + sleep_bonus + sedation * 0.2 - bladder_state.urgency * 0.05))
+                        .clamp(capacity * 0.5, capacity * 0.9);
+                    bladder.micturition_threshold_ml = Self::relax_value(
+                        bladder.micturition_threshold_ml,
+                        micturition_target,
+                        dt_seconds,
+                        900.0,
+                    );
+                    let urge_target = (capacity * (0.4 + sleep_bonus * 0.5 + sedation * 0.15))
+                        .clamp(capacity * 0.3, capacity * 0.7);
+                    bladder.urge_threshold_ml = Self::relax_value(
+                        bladder.urge_threshold_ml,
+                        urge_target,
+                        dt_seconds,
+                        600.0,
+                    );
+                }
+
+                if let Some(brain) = brain_after {
+                    let voiding_signal =
+                        matches!(bladder_state.phase, BladderPhase::Voiding) as i32 as f32;
+                    let spinal_sym = spinal_after.map(|s| s.sympathetic_outflow).unwrap_or(0.6);
+                    let spinal_para = spinal_after
+                        .map(|s| s.parasympathetic_outflow)
+                        .unwrap_or(0.5);
+                    let reflex_gain = spinal_after.map(|s| s.reflex_gain).unwrap_or(1.0);
+                    let para_target = (0.3
+                        + brain.brainstem_drive * 0.4
+                        + spinal_para * 0.3
+                        + bladder_state.urgency * 0.5
+                        + voiding_signal * 0.3)
+                        .clamp(0.05, 1.1);
+                    bladder.parasympathetic_drive = Self::relax_value(
+                        bladder.parasympathetic_drive,
+                        para_target,
+                        dt_seconds,
+                        120.0,
+                    )
+                    .clamp(0.0, 1.0);
+                    let sym_target =
+                        (0.55 + (1.0 - brain.brainstem_drive) * 0.35 + spinal_sym * 0.4
+                            - bladder_state.urgency * 0.4
+                            - voiding_signal * 0.4)
+                            .clamp(0.1, 1.0);
+                    bladder.sympathetic_drive =
+                        Self::relax_value(bladder.sympathetic_drive, sym_target, dt_seconds, 160.0)
+                            .clamp(0.0, 1.0);
+                    let voluntary = brain.consciousness;
+                    let somatic_target = ((0.55 + voluntary * 0.35 - brain.sleep_depth * 0.3)
+                        * (1.0 - bladder_state.urgency * 0.55)
+                        + reflex_gain * 0.1
+                        - voiding_signal * 0.5)
+                        .clamp(0.1, 0.95);
+                    bladder.somatic_drive =
+                        Self::relax_value(bladder.somatic_drive, somatic_target, dt_seconds, 110.0)
+                            .clamp(0.0, 1.0);
+                }
+            }
+        }
+
+        if let Some(pancreas) = pancreas_after {
+            if let Some(liver) = self.find_organ_typed_mut::<Liver>() {
+                let insulin_target = (pancreas.insulin / 60.0).clamp(0.1, 1.0);
+                let glucagon_target = (pancreas.glucagon / 120.0).clamp(0.1, 1.2);
+                liver.insulin_signal =
+                    Self::relax_value(liver.insulin_signal, insulin_target, dt_seconds, 240.0);
+                liver.glucagon_signal =
+                    Self::relax_value(liver.glucagon_signal, glucagon_target, dt_seconds, 240.0);
+            }
+        }
+
+        if let Some((_, urine_flow)) = kidneys_after {
+            let produced = (urine_flow * dt_seconds / 60.0).max(0.0);
+            if produced > 0.0 {
+                if let Some(bladder) = self.find_organ_typed_mut::<Bladder>() {
+                    bladder.volume_ml += produced;
+                }
+            }
+        }
+
+        if let Some(heart) = self.find_organ_typed_mut::<Heart>() {
+            if let Some(brain) = brain_after {
+                let mut tone_target =
+                    (brain.brainstem_drive - 0.5) * 1.2 + (brain.autonomic_variability - 0.5) * 0.8;
+                if let Some(spinal) = spinal_after {
+                    tone_target +=
+                        (spinal.sympathetic_outflow - spinal.parasympathetic_outflow) * 0.6;
+                }
+                heart.autonomic_tone = Self::relax_value(
+                    heart.autonomic_tone,
+                    tone_target.clamp(-1.0, 1.0),
+                    dt_seconds,
+                    40.0,
+                )
+                .clamp(-1.0, 1.0);
+            }
+        }
+
+        if let Some(pancreas) = pancreas_after {
+            if let Some(stomach) = self.find_organ_typed_mut::<Stomach>() {
+                let acid_current = stomach.acid_level as f32;
+                let acid_target = (acid_current - pancreas.somatostatin * 5.0).clamp(10.0, 100.0);
+                let acid_next = Self::relax_value(acid_current, acid_target, dt_seconds, 120.0);
+                stomach.acid_level = acid_next.round().clamp(0.0, 100.0) as u8;
+                stomach.vagal_tone = Self::relax_value(
+                    stomach.vagal_tone,
+                    (0.4 + pancreas.incretin_signal * 0.2).clamp(0.2, 0.9),
+                    dt_seconds,
+                    120.0,
+                );
+            }
+        }
+    }
+
+    #[inline]
+    fn relax_value(current: f32, target: f32, dt_seconds: f32, time_constant: f32) -> f32 {
+        if time_constant <= 0.0 {
+            target
+        } else {
+            let alpha = (dt_seconds / time_constant).clamp(0.0, 1.0);
+            current + (target - current) * alpha
         }
     }