feat(ffi): add bloodstream and bladder metrics API

- add C FFI enums MLBladderPhase, MLMetabolicState, MLPerfusionState
- add C FFI structs MLBloodstreamMetrics and MLBladderMetrics
- add ml_patient_bloodstream_metrics and ml_patient_bladder_metrics
  to populate metrics for a patient (mirrored in src/ffi.rs)
- update examples/c/ffi_example.c to print new metrics
- add tests for FFI metrics (tests/ffi.rs)

organ model expansions
- bloodstream: add metrics() snapshot and detailed physiology:
  plasma proteins/oncotic pressure, lymph return, RBC cohort tracking,
  erythropoiesis/clearance with HIF, iron/folate/B12 stores, platelets,
  coagulation/fibrinolysis, immune cell counts, complement, acid–base
- bladder: introduce adaptive compliance, reflex gating, cortical/voluntary
  modulators, safety indices; add metrics(), summary, and unit tests
- brain: add homeostatic drives (respiratory, thirst, hunger, thermo, pain),
  brainstem nuclei (NTS/RVLM/CVLM, nAmb/DMV, RTN), sleep cycle timing,
  cerebrovascular autoregulation; wire drives into autonomic control
- heart: add phase-based cycle (valves and atria), conduction system,
  RAAS regulation, improved coronary perfusion
- intestines: add micronutrient absorption feeding erythropoiesis

patient coupling
- expose Patient::bloodstream_metrics() and ::bladder_metrics()
- integrate new organ signals (kidney osmolality, spleen culling, liver
  proteins) and brain–lung/continence control pathways
- re-export BladderMetrics and BloodstreamMetrics in lib.rs

note
- existing FFI remains compatible; this is a surface addition
- ffi/medicallib.h kept in sync with src/ffi.rs

.gitea/workflows/ci-reusable.yml

@@ -79,10 +79,19 @@ jobs:
           CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER: x86_64-linux-gnu-g++
           CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER: x86_64-w64-mingw32-gcc
 
+      - name: Build demo app (Cross-Compile)
+        if: inputs.upload-artifacts && inputs.target != ''
+        run: cargo build --release --example demo_app --features demo-monitor --target=${{ inputs.target }}
+        env:
+          CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER: x86_64-linux-gnu-g++
+          CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER: x86_64-w64-mingw32-gcc
+
       - name: Extract version and create package
         if: inputs.upload-artifacts
         shell: bash
         run: |
+          set -euo pipefail
+
           VERSION=$(sed -n 's/^version\s*=\s*"\([^"]\+\)"/\1/p' Cargo.toml | head -n1)
           TARGET_ARCH="x86_64"
           TARGET_TRIPLE="${{ inputs.target }}"
@@ -90,17 +99,29 @@ jobs:
           # Determine package name and library extension based on target
           if [[ "$TARGET_TRIPLE" == "x86_64-unknown-linux-gnu" ]]; then
             PKG_BASENAME="medicallib_rust-v${VERSION}-${TARGET_ARCH}-unknown-linux-gnu"
+            DEMO_PKG_BASENAME="medicallib_demo_app-v${VERSION}-${TARGET_ARCH}-unknown-linux-gnu"
             LIB_NAME="libmedicallib_rust.so"
+            DEMO_BINARY_NAME="demo_app"
             ARCHIVE_TYPE="tar.gz"
           elif [[ "$TARGET_TRIPLE" == "x86_64-pc-windows-gnu" ]]; then
             PKG_BASENAME="medicallib_rust-v${VERSION}-${TARGET_ARCH}-pc-windows-gnu"
+            DEMO_PKG_BASENAME="medicallib_demo_app-v${VERSION}-${TARGET_ARCH}-pc-windows-gnu"
             LIB_NAME="medicallib_rust.dll"
+            DEMO_BINARY_NAME="demo_app.exe"
             ARCHIVE_TYPE="zip"
           else
             echo "::error::Unsupported target for packaging: $TARGET_TRIPLE"
             exit 1
           fi
 
+          DEMO_BINARY_SOURCE="target/${TARGET_TRIPLE}/release/examples/${DEMO_BINARY_NAME}"
+
+          if [[ ! -f "$DEMO_BINARY_SOURCE" ]]; then
+            echo "::error::Demo binary not found at $DEMO_BINARY_SOURCE"
+            exit 1
+          fi
+
+          mkdir -p dist
           PKG_DIR="dist/${PKG_BASENAME}"
           echo "Creating package ${PKG_BASENAME}..."
           mkdir -p "${PKG_DIR}/include" "${PKG_DIR}/lib"
@@ -109,11 +130,18 @@ jobs:
           cp ffi/medicallib.h "${PKG_DIR}/include/"
           cp "target/${TARGET_TRIPLE}/release/${LIB_NAME}" "${PKG_DIR}/lib/"
 
+          DEMO_DIR="dist/${DEMO_PKG_BASENAME}"
+          echo "Creating demo package ${DEMO_PKG_BASENAME}..."
+          mkdir -p "${DEMO_DIR}/bin"
+          cp "$DEMO_BINARY_SOURCE" "${DEMO_DIR}/bin/${DEMO_BINARY_NAME}"
+
           # Create the appropriate archive
           if [[ "$ARCHIVE_TYPE" == "tar.gz" ]]; then
             tar -C dist -czf "dist/${PKG_BASENAME}.tar.gz" "${PKG_BASENAME}"
+            tar -C dist -czf "dist/${DEMO_PKG_BASENAME}.tar.gz" "${DEMO_PKG_BASENAME}"
           elif [[ "$ARCHIVE_TYPE" == "zip" ]]; then
             (cd dist && zip -r9 "${PKG_BASENAME}.zip" "${PKG_BASENAME}")
+            (cd dist && zip -r9 "${DEMO_PKG_BASENAME}.zip" "${DEMO_PKG_BASENAME}")
           fi
 
       - name: Upload Artifact
@@ -123,4 +151,4 @@ jobs:
           # Create a unique name based on the target OS
           name: medicallib-rust-${{ contains(inputs.target, 'windows') && 'Windows' || 'Linux' }}-x86_64-${{ github.run_number }}
           path: dist/
-          if-no-files-found: error
+          if-no-files-found: error

.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" \

.gitignore

@@ -17,3 +17,5 @@ coverage/
 
 
 .claude/settings.local.json
+ffi/medicallib.h
+todo.md

CLAUDE.md

@@ -0,0 +1,99 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Build, Test, and Development Commands
+
+### Core workflows
+- **Build library**: `cargo build` (debug) or `cargo build --release` (optimized)
+- **Build FFI shared library**: `cargo build --release --features ffi` (generates C header via cbindgen)
+- **Run tests**: `cargo test` (all tests) or `cargo test --test <name>` (single integration test file)
+- **Run examples**: `cargo run --example usage`, `cargo run --example patient`, `cargo run --example tracing_demo`
+- **Run demo monitor**: `cargo run --example demo_app --features demo-monitor`
+- **Benchmarks**: `cargo bench` (runs Criterion benchmarks; results in `target/criterion/`)
+- **Format code**: `cargo fmt --all` (run before committing)
+- **Lint**: `cargo clippy --all-targets -- -D warnings` (enforce before committing)
+
+### Packaging binary distributions
+- **Linux/macOS**: Run `../scripts/package.sh [target-triple]` from `medicallib_rust/`
+- **Windows**: Run `..\scripts\package.ps1 [target-triple]` from `medicallib_rust\`
+- Artifacts placed in `medicallib_rust/dist/` as both `.tar.gz` and `.zip`
+
+## Architecture Overview
+
+### Core structure
+- **`src/lib.rs`**: Crate facade re-exporting public API (`Patient`, `Organ`, types, errors)
+- **`src/types.rs`**: Domain types (`Blood`, `BloodPressure`, `OrganType`, `VitalSign`)
+- **`src/error.rs`**: `MedicalError` enum using `thiserror`
+- **`src/patient.rs`**: `Patient` struct orchestrating `Vec<Box<dyn Organ>>` with inter-organ signal routing
+- **`src/organs/mod.rs`**: `Organ` trait and `OrganInfo`; per-organ modules (heart, lungs, brain, etc.)
+- **`src/ekg/mod.rs`**: EKG monitoring system with configurable leads
+- **`src/ffi.rs`**: C-compatible FFI layer (feature `ffi`); header auto-generated to `ffi/medicallib.h` by `build.rs` using cbindgen
+
+### Organ system
+- Each organ module implements the `Organ` trait (`id()`, `organ_type()`, `update(dt)`, `summary()`, `as_any()`, `as_any_mut()`)
+- `Patient` owns organs as trait objects, calls `update()` each tick, and routes signals between organs
+- Inter-organ communication examples:
+  - Lungs SpO2 → Heart rate adjustment
+  - Kidneys GFR → Bladder volume accumulation
+  - Brain autonomic signals → Heart rate variability and respiratory drive
+  - Bloodstream perfusion → multiple organ metabolic states
+
+### FFI boundary
+- **Opaque handle**: `MLPatient` pointer to boxed `Patient`
+- **Functions**: `ml_patient_new/free/update`, `ml_patient_summary`, `ml_patient_organ_summary`, `medicallib_bmi`
+- **Memory**: All returned strings allocated by Rust must be freed via `ml_string_free`
+- **Build script**: `build.rs` runs cbindgen when `--features ffi` is enabled, updates `ffi/medicallib.h` if changed
+- **Validation**: Any change to `src/ffi.rs` must be tested against `examples/c/ffi_example.c`
+
+### Testing and benchmarks
+- **Integration tests**: `tests/` directory (e.g., `tests/patient.rs`, `tests/ffi.rs`)
+- **Benchmarks**: `benches/heart.rs` uses Criterion; compare results across runs for performance regressions
+- **Unit tests**: In-module `#[cfg(test)]` blocks for focused invariants
+
+## Important Development Notes
+
+### When modifying FFI
+1. Edit `src/ffi.rs`
+2. Run `cargo build --features ffi` to regenerate `ffi/medicallib.h` via cbindgen
+3. Verify C example still compiles: `gcc -o ffi_example examples/c/ffi_example.c -L target/release -lmedicallib_rust`
+4. Update `cbindgen.toml` only if header generation settings need adjustment
+
+### Adding new organs
+1. Create module in `src/organs/<organ_name>.rs`
+2. Define struct implementing `Organ` trait
+3. Add module declaration and public re-export in `src/organs/mod.rs`
+4. Update `Patient` signal structs and `couple_organs()` method if inter-organ communication needed
+5. Add corresponding `OrganType` variant in `src/types.rs`
+6. Update FFI constants in `src/ffi.rs` if organ needs FFI exposure
+
+### Cargo features
+- **`serde`**: Enables serialization on public types
+- **`ffi`**: Exposes C ABI; triggers cbindgen in `build.rs`
+- **`demo-monitor`**: Required for `demo_app` example with colorized dashboard
+
+### CI workflows
+- GitHub Actions: `.github/workflows/ci.yml`
+- Gitea Actions: `.gitea/workflows/ci.yml`
+- Both run tests, clippy, formatting checks, and cross-platform builds
+
+## Key Patterns
+
+### Patient simulation loop
+```rust
+let mut patient = Patient::new("case-01")?.initialize_default();
+loop {
+    patient.update(dt_seconds);
+    let summary = patient.patient_summary();
+    // Process vitals...
+}
+```
+
+### Accessing specific organ
+```rust
+let heart = patient.find_organ_typed::<Heart>()?;
+println!("HR: {}", heart.heart_rate_bpm());
+```
+
+### Inter-organ signals
+Patient's `couple_organs()` method reads state from one organ (e.g., `Lungs::spo2_pct()`) and injects it into another (e.g., `Heart::receive_spo2_signal()`). Add new signal fields to the internal `*Signals` structs in `patient.rs` when coupling new organ interactions.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "medicallib_rust"
-version = "0.1.1"
+version = "0.3.0"
 edition = "2021"
 description = "MedicalSim core library rewrite in Rust: basic clinical calculations and types."
 authors = ["MedicalSim Team"]
@@ -14,6 +14,7 @@ crate-type = ["rlib", "cdylib"]
 default = []
 serde = ["dep:serde"]
 ffi = []
+demo-monitor = []
 
 [dependencies]
 thiserror = "1"
@@ -24,6 +25,11 @@ tracing = { version = "0.1", optional = true }
 criterion = { version = "0.5", default-features = false, features = ["cargo_bench_support"] }
 tracing-subscriber = { version = "0.3" }
 
+[[example]]
+name = "demo_app"
+path = "examples/demo_app.rs"
+required-features = ["demo-monitor"]
+
 [[bench]]
 name = "heart"
 harness = false

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)

docs/research_summary.md

@@ -0,0 +1,424 @@
+# Research Summary
+
+## Heart
+
+**Current simulation coverage**
+- Lumped ventricular pump tracks heart rate, arterial pressures, stroke volume, end-diastolic/systolic volumes, ejection fraction, contractility, preload/afterload and systemic vascular resistance, all coupled to cardiac output control (`src/organs/heart.rs:20-218`).
+- Baroreflex-like autonomic loop adjusts sinoatrial pacing, AV delay, vascular resistance and contractility while classifying rhythm states and arrhythmia burden (`src/organs/heart.rs:125-260`).
+- Coronary perfusion, myocardial oxygen supply/demand balance and stroke work are approximated through simple pressure-driven formulas (`src/organs/heart.rs:199-247`).
+
+**Physiology findings and observed gaps**
+- Model lacks explicit atrial chambers and valve mechanics, yet real hearts rely on four coordinated valves guiding flow through right/left atria and ventricles for one-way circulation and chamber filling.[1][2]
+- The cardiac cycle here omits staged systole/diastole events (atrial kick, isovolumic contraction/relaxation, rapid and reduced filling) that shape physiologic pressure-volume loops and heart sounds.[6]
+- Electrical conduction is reduced to SA node rate and an AV delay; physiological activation propagates through the bundle of His, bundle branches and Purkinje fibers to synchronize ventricular contraction and prevent dys-synchrony.[3]
+- Coronary supply is approximated by linear clamps, whereas left ventricular perfusion primarily occurs during diastole and depends on the aortic diastolic pressure minus LV end-diastolic pressure (coronary perfusion pressure).[4]
+- No endocrine or renal modulation is represented even though the renin-angiotensin-aldosterone system governs long-term blood pressure, volume status and sympathetic tone that in turn alter preload/afterload.[5]
+
+**Opportunities for improvement**
+- Introduce discrete atrial compartments and valve state logic (open/closed/regurgitant) to capture atrial kick, regurgitation, shunts and valve pathology scenarios.[1][2][6]
+- Extend conduction modeling with explicit His-Purkinje pathways, refractory periods and conduction delays to support bundle branch blocks, paced rhythms and ventricular dyssynchrony cases.[3]
+- Replace fixed coronary supply proxies with a diastolic perfusion model that references coronary perfusion pressure, heart rate-dependent diastolic time fraction and metabolic autoregulation.[4]
+- Layer hormonal regulation (e.g., RAAS-driven blood volume and vascular tone adjustments) atop existing autonomic controls to reflect chronic adaptations and pharmacologic interventions.[5]
+- Incorporate phase-based cardiac cycle state machine (atrial systole, isovolumic contraction, ejection, isovolumic relaxation, filling) to align simulated pressures/volumes with physiologic waveforms and auscultation cues.[6]
+
+**Sources**
+1. Cleveland Clinic - Heart Valves: What They Are and How They Work.[1]
+2. Cleveland Clinic - Chambers of the Heart.[2]
+3. Cleveland Clinic - Heart Conduction System.[3]
+4. StatPearls/NCBI - Coronary Perfusion Pressure.[4]
+5. Cleveland Clinic - Renin-Angiotensin-Aldosterone System (RAAS).[5]
+6. Merck Manual - Diagram of the Cardiac Cycle.[6]
+
+## Brain
+
+**Current simulation coverage**
+- Sleep-wake regulation couples circadian phase, homeostatic sleep pressure, and a stage state machine to drive cortical arousal, sleep stage transitions, and EEG proxies (`src/organs/brain.rs:54-219`).
+- Brainstem autonomic drive aggregates respiratory, pain, thirst, hunger, and thermoregulatory inputs to modulate sympathetic tone and variability (`src/organs/brain.rs:220-298`).
+- Cerebral perfusion, intracranial pressure, oxygenation, and cerebral blood flow are updated each tick via simplified clamp models tied to metabolic demand and autonomic output (`src/organs/brain.rs:299-373`).
+- Neurotransmitter proxies for glutamate, GABA, and dopamine modulate metabolic demand, arousal, seizure risk, and cognitive load (`src/organs/brain.rs:374-445`).
+- Consciousness index, seizure risk, and syncope propensity summarize global cortical state for downstream consumers (`src/organs/brain.rs:446-480`).
+
+**Physiology findings and observed gaps**
+- The sleep model advances through staged NREM and REM sequences but lacks representation of REM atonia, stage-specific EEG waveforms, and variable cycle length that characterize physiologic sleep architecture.[7]
+- Brainstem autonomic control is condensed into a single drive, omitting the reflex circuitry across nucleus tractus solitarii, ventrolateral medulla, and dorsal vagal outputs that regulate cardiovascular and respiratory coupling.[8]
+- Cerebral perfusion is linearized around a fixed CPP target, whereas real brains maintain ~50 mL/100 g/min flow using autoregulation across 60-160 mmHg CPP and react strongly to CO2 shifts, ischemic thresholds, and gray/white matter differences.[9]
+- Neurotransmitter variables float within heuristically clamped ranges, yet physiological excitatory-inhibitory balance depends on compartmentalized glutamatergic and GABAergic signaling, receptor kinetics, and astrocytic clearance that drive excitotoxic risk.[10][11]
+- Hunger, thirst, and thermoregulatory drives evolve independently of endocrine and hypothalamic feedback, diverging from integrated osmo- and volumetric sensing networks that coordinate angiotensin, vasopressin, and circadian cues.[12]
+
+**Opportunities for improvement**
+- Extend the sleep state machine with polysomnographic markers (e.g., REM atonia, spindle counts) and adaptive cycle timing informed by age or prior sleep debt to better match clinical sleep staging.[7]
+- Model key brainstem nuclei, allowing baroreflex, chemoreflex, and vagal pathways to feed back into cardiovascular and respiratory organs with latency and gain parameters derived from physiology texts.[8]
+- Replace static CPP/CBF clamps with an autoregulatory module that tracks vessel resistance, CO2 reactivity, and ischemic thresholds to capture plateau and failure zones of cerebral flow.[9]
+- Introduce neurotransmitter pools and receptor-specific dynamics (AMPA/NMDA, GABA_A/GABA_B) with astrocytic buffering to simulate excitotoxic cascades and pharmacologic interventions.[10][11]
+- Tie hunger, thirst, and thermoregulation drives to hypothalamic and endocrine mediators (e.g., ghrelin, vasopressin, angiotensin II) so fluid and energy balance respond to hormonal and circadian signals.[12]
+
+**Sources**
+7. StatPearls - Physiology of Sleep.[7]
+8. Frontiers in Physiology - Synaptic Mechanisms Underlying Elevated Sympathetic Outflow.[8]
+9. Stroke Manual - Regulation of Cerebral Blood Flow.[9]
+10. NCBI Bookshelf - Glutamate and Aspartate Are the Major Excitatory Transmitters in the Brain.[10]
+11. StatPearls - GABA Receptor.[11]
+12. Springer Review - Thirst: Neuroendocrine Regulation in Mammals.[12]
+
+## Bladder
+
+**Current simulation coverage**
+- Three-phase state machine (`Filling`, `Voiding`, `PostVoidRefractory`) governs storage dynamics, reflex triggers, and refractory timing to avoid immediate reactivation (`src/organs/bladder.rs:5-133`).
+- Afferent stretch and urgency perception derive from volume thresholds and compliance normalization so filling maps to sensation (`src/organs/bladder.rs:58-96`).
+- Autonomic (parasympathetic/sympathetic) and somatic drives converge toward phase-specific targets to coordinate detrusor activation with internal and external sphincter tone (`src/organs/bladder.rs:34-88`).
+- Pressure dynamics blend passive compliance, abdominal baseline, and detrusor contraction to clamp intravesical pressure during filling and voiding (`src/organs/bladder.rs:97-147`).
+- Cortical inhibition and pontine guarding/void loops drive hypogastric, pudendal, and detrusor outputs with metrics exposed through `Bladder::metrics` and FFI for voluntary continence modeling (`src/organs/bladder.rs:170-452`; `src/ffi.rs`).[14][15]
+
+**Physiology findings and observed gaps**
+- Compliance and capacity stay fixed, yet healthy bladders accommodate volume with minimal pressure rise and elevate detrusor pressure only near voiding; sustained storage pressures above safety limits threaten upper tract health.[13][17]
+- Guarding-loop magnitudes still use heuristic gains; calibrating cortical-pontine gating and pudendal discharge against human EMG and urodynamic datasets is needed to capture pathology-specific continence changes.[14][15]
+- Urgency is volume-only, whereas mature continence uses cortical oversight of the pontine micturition center to suppress reflex voiding until socially appropriate.[14][15]
+- Internal and external sphincters are merged, despite smooth-muscle alpha-adrenergic tone and striated, pudendal-innervated control failing independently in disease.[16]
+- Urge and micturition thresholds remain static, even though typical reflex activation spans roughly 250-400 mL and shifts with age, hydration, and neurologic status.[14][18]
+
+**Opportunities for improvement**
+- Replace static compliance with a pressure-volume curve that adapts to bladder history, hydration, or pathology while tracking detrusor pressure against safety limits.[13][17]
+- Model explicit guarding and voiding reflex pathways (pontine storage/micturition centers, hypogastric, pelvic, pudendal nerves) so autonomic and somatic loops respond to systemic inputs.[14][15]
+- Separate internal and external sphincter models with receptor-specific pharmacology to simulate outlet obstruction, pelvic floor dysfunction, or targeted therapies.[16]
+- Couple urgency and continence to cortical and behavioral inputs so developmental milestones, stress, or voluntary suppression can modulate voiding thresholds.[14]
+- Parameterize urge and micturition thresholds by age, renal output, or neurologic status to span pediatric, neurogenic, and overactive bladder scenarios.[18]
+
+**Sources**
+13. StatPearls - Urodynamic Testing and Interpretation.[13]
+14. StatPearls - Physiology, Urination.[14]
+15. Nature Reviews Neuroscience - The Neural Control of Micturition.[15]
+16. StatPearls - Anatomy of the bladder wall and sphincter receptor distributions.[16]
+17. Physiological Reviews - Detrusor mechanics and compliance regulation in health and disease.[17]
+18. Indiana University Pressbooks - Typical micturition reflex thresholds and nerve pathways.[18]
+
+## Bloodstream
+
+**Current simulation coverage**
+- Maintains plasma volume, red cell volume, total circulating volume, hematocrit, and hemoglobin while syncing cardiac output, mean arterial pressure, and oxygen saturation targets (`src/organs/bloodstream.rs:18-170`).
+- Computes arterial/venous oxygen content, delivery, consumption, supply-demand ratio, and circulation time, feeding perfusion and metabolic state classifiers (`src/organs/bloodstream.rs:70-210`).
+- Aggregates metabolic waste load, lactate, pH proxy, temperature, glucose, and clearance indices for renal and hepatic pathways (`src/organs/bloodstream.rs:120-270`).
+- Maintains albumin and globulin pools with hepatic synthesis targets, Starling oncotic pressure terms, lymphatic return modulation, and edema risk scoring in the plasma volume controller (`src/organs/bloodstream.rs:170-230`).[19][20]
+- Tracks erythrocyte age cohorts with spleen-mediated clearance, platelet tagging, and reticuloendothelial iron recycling feeding hepatic stores and transferrin saturation metrics (`src/organs/bloodstream.rs:240-320`).[21][22]
+- Couples hypoxia-inducible EPO drive with micronutrient sufficiency (iron saturation, folate, cobalamin) to gate erythropoiesis and reticulocyte surges (`src/organs/bloodstream.rs:320-360`).[23][24]
+- Integrates platelet mass, coagulation factor activity, fibrinogen dynamics, fibrinolysis feedback, and thrombosis/bleeding risk indices modulated by splenic platelet reservoirs (`src/organs/bloodstream.rs:360-820`).[25][26]
+- Drives leukocyte, differential counts, complement activation, and inflammation indices from spleen immune activity for downstream organs and telemetry surfaces (`src/organs/bloodstream.rs:720-860`).[27][28]
+- Replaces the static pH clamp with bicarbonate, base excess, anion gap, arterial PCO2, and lactate guided respiratory/renal compensation to update systemic pH targets (`src/organs/bloodstream.rs:851-910`).[29][30]
+- Sets ventilation-perfusion, pulmonary gas exchange targets, and renal/hepatic clearance goals to coordinate with lung and kidney controllers (`src/organs/bloodstream.rs:150-310`).
+
+**Physiology findings and observed gaps**
+- Acute-phase shifts, capillary leak syndromes, and protein-losing pathologies are not yet parameterized, limiting how the new oncotic module responds to inflammation or liver dysfunction.[19][20]
+- Cohort-based erythrocyte turnover lacks explicit macrophage phenotypes, hemolysis triggers, or disease-specific remodeling compared with observed splenic clearance pathways.[21][22]
+- Hemostasis dynamics still rely on generic activation/fibrinolysis curves and omit factor-specific deficiencies, platelet granule secretion, and transfusion or antithrombotic therapy responses.[25][26]
+- Leukocyte modeling excludes adaptive lymphocyte subsets, cytokine networks, and pathogen-specific complement cascades necessary for sepsis or immunosuppression case studies.[27][28]
+- Acid-base controller does not yet simulate strong ion difference, renal ammoniagenesis, or mixed metabolic-respiratory disorders beyond linear compensation curves.[29][30]
+
+**Opportunities for improvement**
+- Calibrate acute-phase protein responses and capillary permeability effects within the new oncotic and lymphatic model to capture edema and hypoalbuminemia scenarios.[19][20]
+- Add macrophage/monocyte phenotypes, hemolysis triggers, and disease-specific erythrocyte remodeling pathways to the cohort turnover logic.[21][22]
+- Expand coagulation modeling with von Willebrand interactions, factor-specific deficits, platelet granule release, and transfusion protocols to reflect trauma and anticoagulation management.[25][26]
+- Introduce cytokine-mediated leukocyte recruitment, adaptive immune compartments, and pathogen load feedback to enrich inflammation signaling.[27][28]
+- Extend acid-base buffering with strong ion difference, renal ammoniagenesis, and ventilatory control loops tied to organ dysfunction scenarios.[29][30]
+
+**Sources**
+19. Hahn RG. Plasma Volume Oscillations Induced by Hyperoncotic Albumin Infusion. Life (Basel). 2025;15(1):111.[19]
+20. Wu JW, Mack GW. Effect of lymphatic outflow on albumin flux from exercising skeletal muscle. J Appl Physiol. 2001;90(5):1912-1918.[20]
+21. Vautrinot J, Poole AW. Platelets mediate the clearance of senescent red blood cells. Blood. 2024;143(7):800-812.[21]
+22. Mohandas N, Gallagher PG. Accelerated aging of red blood cells in pathologic states. Blood. 2021;137(18):2429-2437.[22]
+23. Peng W, Zhan Y, Yu T, et al. Regulation of erythropoiesis by hypoxia-inducible factors and nutrient availability. BMC Med. 2024;22(1):194.[23]
+24. Coneyworth LJ, Ford D, Mathers JC. Vitamin B12 and folate interactions in erythropoiesis and neurological function. Nutrients. 2023;15(5):1120.[24]
+25. Real-time imaging of platelet-initiated plasma clot formation and lysis unveils distinct impacts of anticoagulants. Res Pract Thromb Haemost. 2024.[25]
+26. Thrombopoiesis regulation by hepatic thrombopoietin and splenic clearance ensures platelet homeostasis. J Thromb Thrombolysis. 2025.[26]
+27. The role of complement in thromboinflammation. J Trauma Acute Care Surg. 2024.[27]
+28. Complement orchestrates innate immune cell differentiation in sepsis. iScience. 2025.[28]
+29. Limitations of serum bicarbonate in the ED for diagnosing acid-base disorders. J Emerg Med. 2024.[29]
+30. A physiology-based approach to acid-base disorders. BJA Educ. 2024.[30]
+
+## Esophagus
+
+**Current simulation coverage**
+- State machine cycles swallow initiation, primary/secondary peristalsis, clearing, and reflux exposure while tracking bolus volume and peristaltic progress (`src/organs/esophagus.rs:105-218`).
+- Swallow drive integrates oral dryness and mucosal irritation to retune swallow intervals, vagal tone, and peristaltic strength (`src/organs/esophagus.rs:113-131`).
+- Lower and upper esophageal sphincter tones adapt via stage-specific modifiers and approach dynamics (`src/organs/esophagus.rs:133-150`).
+- Hiatal pressure gradient and reflux propensity are blended with sphincter tone to govern reflux transitions and event rates (`src/organs/esophagus.rs:153-244`).
+- Acid balance updates saliva buffering, mucosal integrity, luminal pH, and estimated reflux frequency each tick (`src/organs/esophagus.rs:221-249`).
+
+**Physiology findings and observed gaps**
+- Physiologic swallowing relies on proximal striated and distal smooth muscle with deglutitive inhibition orchestrated by nucleus ambiguus and enteric circuits, but the model uses a single peristaltic strength scalar without segmental timing.[26][27]
+- Primary peristaltic waves in healthy adults traverse ~3-6 cm/s with durations modulated by bolus consistency and posture, whereas wave speeds and bolus emptying here stay fixed regardless of load or position.[27][28]
+- Esophageal acid clearance depends on saliva-stimulated secondary swallows, gravity assistance, and esophageal shortening; current logic omits clearance latency, posture effects, and bicarbonate secretion variability.[29][30]
+- The anti-reflux barrier combines intrinsic LES tone with diaphragmatic crural pinch and transient LES relaxations triggered by gastric distention, yet the simulation only scales a hiatal gradient without diaphragmatic coupling or TLESR triggers.[31]
+
+**Opportunities for improvement**
+- Split the tube into proximal striated and distal smooth segments with deglutitive inhibition timing and enteric reflex loops to cover neurogenic dysphagia and achalasia variants.[26][27]
+- Parameterize peristaltic velocity and bolus transport against meal consistency, volume, and posture, and allow failed primary waves to spawn variable secondary peristalsis.[27][28]
+- Extend acid clearance to track saliva flow, sequential swallows, gravitational drainage, and bicarbonate buffering so supine, xerostomia, and nocturnal reflux scenarios emerge.[29][30]
+- Model diaphragmatic contributions and transient LES relaxation triggers tied to gastric load, belching, and vagal reflexes to enable GERD, hiatal hernia, and fundoplication training cases.[31]
+
+**Sources**
+26. StatPearls - Physiology, Esophagus.[26]
+27. GI Motility Online - Physiology of esophageal motility.[27]
+28. TSRA Primer - Esophageal Motility & Function Testing.[28]
+29. PubMed - Esophageal acid clearance testing and clinical significance.[29]
+30. PubMed - Salivary bicarbonate secretion in gastroesophageal reflux disease.[30]
+31. Gastroenterology & Hepatology - Gastroesophageal Reflux Disease: Pathophysiology.[31]
+## Gallbladder
+
+**Current simulation coverage**
+- Tracks bile reservoir dynamics (volume, acid concentration, hepatic inflow, bile acid pool, recycling efficiency, mucosal absorption, and gallstone index) within the gallbladder struct (`src/organs/gallbladder.rs:24-102`).
+- Meal-drive controller sequences fasting clock, meal signal decay, CCK level targeting, and vagal tone adjustments to gate activation cues (`src/organs/gallbladder.rs:103-145`).
+- Phase state machine (Filling -> Primed -> Contraction -> Expulsion -> Recovery) tunes sphincter of Oddi tone and bile outflow during each stage (`src/organs/gallbladder.rs:146-208`).
+- Bile pool updater concentrates or dilutes bile, clamps cholesterol saturation, and updates the gallstone nucleation index for downstream risk reporting (`src/organs/gallbladder.rs:209-233`).
+
+**Physiology findings and observed gaps**
+- Real gallbladders absorb about 90% of bile water during fasting and eject 50-75% of their contents when CCK triggers contraction alongside sphincter of Oddi relaxation; the model uses fixed constants rather than hormone- and pressure-driven coupling.[32]
+- Interdigestive motility features motilin-driven emptying pulses and sphincter phasic contractions preceding migrating motor complex phase III, but the simulation lacks motilin signaling and oscillatory sphincter behavior.[33][37]
+- Enterohepatic circulation recycles a roughly 3 g bile acid pool 4-12 times per day with 95% ileal reabsorption; the current model does not exchange bile acids with intestinal or hepatic compartments, obscuring pool depletion or malabsorption states.[34]
+- Gallstone formation requires cholesterol supersaturation, mucin-mediated nucleation, and gallbladder stasis, whereas the simulation reduces risk to a single scalar that omits mucin dynamics, bile composition shifts, and sludge progression.[35][36]
+
+**Opportunities for improvement**
+- Replace fixed absorption and outflow clamps with transport models that concentrate bile via electrolyte exchange, allow fractional emptying, and coordinate sphincter relaxation with CCK levels to match post-prandial kinetics.[32]
+- Introduce motilin and vagovagal reflex inputs that trigger intermittent fasting-phase contractions and modulate sphincter of Oddi tone, enabling biliary dyskinesia and post-cholecystectomy motility scenarios.[33][37]
+- Link the gallbladder bile acid pool to a shared enterohepatic circuit with hepatic synthesis, intestinal reuptake, and fecal losses so bile acid sequestrants or ileal disease deplete the pool and alter digestion.[34]
+- Expand the gallstone framework to track bile lipid composition, mucin secretion, sludge accumulation, and stasis duration to differentiate cholesterol versus pigment stone risks and evaluate preventive therapies.[35][36]
+
+**Sources**
+32. Merck Manual Professional Edition - Overview of Biliary Function.[32]
+33. PubMed - Cyclic motility of the sphincter of Oddi.[33]
+34. PMC - Nuclear receptor control of enterohepatic circulation.[34]
+35. StatPearls - Gallstones (Cholelithiasis).[35]
+36. PubMed - Role of gallbladder mucin in pathophysiology of gallstones.[36]
+37. PubMed - Differential effects of motilin on interdigestive motility.[37]
+
+
+
+## Intestines
+
+**Current simulation coverage**
+- Maintains macronutrient absorption, electrolyte reclamation, water reuptake, bile acid recycling, microbiome balance, and inflammatory tone fields within the intestinal struct (`src/organs/intestines.rs:15-113`).
+- Internal feeding clock injects nutrient loads, updates motilin and GLP-1 proxies, and drives phase transitions among interdigestive, fed, MMC, ileal brake, and dysmotility states (`src/organs/intestines.rs:111-173`).
+- Motility updater blends peristaltic and segmentation indices, lumen volume, and enteric tone to set motility_index, segmentation_index, and mmc_activity scaling (`src/organs/intestines.rs:174-197`).
+- Absorption, microbiome, and mucosal routines convert nutrient energy into carbohydrate/fat/protein uptake, adjust electrolyte-water handling, SCFA production, pH, mucosal integrity, inflammation, and bile acid recirculation (`src/organs/intestines.rs:198-287`).
+
+**Physiology findings and observed gaps**
+- Physiologically the small intestine absorbs ~95% of carbohydrates and proteins, 90% of water, and recovers bile salts in the ileum while the colon reclaims the last 1-2 L with electrolyte-coupled transport; the model uses fixed rates without segment-specific transporters or fluid budgets.[38][43]
+- MMC cycles repeat every ~90-120 minutes with distinct Phase I-IV patterns governed by motilin pulses that prevent bacterial overgrowth; simulation only tracks a scalar mmc_activity and phase enum without propagating cyclical motor waves or bacterial clearing.[39]
+- Ileal brake hormones GLP-1 and PYY respond to distal nutrient exposure to slow gastric emptying and upper gut motility, yet the model lacks nutrient-specific triggers or feedback to upstream organs despite tracking hormone_glp1.[40][41]
+- Terminal ileum bile-salt reabsorption and vitamin B12 uptake depend on mucosal transporters and flow, whereas the simulation clamps bile acid recirculation to a motility-dependent target without hepatic pool linkage or malabsorption states.[38]
+- Microbiota ferment 30 g/day of carbohydrates to produce ~300 mmol SCFAs that drive sodium/water absorption and fuel colonocytes; current logic approximates SCFA generation linearly from fiber load and does not expose ion transport coupling or microbial community shifts.[42][43]
+
+**Opportunities for improvement**
+- Partition the intestine into duodenal, jejunal, ileal, and colonic segments with transporter-limited nutrient and water absorption, dynamic bile acid pools, and luminal fluid accounting to capture malabsorption and diarrhea phenotypes.[38][43]
+- Implement MMC phase cycling driven by motilin bursts with spatial propagation, allowing fasting length, vagal tone, or opioids to disrupt waves and precipitate SIBO scenarios.[39]
+- Couple nutrient sensing to GLP-1/PYY secretion, feeding-clock intervals, and feedback onto stomach, pancreas, and gallbladder controllers so fat vs carbohydrate loads elicit distinct ileal brake responses.[40][41]
+- Expand microbiome modeling to track fiber species, SCFA spectra, lumen pH, and epithelial fuel utilization, enabling dysbiosis, antibiotic, or prebiotic interventions to shift absorption and mucosal integrity.[42]
+
+**Sources**
+38. StatPearls - Physiology, Small Bowel.[38]
+39. Gastroenterology & Hepatology Board Review - Small Intestinal Motility Disorders.[39]
+40. PMC - Effects of GLP-1 and incretin-based therapies on gastrointestinal motor function.[40]
+41. PubMed - PYY and GLP-1 contribute to feedback inhibition from the canine ileum and colon.[41]
+42. PubMed - Colonic health: fermentation and short chain fatty acids.[42]
+43. PubMed - Colonic absorption: the importance of short chain fatty acids in man.[43]
+## Kidneys
+
+**Current simulation coverage**
+- Tracks glomerular filtration rate, renal plasma flow, filtration fraction, osmolality metrics, and endocrine proxies within the kidney struct (`src/organs/kidneys.rs:14-94`).
+- Autoregulation routine classifies perfusion into Autoregulated, Hypoperfused, Hyperperfused, or Obstructed states based on renal plasma flow and obstruction heuristics (`src/organs/kidneys.rs:100-151`).
+- Perfusion and hormonal controllers adjust sympathetic tone, renin release, aldosterone drive, and ADH sensitivity in response to plasma volume and osmolality (`src/organs/kidneys.rs:115-151`).
+- Tubular handling, acid-base, and erythropoietin updates set sodium reabsorption, potassium and urea excretion, urine flow/osmolality, serum osmolality, plasma volume, and EPO secretion each tick (`src/organs/kidneys.rs:152-231`).
+
+**Physiology findings and observed gaps**
+- Healthy kidneys filter ~120 mL/min from ~600-720 mL/min renal plasma flow and hold GFR constant across 80-180 mmHg via coupled myogenic and macula densa feedback; the model uses fixed thresholds without afferent/efferent resistance dynamics or nephron flow sensing.[44][45]
+- Segmental transport normally reclaims ~65-70% of sodium and water in the proximal tubule, ~25% in Henle segments, and fine-tunes electrolytes distally; the simulation collapses everything into a single tubular reabsorption fraction, limiting malabsorption or diuretic scenarios.[46]
+- Urine concentration depends on the countercurrent multiplier, medullary gradient maintenance, and ADH-gated aquaporins to span ~50-1200 mOsm; current clamps ignore gradient washout and aquaporin trafficking.[47]
+- Renal acid-base balance requires bicarbonate reclamation plus ammonium and titratable acid excretion across segments, whereas the model condenses compensation into a single acid_base_balance scalar.[48]
+- Juxtaglomerular renin release integrates baroreceptor, macula densa, and sympathetic inputs, yet renin and aldosterone here follow simplified algebra that cannot capture RAAS pharmacology or dysregulation.[49]
+- Erythropoietin secretion arises from hypoxia-responsive peritubular interstitial cells and intercalated cells, but the simulation ties EPO to a coarse renal oxygenation clamp only.[50]
+
+**Opportunities for improvement**
+- Add afferent/efferent arteriole resistance modeling with myogenic and tubuloglomerular feedback loops plus RAAS modulation to reproduce autoregulatory plateaus and pressure-natriuresis shifts.[44][45][49]
+- Break the nephron into proximal, loop, distal, and collecting segments with transporter-limited sodium/water reabsorption and endocrine regulation, enabling segment-specific injuries and diuretic effects.[46][47]
+- Implement countercurrent multiplier/ exchanger dynamics with medullary gradient washout, aquaporin trafficking, and osmolality feedback to simulate diabetes insipidus, SIADH, or osmotic diuresis.[47]
+- Expand acid-base handling to compute bicarbonate reclamation, titratable acid, and ammonium excretion, linking to respiratory compensation and chronic kidney disease buffering limits.[48]
+- Drive erythropoietin output from local oxygen tension, fibrosis, and inflammatory cues to support anemia-of-CKD progression and ESA therapy responses.[50]
+
+**Sources**
+44. StatPearls - Physiology, Glomerular Filtration Rate.[44]
+45. PubMed - Renal autoregulation in health and disease.[45]
+46. PMC - Mechanistic insights into renal ion and water transport in the distal nephron.[46]
+47. Kidney: Physiology of the Tubular Reabsorption.[47]
+48. PubMed - Acid-Base Homeostasis.[48]
+49. StatPearls - Physiology, Renin Angiotensin System.[49]
+50. PubMed - Renal epithelium regulates erythropoiesis via HIF-dependent suppression of erythropoietin.[50]
+
+## Liver
+
+**Current simulation coverage**
+- Multi-state hepatic controller transitions between postabsorptive, fed, fasting, acute phase, and regenerating modes while updating glycogen, lipids, ammonia clearance, and hormone signals each tick (`src/organs/liver.rs:1`).
+- Meal-driven hormone routine modulates insulin, glucagon, and cortisol proxies alongside glycogenolysis, gluconeogenesis, and lipogenesis rates to shape fuel handling (`src/organs/liver.rs:73`).
+- Bile synthesis, secretion, detox capacity, Kupffer activation, and portal hemodynamics are adjusted through bile/enzymatic update loops (`src/organs/liver.rs:176`).
+- Protein synthesis block tracks albumin, clotting factor output, and hepatic fat fraction to summarize synthetic function (`src/organs/liver.rs:214`).
+
+**Physiology findings and observed gaps**
+- The simulation uses static portal and arterial flow clamps, but healthy livers receive ~80% portal venous inflow with a hepatic arterial buffer response that compensates dynamically for portal changes.[51][52]
+- Hepatic lobules exhibit periportal-pericentral zonation governing carbohydrate, lipid, and ammonia metabolism, whereas the model treats hepatocytes as a single compartment.[55]
+- Enterohepatic bile acid cycling involves secretion, ileal reabsorption, and hepatic reconjugation; current logic generates bile locally without coupling to intestinal pools or transporter limits.[54]
+- Fasting gluconeogenesis in humans scales from ~1 to 2 mg·kg⁻¹·min⁻¹ with prolonged fasts driving Cori-cycle recycling; fixed-rate clamps in the model underrepresent these range shifts.[56]
+- Kupffer cell activation drives cytokine and acute phase cascades based on pattern-recognition signaling; present implementation raises a scalar without linking to inflammatory inputs or downstream APR protein switches.[53]
+
+**Opportunities for improvement**
+- Implement dual-inflow hemodynamics with arterial buffer feedback and sinusoidal resistance modulation to recreate portal hypertension and ischemia scenarios.[51][52]
+- Add zonated hepatocyte segments with zone-specific enzyme sets (urea cycle periportal, glycolysis/pericentral lipogenesis) to capture differential injury and drug metabolism.[55]
+- Couple bile acid production to an enterohepatic pool shared with the intestines, including transporter saturation and fecal loss terms for cholestasis modeling.[54]
+- Replace fixed gluconeogenesis/glycogenolysis clamps with hormone- and substrate-responsive pathways calibrated to fasting studies, enabling hypoglycemia and stress testing.[56]
+- Expand Kupffer signaling to accept pathogen/toxin inputs and drive acute phase protein synthesis, oxidative stress, and stellate activation responses.[53]
+
+**Sources**
+51. World Journal of Gastroenterology - Liver hemodynamics reference values.[51]
+52. American Society of Anesthesiologists - Hepatic arterial buffer response overview.[52]
+53. StatPearls - Physiology, Liver.[53]
+54. StatPearls - Physiology, Bile Secretion.[54]
+55. Elsevier - Zonation of hepatic fatty acid metabolism review.[55]
+56. American Journal of Physiology - Gluconeogenesis and the Cori cycle in prolonged fasting.[56]
+
+## Lungs
+
+**Current simulation coverage**
+- Breathing phase loop advances inhalation, exhalation, and pause states while updating diaphragm kinematics, tidal volume, and respiratory rate targets (`src/organs/lungs.rs:37`).
+- Ventilatory state machine shifts between resting, hypercapnic, hypoxic, exercise, and distress modes with chemoreceptor and muscle drive scalars (`src/organs/lungs.rs:108`).
+- Gas exchange routine adjusts alveolar PO₂/PCO₂, shunt fraction, SpO₂, and CO₂ elimination based on ventilation and metabolic demand (`src/organs/lungs.rs:246`).
+- Pulmonary vascular block tunes pulmonary artery and wedge pressures along with V/Q ratio and dead space fractions (`src/organs/lungs.rs:292`).
+
+**Physiology findings and observed gaps**
+- The model collapses regional ventilation/perfusion into single ratios even though human lungs show gravity-dependent gradients (low V/Q at bases, higher at apices) crucial for hypoxemia phenotyping.[57]
+- Lung compliance is treated as a scalar, yet in vivo compliance reflects surfactant dynamics, chest wall interaction, and disease-specific hysteresis that shift the pressure–volume curve.[58]
+- Diffusing capacity is estimated by linear clamps, whereas normal DL(O₂) ≈ 20–25 ml·min⁻¹·mmHg⁻¹ and increases threefold with exercise due to capillary recruitment—effects absent in the current abstraction.[59][60]
+- Chemoreceptor control is condensed into a single drive, but central and peripheral chemoreceptors differ in latency and CO₂/O₂ sensitivity; blended logic masks disorders like carotid body failure.[61]
+- Distress flag drives shunt fraction heuristics without modeling airway resistance, surfactant loss, or V/Q scatter that define ARDS phenotypes.[57]
+
+**Opportunities for improvement**
+- Introduce multi-compartment V/Q modeling (apex/mid/base) with gravity and posture modifiers to support shunt-vs-dead-space diagnostics.[57]
+- Track static and dynamic compliance separately with surfactant depletion, fibrosis, and chest wall modifiers to capture recruitment and hysteresis behavior.[58]
+- Add diffusing-capacity calculations tied to capillary blood volume and exercise state so DL and end-tidal gradients respond to flow changes.[59][60]
+- Split chemoreceptor control into central CO₂/pH and peripheral O₂/CO₂ pathways with time constants and hypoxic potentiation to emulate ventilatory drive disorders.[61]
+- Expand distress modeling to include airway resistance, alveolar flooding, and recruitable units rather than a single shunt scalar.[57]
+
+**Sources**
+57. StatPearls - Physiology, Pulmonary Ventilation and Perfusion.[57]
+58. StatPearls - Physiology, Pulmonary Compliance.[58]
+59. MedMuv - Diffusion capacity of the lungs for oxygen.[59]
+60. European Respiratory Journal - Reference values for alveolar membrane diffusion capacity.[60]
+61. NCBI Bookshelf - Chemical Regulation of Respiration.[61]
+
+## Pancreas
+
+**Current simulation coverage**
+- State machine toggles basal, postprandial anabolic, hypoglycemic counterregulation, and beta-cell exhaustion modes while updating endocrine outputs (`src/organs/pancreas.rs:15`).
+- Meal simulator modulates glucose, incretin, and autonomic tone inputs to drive insulin, glucagon, somatostatin, and pancreatic polypeptide responses (`src/organs/pancreas.rs:55`).
+- Exocrine routines adjust enzyme secretion, bicarbonate output, acinar flow, and ductal pressure against incretin and autonomic cues (`src/organs/pancreas.rs:146`).
+- Chronic stress logic tracks beta-cell mass fraction and islet stress index to approximate long-term endocrine reserve (`src/organs/pancreas.rs:119`).
+
+**Physiology findings and observed gaps**
+- Ductal secretion depends on CFTR-mediated chloride/bicarbonate exchange achieving ~140 mM bicarbonate, yet the model lacks CFTR or flow-dependent coupling to maintain alkaline secretion.[62][63]
+- Incretin physiology (GLP-1/GIP) enhances glucose-stimulated insulin secretion and suppresses glucagon in a glucose-dependent fashion; current logic uses fixed incretin boosts without receptor kinetics.[64]
+- Chronic ER stress triggers reversible beta-cell de-differentiation before apoptosis, implying nonlinear mass dynamics beyond the linear decay implemented here.[65]
+- Enzyme composition adapts to macronutrient content (e.g., fat increases lipase output), but the simulation scales enzymes uniformly with incretin tone.[66]
+- Autonomic tone integrates vagal and sympathetic signaling that co-modulate endocrine and exocrine release; the single autonomic scalar omits frequency-specific vagal bursts and adrenergic suppression.[62]
+
+**Opportunities for improvement**
+- Add CFTR and SLC26 exchanger models with flow-dependent secretion and sensitivity to ductal pressure to emulate cystic fibrosis and pancreatitis.[62][63]
+- Implement incretin receptor kinetics with glucose thresholds and pharmacologic agonist profiles to study GLP-1 therapies.[64]
+- Model beta-cell stress with reversible identity states and thresholds for apoptosis, capturing adaptation vs. failure under chronic load.[65]
+- Differentiate enzyme synthesis pathways for amylase, proteases, and lipase responding to nutrient sensing and CCK feedback.[66]
+- Split autonomic inputs into vagal (bursting) and sympathetic (tonic) components to simulate stress-induced endocrine shifts.[62]
+
+**Sources**
+62. Cells - Bicarbonate Transport in the Exocrine Pancreas.[62]
+63. NCBI Bookshelf - Water and Ion Secretion from the Pancreatic Ductal System.[63]
+64. Diabetes - Multiple actions of GLP-1 on glucose-stimulated insulin secretion.[64]
+65. Cell Reports - Adaptation to chronic ER stress enforces beta-cell plasticity.[65]
+66. Pancreapedia - Secretion of the human exocrine pancreas in health and disease.[66]
+
+## Spleen
+
+**Current simulation coverage**
+- Splenic controller tracks immune activity, red pulp volume, platelet reservoir, sympathetic tone, cytokine output, and contraction fraction states (`src/organs/spleen.rs:13`).
+- State machine transitions among homeostatic, sympathetic contraction, hyperimmune activation, sequestration, and hypofunction modes driving pulp volumes and cytokines (`src/organs/spleen.rs:45`).
+- Contraction and immune routines update platelet release, erythrocyte culling, IgM production, and cytokine signals each tick (`src/organs/spleen.rs:72`).
+
+**Physiology findings and observed gaps**
+- Real spleens hold ~1/3 of circulating platelets and mobilize contracted red pulp during sympathetic surges; model contraction lacks integration with circulating platelet counts or venous return.[69][71]
+- White pulp architecture (periarteriolar lymphoid sheaths, marginal zone B cells) drives rapid responses to blood-borne antigens, whereas simulation aggregates immune activity into a single scalar.[67][70]
+- Splenic contraction alters hemoglobin and hematocrit during apnea/diving; current logic adjusts reservoir without systemic hematologic feedbacks.[69]
+- Marginal zone B cells and macrophages maintain humoral defense; absence of compartment-specific responses limits modeling of asplenia risks.[70]
+- Chronic splenomegaly and hypersplenism alter sequestration thresholds; static volume clamps miss disease-dependent compliance changes.[71]
+
+**Opportunities for improvement**
+- Couple splenic reservoir to systemic platelet/erythrocyte pools and venous return to reflect contraction-induced hematologic shifts.[69][71]
+- Represent white pulp, marginal zone, and red pulp compartments with discrete immune cell populations and activation kinetics.[67][70]
+- Add sympathetic burst inputs tied to cardiovascular simulations to trigger dynamic spleen contraction during exercise or hemorrhage.[69]
+- Model splenic compliance changes in infiltrative disease to capture hypersplenism and cytopenia risks.[71]
+- Track antigen capture and antibody production timelines to assess vaccine efficacy in asplenic states.[67][70]
+
+**Sources**
+67. StatPearls - Physiology, Spleen.[67]
+68. Kenhub - Microscopic anatomy of the spleen.[68]
+69. Journal of Applied Physiology - Spleen as an erythrocyte reservoir during diving responses.[69]
+70. Journal of Immunology - B cells are crucial for splenic marginal zone development.[70]
+71. StatPearls - Splenomegaly.[71]
+
+## Spinal Cord
+
+**Current simulation coverage**
+- Spinal cord organ tracks signal integrity, ascending/descending conduction velocities, reflex gain, autonomic outflows, locomotor CPG tone, nociceptive facilitation, and perfusion metrics (`src/organs/spinal_cord.rs:14`).
+- State machine differentiates intact, concussed, inflammatory, ischemic, and neurogenic shock presentations with corresponding autonomic targets (`src/organs/spinal_cord.rs:48`).
+- Integrity and perfusion routines update glial scar index, inflammation, sympathetic/parasympathetic outputs, and locomotor CPG tone over time (`src/organs/spinal_cord.rs:71`).
+
+**Physiology findings and observed gaps**
+- Acute SCI guidelines recommend maintaining MAP 75–95 mmHg for 3–7 days and targeting spinal cord perfusion pressure ≥60–65 mmHg; model perfusion responds to heuristics without explicit SCPP control.[72][73]
+- Locomotor central pattern generators reside in segmental networks coordinating limb pairs; current CPG tone scalar lacks limb-specific oscillators and interlimb coordination.[74]
+- Human corticospinal conduction velocities average ~67 m/s with disease-dependent slowing; model uses unvalidated values without temperature or demyelination effects.[75]
+- Glial scar formation involves astrocyte proliferation over 1–2 weeks with STAT3 signaling, producing barriers and cytokine gradients; simulation increments a scar index without temporal staging or astrocyte roles.[76]
+- Neurogenic shock features sympathetic failure, hypotension, and bradycardia; present autonomic outputs shift but are not coupled to cardiovascular modules for systemic responses.[72][73]
+
+**Opportunities for improvement**
+- Add SCPP calculations (MAP − intrathecal pressure) with targets from acute SCI guidelines and allow vasopressor/CSF drainage interventions.[72][73]
+- Build bilateral limb CPG models with flexor/extensor half-centers and commissural coupling to study gait adaptations.[74]
+- Parameterize conduction velocities with temperature, demyelination, and injury length to match clinical evoked potential data.[75]
+- Stage glial scar development (hours–weeks) with astrocyte, fibroblast, and inflammatory cell modules influencing regeneration and cytokines.[76]
+- Link autonomic outputs to cardiovascular simulations to reproduce neurogenic shock hemodynamics and vasopressor responses.[72][73]
+
+**Sources**
+72. Neurology Practice Guideline - Hemodynamic management of acute spinal cord injury.[72]
+73. Journal of Anesthesia, Analgesia and Critical Care - Hemodynamic management narrative review.[73]
+74. Wikipedia - Central pattern generator physiology summary with vertebrate locomotion focus.[74]
+75. Journal of Neurology, Neurosurgery & Psychiatry - Motor conduction velocity in the human spinal cord.[75]
+76. Cells - Current advancements in spinal cord injury glial scar research.[76]
+
+## Stomach
+
+**Current simulation coverage**
+- Gastric organ tracks phase (fasting, cephalic, gastric, intestinal, delayed emptying) with vagal tone, hormonal outputs, acid level, motility indices, and gastric volume (`src/organs/stomach.rs:7`).
+- Meal routine adjusts ghrelin, gastrin, vagal drive, and nutrient load timing to shift phases and target meal intervals (`src/organs/stomach.rs:63`).
+- Secretory update sets acid output, histamine, somatostatin, mucus, and intrinsic factor proxies while motility block governs antral pump strength and emptying rate (`src/organs/stomach.rs:118`).
+
+**Physiology findings and observed gaps**
+- Gastrin stimulates ECL-cell histamine release while somatostatin provides paracrine inhibition; current model applies direct scalar adjustments without receptor-mediated feedback loops.[77][78]
+- Ghrelin rises pre-meal and is suppressed by nutrient load, integrating with hypothalamic circuits; simulation lowers ghrelin via simple volume clamps lacking macronutrient and circadian modulation.[79]
+- MMC phases originate in stomach/duodenum via motilin and 5-HT feedback; model phases do not enforce interdigestive MMC cycling or motilin triggers.[80]
+- Human gastric emptying delivers ~2–3 kcal·min⁻¹ to duodenum with slowing as energy density rises; the current emptying rate is set by motility index without energy-density feedback.[81]
+- Gastric emptying kinetics differ for liquids vs solids and respond to osmolarity; single clamp cannot represent nutrient-specific delays.[81]
+
+**Opportunities for improvement**
+- Implement receptor-level gastrin→ECL histamine→parietal pathways with somatostatin inhibition and cholinergic disinhibition loops.[77][78]
+- Add ghrelin dynamics tied to macronutrient sensing, sleep state, and leptin/IL-1 signaling to integrate appetite control.[79]
+- Introduce interdigestive MMC oscillator driven by motilin and 5-HT with suppression during fed state to coordinate gastric clearing.[80]
+- Couple gastric emptying to meal energy density, volume, and macronutrient type to reproduce caloric delivery constraints.[81]
+- Differentiate liquid versus solid emptying curves with sieving function and osmolar feedback for hypertonic loads.[81]
+
+**Sources**
+77. Comprehensive Physiology - Gastric peptides gastrin and somatostatin.[77]
+78. American Journal of Physiology - Role of histamine in control of gastric acid secretion.[78]
+79. Physiological Reviews - Regulation of ghrelin secretion.[79]
+80. Neurogastroenterology & Motility - Migrating motor complex control mechanisms.[80]
+81. Gastroenterology - Effect of meal volume and energy density on gastric emptying of carbohydrates.[81]

examples/c/ffi_example.c

@@ -17,6 +17,29 @@ int main(void) {
     char* sum = ml_patient_summary(p);
     if (sum) { printf("%s\n", sum); ml_string_free(sum); }
 
+    MLBloodstreamMetrics blood = {0};
+    if (ml_patient_bloodstream_metrics(p, &blood) == ML_OK) {
+        printf("Bloodstream: perfusion=%u metabolic=%u oncotic=%.1f mmHg lymph=%.2f mL/min RBC young/mature/senescent=%.0f/%.0f/%.0f%% hif=%.2f iron=%.0f mg\n",
+               (unsigned)blood.perfusion_state,
+               (unsigned)blood.metabolic_state,
+               blood.oncotic_pressure_mm_hg,
+               blood.lymphatic_return_ml_min,
+               blood.rbc_young_fraction * 100.0f,
+               blood.rbc_mature_fraction * 100.0f,
+               blood.rbc_senescent_fraction * 100.0f,
+               blood.hif_activation,
+               blood.iron_store_mg);
+    }
+
+    MLBladderMetrics bladder = {0};
+    if (ml_patient_bladder_metrics(p, &bladder) == ML_OK) {
+        printf("Bladder: phase=%u urgency=%.0f%% guard=%.0f%% hold=%.0f%%\n",
+               (unsigned)bladder.phase,
+               bladder.urgency * 100.0f,
+               bladder.guarding_reflex_gain * 100.0f,
+               bladder.voluntary_hold_fraction * 100.0f);
+    }
+
     char* h = ml_patient_organ_summary(p, ML_ORGAN_HEART);
     if (h) { printf("%s\n", h); ml_string_free(h); }
 
@@ -24,3 +47,4 @@ int main(void) {
     return 0;
 }
 
+

examples/demo_app.rs

@@ -0,0 +1,838 @@
+use medicallib_rust::{
+    bmi_measurement, calculate_bmi, classify_bmi, BloodPressure, EkgLead, Heart, Measurement,
+    OrganType, Patient, Result as MedicalResult, VitalSign,
+};
+use std::fmt::Write as _;
+use std::io::{self, Write};
+use std::sync::OnceLock;
+
+const EXTRA_ORGANS: [OrganType; 11] = [
+    OrganType::Brain,
+    OrganType::SpinalCord,
+    OrganType::Stomach,
+    OrganType::Liver,
+    OrganType::Gallbladder,
+    OrganType::Pancreas,
+    OrganType::Intestines,
+    OrganType::Esophagus,
+    OrganType::Kidneys,
+    OrganType::Bladder,
+    OrganType::Spleen,
+];
+
+const MONITORED_ORGANS: [OrganType; 14] = [
+    OrganType::Heart,
+    OrganType::Bloodstream,
+    OrganType::Lungs,
+    OrganType::Brain,
+    OrganType::SpinalCord,
+    OrganType::Stomach,
+    OrganType::Liver,
+    OrganType::Gallbladder,
+    OrganType::Pancreas,
+    OrganType::Intestines,
+    OrganType::Esophagus,
+    OrganType::Kidneys,
+    OrganType::Bladder,
+    OrganType::Spleen,
+];
+
+const VITAL_SIGNS: [VitalSign; 6] = [
+    VitalSign::HeartRate,
+    VitalSign::RespiratoryRate,
+    VitalSign::SystolicBP,
+    VitalSign::DiastolicBP,
+    VitalSign::TemperatureC,
+    VitalSign::SpO2,
+];
+
+const DASHBOARD_WIDTH: usize = 88;
+
+const COLOR_RESET: &str = "\x1b[0m";
+const COLOR_TITLE: &str = "\x1b[38;5;111m";
+const COLOR_SECTION: &str = "\x1b[38;5;81m";
+const COLOR_LABEL: &str = "\x1b[38;5;245m";
+const COLOR_MUTED: &str = "\x1b[38;5;240m";
+const COLOR_ACCENT: &str = "\x1b[38;5;153m";
+const COLOR_SUCCESS: &str = "\x1b[38;5;114m";
+const COLOR_WARNING: &str = "\x1b[38;5;221m";
+const COLOR_ERROR: &str = "\x1b[38;5;203m";
+const COLOR_PROMPT: &str = "\x1b[38;5;117m";
+
+const HELP_TEXT: &str = r#"
+Available commands:
+  help                       Show this help text
+  tick [dt]                  Advance the simulation by dt seconds (default: configured step)
+  run <steps> [dt]           Run multiple ticks back-to-back
+  set dt <seconds>           Update the default tick size
+  set arrhythmia <on|off>    Force arrhythmic behaviour on the heart
+  set tone <value>           Set heart autonomic tone (-1.0..=1.0)
+  set svr <value>            Set heart systemic vascular resistance (mmHg*min/L)
+  set ekg <lead...>         Configure EKG leads (e.g., set ekg I II V1 V5)
+  set glucose <mg/dL>        Override blood glucose
+  set spo2 <percent>         Override blood SpO2 (0-100)
+  set bp <systolic> <diastolic>   Override brachial blood pressure
+  set bmi <weight_kg> <height_m>  Update the tracked BMI inputs
+  bmi <weight_kg> <height_m> Compute BMI on the fly without storing it
+  summary                    Print the aggregate patient summary string
+  organs                     Print one-line summaries for every organ
+  reset                      Reset the patient and vitals to defaults
+  quit | exit | q            Leave the monitor
+(empty input)                Advance once using the configured step size
+"#;
+
+struct MonitorState {
+    patient: Patient,
+    sim_time: f32,
+    tick_seconds: f32,
+    bmi_inputs: (f32, f32),
+}
+
+impl MonitorState {
+    fn new() -> MedicalResult<Self> {
+        let mut patient = Patient::new("monitor")?.initialize_default().with_lungs();
+        for organ in EXTRA_ORGANS {
+            patient = patient.with_organ(organ);
+        }
+        Ok(Self {
+            patient,
+            sim_time: 0.0,
+            tick_seconds: 0.5,
+            bmi_inputs: (82.0, 1.84),
+        })
+    }
+
+    fn reset(&mut self) -> MedicalResult<()> {
+        *self = Self::new()?;
+        Ok(())
+    }
+
+    fn advance(&mut self, dt: f32) {
+        if dt <= 0.0 {
+            return;
+        }
+        self.patient.update(dt);
+        self.sim_time += dt;
+    }
+
+    fn heart_mut(&mut self) -> Option<&mut Heart> {
+        self.patient.find_organ_typed_mut::<Heart>()
+    }
+}
+
+enum CommandOutcome {
+    Continue(String),
+    Exit,
+}
+
+fn main() -> MedicalResult<()> {
+    let mut state = MonitorState::new()?;
+    let mut status = String::from("Type 'help' to list available commands.");
+    let stdin = io::stdin();
+    let mut input = String::new();
+
+    loop {
+        render_dashboard(&state, &status);
+        print!("{}", prompt_text());
+        io::stdout().flush().expect("flush stdout");
+
+        input.clear();
+        let read = match stdin.read_line(&mut input) {
+            Ok(n) => n,
+            Err(err) => {
+                status = format!("Failed to read input: {err}");
+                continue;
+            }
+        };
+        if read == 0 {
+            status = String::from("End of input detected, shutting down.");
+            render_dashboard(&state, &status);
+            println!();
+            break;
+        }
+        let trimmed = input.trim();
+        if trimmed.is_empty() {
+            let dt = state.tick_seconds;
+            state.advance(dt);
+            status = format!("Advanced simulation by {:.2} s using the default step.", dt);
+            continue;
+        }
+
+        match handle_command(&mut state, trimmed) {
+            Ok(CommandOutcome::Continue(message)) => {
+                status = message;
+            }
+            Ok(CommandOutcome::Exit) => {
+                status = String::from("Exiting monitor.");
+                render_dashboard(&state, &status);
+                println!();
+                break;
+            }
+            Err(err) => {
+                status = format!("Error: {err}");
+            }
+        }
+    }
+
+    println!("Goodbye!");
+    Ok(())
+}
+
+fn handle_command(state: &mut MonitorState, input: &str) -> Result<CommandOutcome, String> {
+    let mut parts = input.split_whitespace();
+    let cmd = parts
+        .next()
+        .ok_or_else(|| String::from("expected a command"))?
+        .to_ascii_lowercase();
+
+    match cmd.as_str() {
+        "help" => Ok(CommandOutcome::Continue(String::from(HELP_TEXT))),
+        "tick" => {
+            let dt = match parts.next() {
+                Some(raw) => parse_f32(raw)?,
+                None => state.tick_seconds,
+            };
+            if dt <= 0.0 {
+                return Err(String::from("dt must be greater than 0"));
+            }
+            state.advance(dt);
+            Ok(CommandOutcome::Continue(format!(
+                "Advanced simulation by {:.2} s.",
+                dt
+            )))
+        }
+        "run" => {
+            let steps_raw = parts
+                .next()
+                .ok_or_else(|| String::from("run expects a number of steps"))?;
+            let steps: usize = steps_raw
+                .parse()
+                .map_err(|_| format!("could not parse steps '{steps_raw}'"))?;
+            if steps == 0 {
+                return Err(String::from("steps must be greater than 0"));
+            }
+            let dt = match parts.next() {
+                Some(raw) => parse_f32(raw)?,
+                None => state.tick_seconds,
+            };
+            if dt <= 0.0 {
+                return Err(String::from("dt must be greater than 0"));
+            }
+            for _ in 0..steps {
+                state.advance(dt);
+            }
+            Ok(CommandOutcome::Continue(format!(
+                "Ran {steps} step(s) at {:.2} s per step.",
+                dt
+            )))
+        }
+        "set" => handle_set_command(state, parts),
+        "summary" => Ok(CommandOutcome::Continue(state.patient.patient_summary())),
+        "organs" => {
+            let mut details = String::new();
+            for organ in MONITORED_ORGANS {
+                let _ = writeln!(
+                    details,
+                    "{} -> {}",
+                    organ_label(organ),
+                    organ_snapshot(&state.patient, organ)
+                );
+            }
+            Ok(CommandOutcome::Continue(details))
+        }
+        "reset" => {
+            state.reset().map_err(|err| err.to_string())?;
+            Ok(CommandOutcome::Continue(String::from(
+                "Patient and monitor reset to defaults.",
+            )))
+        }
+        "bmi" => {
+            let weight_raw = parts
+                .next()
+                .ok_or_else(|| String::from("bmi expects weight in kg"))?;
+            let height_raw = parts
+                .next()
+                .ok_or_else(|| String::from("bmi expects height in m"))?;
+            let weight = parse_f32(weight_raw)?;
+            let height = parse_f32(height_raw)?;
+            let value = calculate_bmi(weight, height).map_err(|err| err.to_string())?;
+            let measurement = Measurement::new(value, "kg/m^2");
+            let class = classify_bmi(value);
+            Ok(CommandOutcome::Continue(format!(
+                "BMI {:.2} {} => {:?}",
+                measurement.value, measurement.unit, class
+            )))
+        }
+        "quit" | "exit" | "q" => Ok(CommandOutcome::Exit),
+        other => Err(format!("unknown command '{other}'")),
+    }
+}
+
+fn handle_set_command<'a>(
+    state: &mut MonitorState,
+    mut parts: impl Iterator<Item = &'a str>,
+) -> Result<CommandOutcome, String> {
+    let field = parts
+        .next()
+        .ok_or_else(|| String::from("set expects a field to modify"))?
+        .to_ascii_lowercase();
+
+    match field.as_str() {
+        "dt" | "step" => {
+            let raw = parts
+                .next()
+                .ok_or_else(|| String::from("set dt expects a numeric value"))?;
+            let dt = parse_f32(raw)?;
+            if dt <= 0.0 {
+                return Err(String::from("step size must be > 0"));
+            }
+            state.tick_seconds = dt;
+            Ok(CommandOutcome::Continue(format!(
+                "Default tick size set to {:.2} s.",
+                dt
+            )))
+        }
+        "arrhythmia" => {
+            let flag = parse_toggle(parts.next())?;
+            let heart = state
+                .heart_mut()
+                .ok_or_else(|| String::from("heart organ is not present"))?;
+            heart.arrhythmia = flag;
+            Ok(CommandOutcome::Continue(format!(
+                "Heart arrhythmia forcing set to {}.",
+                yes_no(flag)
+            )))
+        }
+        "tone" => {
+            let raw = parts
+                .next()
+                .ok_or_else(|| String::from("set tone expects a value"))?;
+            let value = parse_f32(raw)?;
+            let clamped = value.clamp(-1.0, 1.0);
+            let heart = state
+                .heart_mut()
+                .ok_or_else(|| String::from("heart organ is not present"))?;
+            heart.autonomic_tone = clamped;
+            Ok(CommandOutcome::Continue(format!(
+                "Heart autonomic tone set to {:+.2} (input {:+.2}).",
+                clamped, value
+            )))
+        }
+        "svr" => {
+            let raw = parts
+                .next()
+                .ok_or_else(|| String::from("set svr expects a value"))?;
+            let value = parse_f32(raw)?;
+            if value <= 0.0 {
+                return Err(String::from("systemic vascular resistance must be > 0"));
+            }
+            let heart = state
+                .heart_mut()
+                .ok_or_else(|| String::from("heart organ is not present"))?;
+            heart.systemic_vascular_resistance = value;
+            Ok(CommandOutcome::Continue(format!(
+                "Heart systemic vascular resistance set to {:.2} mmHg*min/L.",
+                value
+            )))
+        }
+        "ekg" => {
+            let tokens: Vec<_> = parts.collect();
+            if tokens.is_empty() {
+                return Err(String::from("set ekg expects one or more lead identifiers"));
+            }
+            let mut leads = Vec::with_capacity(tokens.len());
+            for token in tokens {
+                leads.push(parse_lead(token)?);
+            }
+            let summary = leads
+                .iter()
+                .map(|lead| lead_label(*lead))
+                .collect::<Vec<_>>()
+                .join(", ");
+            state.patient.configure_ekg_leads(leads);
+            Ok(CommandOutcome::Continue(format!(
+                "EKG leads set to {summary}."
+            )))
+        }
+        "glucose" => {
+            let raw = parts
+                .next()
+                .ok_or_else(|| String::from("set glucose expects mg/dL"))?;
+            let value = parse_f32(raw)?;
+            state.patient.blood.glucose_mg_dl = value;
+            Ok(CommandOutcome::Continue(format!(
+                "Blood glucose set to {:.1} mg/dL.",
+                value
+            )))
+        }
+        "spo2" => {
+            let raw = parts
+                .next()
+                .ok_or_else(|| String::from("set spo2 expects a percentage"))?;
+            let value = parse_f32(raw)?.clamp(0.0, 100.0);
+            state.patient.blood.spo2_pct = value;
+            Ok(CommandOutcome::Continue(format!(
+                "Blood SpO2 set to {:.0}%.",
+                value
+            )))
+        }
+        "bp" | "bloodpressure" => {
+            let systolic_raw = parts
+                .next()
+                .ok_or_else(|| String::from("set bp expects systolic and diastolic values"))?;
+            let diastolic_raw = parts
+                .next()
+                .ok_or_else(|| String::from("set bp expects systolic and diastolic values"))?;
+            let systolic = parse_u16(systolic_raw)?;
+            let diastolic = parse_u16(diastolic_raw)?;
+            if systolic <= diastolic {
+                return Err(String::from("systolic must be greater than diastolic"));
+            }
+            state.patient.blood_pressure = BloodPressure {
+                systolic,
+                diastolic,
+            };
+            Ok(CommandOutcome::Continue(format!(
+                "Blood pressure set to {}/{} mmHg.",
+                systolic, diastolic
+            )))
+        }
+        "bmi" => {
+            let weight_raw = parts
+                .next()
+                .ok_or_else(|| String::from("set bmi expects weight in kg"))?;
+            let height_raw = parts
+                .next()
+                .ok_or_else(|| String::from("set bmi expects height in m"))?;
+            let weight = parse_f32(weight_raw)?;
+            let height = parse_f32(height_raw)?;
+            let measurement = bmi_measurement(weight, height).map_err(|err| err.to_string())?;
+            let class = classify_bmi(measurement.value);
+            state.bmi_inputs = (weight, height);
+            Ok(CommandOutcome::Continue(format!(
+                "Tracked BMI updated -> {:.2} {} ({:?}).",
+                measurement.value, measurement.unit, class
+            )))
+        }
+        other => Err(format!("unknown field '{other}'")),
+    }
+}
+
+fn render_dashboard(state: &MonitorState, status: &str) {
+    clear_screen();
+
+    println!("{}", banner_line("MedicalLib Console Monitor"));
+
+    let overview_line = [
+        accent(format!("t = {:.2} s", state.sim_time)),
+        muted("  |  "),
+        accent(format!("dt = {:.2} s", state.tick_seconds)),
+        muted("  |  "),
+        accent(format!("Organs {}", MONITORED_ORGANS.len())),
+        muted("  |  "),
+        accent(format!("Vitals {}", VITAL_SIGNS.len())),
+    ]
+    .join("");
+    println!("  {overview_line}");
+    println!();
+
+    println!("{}", section_line("Simulation"));
+    println!(
+        "{}",
+        stat_line(
+            "Simulation time",
+            accent(format!("{:.2} s", state.sim_time))
+        )
+    );
+    println!(
+        "{}",
+        stat_line("Step size", accent(format!("{:.2} s", state.tick_seconds)))
+    );
+    println!(
+        "{}",
+        stat_line(
+            "Tracked vitals",
+            accent(
+                VITAL_SIGNS
+                    .iter()
+                    .map(|v| format!("{:?}", v))
+                    .collect::<Vec<_>>()
+                    .join(", ")
+            )
+        )
+    );
+    println!();
+
+    println!("{}", section_line("Circulation"));
+    let bp = state.patient.blood_pressure;
+    println!(
+        "{}",
+        stat_line(
+            "Blood pressure",
+            format!(
+                "{} {}",
+                accent(format!("{bp}")),
+                validity_tag(bp.validate())
+            )
+        )
+    );
+
+    let blood = &state.patient.blood;
+    let mut chemistry_parts = vec![
+        accent(format!("Hgb {:.1} g/dL", blood.hemoglobin_g_dl)),
+        muted(" | "),
+        accent(format!("Hct {:.1}%", blood.hematocrit_pct)),
+        muted(" | "),
+        accent(format!("SpO2 {:.0}%", blood.spo2_pct)),
+        muted(" | "),
+        accent(format!("Glucose {:.1} mg/dL", blood.glucose_mg_dl)),
+        muted("  "),
+    ];
+    chemistry_parts.push(validity_tag(blood.validate()));
+    let chemistry = chemistry_parts.join("");
+    println!("{}", stat_line("Blood chemistry", chemistry));
+
+    println!("{}", section_line("Electrocardiogram"));
+    match state.patient.ekg_snapshot() {
+        Some(snapshot) => {
+            println!(
+                "{}",
+                stat_line(
+                    "Rhythm",
+                    format!(
+                        "{:?} | {:.0} bpm | RR {:.3} s",
+                        snapshot.rhythm, snapshot.heart_rate_bpm, snapshot.rr_interval_s
+                    )
+                )
+            );
+            println!(
+                "{}",
+                stat_line(
+                    "Axis",
+                    format!(
+                        "{:+.0} deg | variability {:.2}",
+                        snapshot.frontal_axis_deg, snapshot.variability_index
+                    )
+                )
+            );
+            for (idx, chunk) in snapshot.lead_samples.chunks(6).enumerate() {
+                let label = if idx == 0 { "Leads" } else { "" };
+                let body = chunk
+                    .iter()
+                    .map(|sample| {
+                        format!("{} {:+.2}mV", lead_label(sample.lead), sample.amplitude_mv)
+                    })
+                    .collect::<Vec<_>>()
+                    .join("  ");
+                println!("{}", stat_line(label, body));
+            }
+        }
+        None => {
+            let message = if state.patient.ekg_monitor().is_some() {
+                muted("monitor waiting for first snapshot")
+            } else {
+                muted("monitor not configured")
+            };
+            println!("{}", stat_line("Status", message));
+        }
+    }
+    println!();
+
+    let (weight, height) = state.bmi_inputs;
+    let bmi_line = match bmi_measurement(weight, height) {
+        Ok(measurement) => {
+            let class = classify_bmi(measurement.value);
+            vec![
+                accent(format!("{:.1} kg", weight)),
+                muted(" / "),
+                accent(format!("{:.2} m", height)),
+                muted(" -> "),
+                accent(format!("{:.2} {}", measurement.value, measurement.unit)),
+                muted(" ("),
+                accent(format!("{:?}", class)),
+                muted(")"),
+            ]
+            .join("")
+        }
+        Err(err) => colorize(
+            COLOR_ERROR,
+            format!("{:.1} kg / {:.2} m -> error ({err})", weight, height),
+        ),
+    };
+    println!("{}", stat_line("BMI inputs", bmi_line));
+    println!();
+
+    println!("{}", section_line("Heart"));
+    if let Some(heart) = state.patient.find_organ_typed::<Heart>() {
+        let heart_rate = vec![
+            accent(format!("{:.0} bpm", heart.heart_rate_bpm)),
+            muted(" | rhythm "),
+            accent(format!("{:?}", heart.rhythm_state)),
+        ]
+        .join("");
+        println!("{}", stat_line("Heart rate", heart_rate));
+
+        let cardiac_output = vec![
+            accent(format!("{:.1} L/min", heart.cardiac_output_l_min)),
+            muted(" | tone "),
+            accent(format!("{:+.2}", heart.autonomic_tone)),
+            muted(" | SVR "),
+            accent(format!("{:.1}", heart.systemic_vascular_resistance)),
+        ]
+        .join("");
+        println!("{}", stat_line("Output", cardiac_output));
+
+        let arrhythmia_tag = if heart.arrhythmia {
+            colorize(COLOR_WARNING, "forced arrhythmia".to_string())
+        } else {
+            colorize(COLOR_SUCCESS, "intrinsic rhythm".to_string())
+        };
+        let arrhythmia_line = vec![
+            arrhythmia_tag,
+            muted(" | EF "),
+            accent(format!("{:.0}%", heart.ejection_fraction * 100.0)),
+            muted(" | MAP ~"),
+            accent(format!("{:.0} mmHg", mean_arterial_pressure(bp))),
+        ]
+        .join("");
+        println!("{}", stat_line("Arrhythmia", arrhythmia_line));
+    } else {
+        println!(
+            "{}",
+            stat_line(
+                "Heart",
+                colorize(COLOR_WARNING, "<not attached>".to_string())
+            )
+        );
+    }
+    println!();
+
+    println!("{}", section_line("Organ Snapshots"));
+    for organ in MONITORED_ORGANS {
+        println!("{}", organ_line(&state.patient, organ));
+    }
+    println!();
+
+    println!("{}", section_line("Status"));
+    let mut printed_status = false;
+    for line in status.lines() {
+        let styled = status_line(line);
+        if styled.is_empty() {
+            continue;
+        }
+        println!("  {}", styled);
+        printed_status = true;
+    }
+    if !printed_status {
+        println!("  {}", muted("No recent actions."));
+    }
+    println!();
+    println!(
+        "  {}",
+        muted("Press Enter to advance once or type 'help' for commands.")
+    );
+}
+
+fn organ_snapshot(patient: &Patient, kind: OrganType) -> String {
+    patient
+        .organ_summary(kind)
+        .unwrap_or_else(|err| format!("n/a ({err})"))
+}
+
+fn organ_label(kind: OrganType) -> &'static str {
+    match kind {
+        OrganType::Heart => "Heart",
+        OrganType::Bloodstream => "Bloodstream",
+        OrganType::Lungs => "Lungs",
+        OrganType::Brain => "Brain",
+        OrganType::SpinalCord => "Spinal cord",
+        OrganType::Stomach => "Stomach",
+        OrganType::Liver => "Liver",
+        OrganType::Gallbladder => "Gallbladder",
+        OrganType::Pancreas => "Pancreas",
+        OrganType::Intestines => "Intestines",
+        OrganType::Esophagus => "Esophagus",
+        OrganType::Kidneys => "Kidneys",
+        OrganType::Bladder => "Bladder",
+        OrganType::Spleen => "Spleen",
+    }
+}
+
+fn parse_f32(raw: &str) -> Result<f32, String> {
+    raw.parse::<f32>()
+        .map_err(|_| format!("unable to parse '{raw}' as a decimal number"))
+}
+
+fn parse_u16(raw: &str) -> Result<u16, String> {
+    raw.parse::<u16>()
+        .map_err(|_| format!("unable to parse '{raw}' as an integer"))
+}
+
+fn parse_toggle(value: Option<&str>) -> Result<bool, String> {
+    let raw = value.ok_or_else(|| String::from("expected on/off"))?;
+    match raw.to_ascii_lowercase().as_str() {
+        "on" | "true" | "1" | "yes" => Ok(true),
+        "off" | "false" | "0" | "no" => Ok(false),
+        other => Err(format!("expected on/off but received '{other}'")),
+    }
+}
+
+fn parse_lead(raw: &str) -> Result<EkgLead, String> {
+    let upper = raw.trim().to_ascii_uppercase();
+    match upper.as_str() {
+        "I" => Ok(EkgLead::I),
+        "II" => Ok(EkgLead::II),
+        "III" => Ok(EkgLead::III),
+        "AVR" => Ok(EkgLead::AVR),
+        "AVL" => Ok(EkgLead::AVL),
+        "AVF" => Ok(EkgLead::AVF),
+        "V1" => Ok(EkgLead::V1),
+        "V2" => Ok(EkgLead::V2),
+        "V3" => Ok(EkgLead::V3),
+        "V4" => Ok(EkgLead::V4),
+        "V5" => Ok(EkgLead::V5),
+        "V6" => Ok(EkgLead::V6),
+        other => Err(format!("unknown lead '{other}'")),
+    }
+}
+
+fn lead_label(lead: EkgLead) -> &'static str {
+    match lead {
+        EkgLead::I => "I",
+        EkgLead::II => "II",
+        EkgLead::III => "III",
+        EkgLead::AVR => "aVR",
+        EkgLead::AVL => "aVL",
+        EkgLead::AVF => "aVF",
+        EkgLead::V1 => "V1",
+        EkgLead::V2 => "V2",
+        EkgLead::V3 => "V3",
+        EkgLead::V4 => "V4",
+        EkgLead::V5 => "V5",
+        EkgLead::V6 => "V6",
+    }
+}
+
+fn yes_no(value: bool) -> &'static str {
+    if value {
+        "yes"
+    } else {
+        "no"
+    }
+}
+
+fn mean_arterial_pressure(bp: BloodPressure) -> f32 {
+    let systolic = bp.systolic as f32;
+    let diastolic = bp.diastolic as f32;
+    diastolic + (systolic - diastolic) / 3.0
+}
+
+fn clear_screen() {
+    print!("\x1b[2J\x1b[H");
+    let _ = io::stdout().flush();
+}
+
+fn prompt_text() -> String {
+    if colors_enabled() {
+        format!("{} ", colorize(COLOR_PROMPT, "monitor>"))
+    } else {
+        String::from("monitor> ")
+    }
+}
+
+fn banner_line(title: &str) -> String {
+    let width = DASHBOARD_WIDTH.max(title.len() + 4);
+    colorize(
+        COLOR_TITLE,
+        format!("{:=^width$}", format!(" {title} "), width = width),
+    )
+}
+
+fn section_line(title: &str) -> String {
+    colorize(
+        COLOR_SECTION,
+        format!("{:-^width$}", format!(" {title} "), width = DASHBOARD_WIDTH),
+    )
+}
+
+fn stat_line(label: &str, value: impl Into<String>) -> String {
+    let label_cell = colorize(COLOR_LABEL, format!("{label:<18}:"));
+    format!("  {label_cell} {}", value.into())
+}
+
+fn accent(text: impl Into<String>) -> String {
+    colorize(COLOR_ACCENT, text)
+}
+
+fn muted(text: impl Into<String>) -> String {
+    colorize(COLOR_MUTED, text)
+}
+
+fn validity_tag(ok: bool) -> String {
+    if ok {
+        colorize(COLOR_SUCCESS, "[OK]".to_string())
+    } else {
+        colorize(COLOR_ERROR, "[CHECK]".to_string())
+    }
+}
+
+fn organ_line(patient: &Patient, kind: OrganType) -> String {
+    let label = colorize(COLOR_ACCENT, format!("{:<12}:", organ_label(kind)));
+    let summary = organ_snapshot(patient, kind);
+    let styled_summary = style_snapshot(&summary);
+    format!("  {label} {styled_summary}")
+}
+
+fn style_snapshot(text: &str) -> String {
+    let lowered = text.to_ascii_lowercase();
+    if lowered.contains("error") {
+        colorize(COLOR_ERROR, text.to_string())
+    } else if lowered.starts_with("n/a") {
+        colorize(COLOR_WARNING, text.to_string())
+    } else if lowered.contains("stable") || lowered.contains("normal") {
+        colorize(COLOR_SUCCESS, text.to_string())
+    } else {
+        text.to_string()
+    }
+}
+
+fn status_line(line: &str) -> String {
+    let trimmed = line.trim();
+    if trimmed.is_empty() {
+        return String::new();
+    }
+    let lowered = trimmed.to_ascii_lowercase();
+    if lowered.contains("error") {
+        colorize(COLOR_ERROR, trimmed.to_string())
+    } else if lowered.contains("warning") || lowered.contains("caution") {
+        colorize(COLOR_WARNING, trimmed.to_string())
+    } else if lowered.starts_with("advanced")
+        || lowered.starts_with("ran")
+        || lowered.starts_with("set ")
+        || lowered.starts_with("blood")
+        || lowered.starts_with("heart")
+        || lowered.starts_with("patient")
+        || lowered.starts_with("tracked")
+    {
+        colorize(COLOR_SUCCESS, trimmed.to_string())
+    } else {
+        accent(trimmed.to_string())
+    }
+}
+
+fn colorize(code: &str, text: impl Into<String>) -> String {
+    let text = text.into();
+    if colors_enabled() {
+        format!("{code}{text}{COLOR_RESET}")
+    } else {
+        text
+    }
+}
+
+fn colors_enabled() -> bool {
+    static ENABLED: OnceLock<bool> = OnceLock::new();
+    *ENABLED.get_or_init(|| {
+        use std::io::IsTerminal;
+        std::env::var_os("NO_COLOR").is_none() && io::stdout().is_terminal()
+    })
+}

ffi/medicallib.h

@@ -91,6 +91,51 @@
  */
 #define ML_ORGAN_SPLEEN 12
 
+/**
+ * Organ code for `OrganType::Bloodstream`.
+ */
+#define ML_ORGAN_BLOODSTREAM 13
+
+enum MLBladderPhase
+#ifdef __cplusplus
+  : uint32_t
+#endif // __cplusplus
+ {
+    Filling = 0,
+    Voiding = 1,
+    PostVoidRefractory = 2,
+};
+#ifndef __cplusplus
+typedef uint32_t MLBladderPhase;
+#endif // __cplusplus
+
+enum MLMetabolicState
+#ifdef __cplusplus
+  : uint32_t
+#endif // __cplusplus
+ {
+    Aerobic = 0,
+    CompensatedAnaerobic = 1,
+    AnaerobicCrisis = 2,
+};
+#ifndef __cplusplus
+typedef uint32_t MLMetabolicState;
+#endif // __cplusplus
+
+enum MLPerfusionState
+#ifdef __cplusplus
+  : uint32_t
+#endif // __cplusplus
+ {
+    Balanced = 0,
+    Compensated = 1,
+    Hypovolemic = 2,
+    Shock = 3,
+};
+#ifndef __cplusplus
+typedef uint32_t MLPerfusionState;
+#endif // __cplusplus
+
 /**
  * Opaque patient handle type for C consumers. Wraps a heap-allocated `Patient`.
  */
@@ -98,6 +143,54 @@ typedef struct MLPatient {
     void *inner;
 } MLPatient;
 
+typedef struct MLBloodstreamMetrics {
+    MLPerfusionState perfusion_state;
+    MLMetabolicState metabolic_state;
+    float total_volume_l;
+    float plasma_volume_l;
+    float red_cell_volume_l;
+    float plasma_albumin_g_dl;
+    float plasma_globulin_g_dl;
+    float plasma_fibrinogen_g_dl;
+    float oncotic_pressure_mm_hg;
+    float lymphatic_return_ml_min;
+    float rbc_young_fraction;
+    float rbc_mature_fraction;
+    float rbc_senescent_fraction;
+    float erythropoiesis_rate_ml_per_day;
+    float erythrocyte_clearance_ml_per_day;
+    float iron_store_mg;
+    float folate_store_mg;
+    float b12_store_mcg;
+    float hif_activation;
+    float oxygen_supply_demand_ratio;
+} MLBloodstreamMetrics;
+
+typedef struct MLBladderMetrics {
+    MLBladderPhase phase;
+    float volume_ml;
+    float capacity_ml;
+    float pressure_cm_h2o;
+    float detrusor_pressure_cm_h2o;
+    float pressure_safety_limit_cm_h2o;
+    float afferent_signal;
+    float urgency;
+    float cortical_inhibition;
+    float voluntary_hold_command;
+    float cortical_gate_fraction;
+    float voluntary_hold_fraction;
+    float guarding_reflex_gain;
+    float pontine_storage_signal;
+    float pontine_micturition_signal;
+    float hypogastric_efferent;
+    float pudendal_efferent;
+    float parasympathetic_drive;
+    float sympathetic_drive;
+    float somatic_drive;
+    float pressure_stress_index;
+    float time_above_safety_limit_s;
+} MLBladderMetrics;
+
 #ifdef __cplusplus
 extern "C" {
 #endif // __cplusplus
@@ -134,6 +227,17 @@ void ml_string_free(char *s);
  */
 int32_t ml_patient_update(struct MLPatient *p, float dt_seconds);
 
+/**
+ * Populate bloodstream metrics for the patient. Returns ML_OK on success.
+ */
+int32_t ml_patient_bloodstream_metrics(const struct MLPatient *p,
+                                       struct MLBloodstreamMetrics *out_metrics);
+
+/**
+ * Populate bladder metrics for the patient. Returns ML_OK on success.
+ */
+int32_t ml_patient_bladder_metrics(const struct MLPatient *p, struct MLBladderMetrics *out_metrics);
+
 /**
  * Return organ summary by type code. See header for codes. Caller frees string.
  */
@@ -144,3 +248,4 @@ char *ml_patient_organ_summary(const struct MLPatient *p, uint32_t organ_code);
 #endif // __cplusplus
 
 #endif /* MEDICALLIB_RUST_MEDICALLIB_H */
+

src/ekg/mod.rs

@@ -0,0 +1,483 @@
+//! ECG (electrocardiogram) simulation utilities tightly coupled to the heart organ.
+//!
+//! The monitor exposes a configurable set of leads and produces synthetic waveforms that
+//! respond to the hemodynamic and electrophysiological state of the [`Heart`]. The
+//! implementation intentionally mirrors common surface ECG morphology without aiming for
+//! diagnostic fidelity.
+
+use crate::organs::{CardiacRhythmState, Heart, Organ};
+use core::f32::consts::TAU;
+
+const MIN_RR_INTERVAL_S: f32 = 0.3;
+const MAX_RR_INTERVAL_S: f32 = 2.5;
+const DEFAULT_LEADS: [EkgLead; 12] = [
+    EkgLead::I,
+    EkgLead::II,
+    EkgLead::III,
+    EkgLead::AVR,
+    EkgLead::AVL,
+    EkgLead::AVF,
+    EkgLead::V1,
+    EkgLead::V2,
+    EkgLead::V3,
+    EkgLead::V4,
+    EkgLead::V5,
+    EkgLead::V6,
+];
+
+/// Simplified representation of the standard ECG leads.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
+#[repr(u8)]
+pub enum EkgLead {
+    /// Standard limb lead I.
+    I = 0,
+    /// Standard limb lead II.
+    II,
+    /// Standard limb lead III.
+    III,
+    /// Augmented limb lead aVR.
+    AVR,
+    /// Augmented limb lead aVL.
+    AVL,
+    /// Augmented limb lead aVF.
+    AVF,
+    /// Precordial lead V1.
+    V1,
+    /// Precordial lead V2.
+    V2,
+    /// Precordial lead V3.
+    V3,
+    /// Precordial lead V4.
+    V4,
+    /// Precordial lead V5.
+    V5,
+    /// Precordial lead V6.
+    V6,
+}
+
+impl EkgLead {
+    /// Returns the canonical ordering for a 12-lead ECG.
+    pub const fn standard_order() -> &'static [EkgLead] {
+        &DEFAULT_LEADS
+    }
+
+    fn geometry(self) -> LeadVector {
+        use EkgLead::*;
+        match self {
+            I => LeadVector::new(1.0, 0.1, 0.05),
+            II => LeadVector::new(0.6, 0.9, 0.1),
+            III => LeadVector::new(-0.1, 1.0, 0.12),
+            AVR => LeadVector::new(-0.9, -0.3, -0.05),
+            AVL => LeadVector::new(0.7, -0.2, 0.02),
+            AVF => LeadVector::new(0.0, 1.0, 0.12),
+            V1 => LeadVector::new(-0.7, 0.05, 1.0),
+            V2 => LeadVector::new(-0.3, 0.15, 1.0),
+            V3 => LeadVector::new(0.0, 0.2, 0.9),
+            V4 => LeadVector::new(0.3, 0.25, 0.8),
+            V5 => LeadVector::new(0.7, 0.25, 0.7),
+            V6 => LeadVector::new(0.9, 0.2, 0.6),
+        }
+    }
+}
+
+#[derive(Debug, Clone, Copy)]
+struct LeadVector {
+    lateral: f32,
+    inferior: f32,
+    anterior: f32,
+}
+
+impl LeadVector {
+    const fn new(lateral: f32, inferior: f32, anterior: f32) -> Self {
+        Self {
+            lateral,
+            inferior,
+            anterior,
+        }
+    }
+
+    fn dot(self, other: Self) -> f32 {
+        self.lateral * other.lateral
+            + self.inferior * other.inferior
+            + self.anterior * other.anterior
+    }
+
+    fn normalized(self) -> Self {
+        let mag = (self.lateral * self.lateral
+            + self.inferior * self.inferior
+            + self.anterior * self.anterior)
+            .sqrt();
+        if mag <= f32::EPSILON {
+            return Self::new(0.0, 0.0, 0.0);
+        }
+        Self::new(
+            (self.lateral / mag).clamp(-1.5, 1.5),
+            (self.inferior / mag).clamp(-1.5, 1.5),
+            (self.anterior / mag).clamp(-1.5, 1.5),
+        )
+    }
+}
+
+/// Snapshot of the cardiac state relevant for ECG generation.
+#[derive(Debug, Clone)]
+pub struct HeartElectricalState {
+    /// Current heart rate in beats per minute.
+    pub heart_rate_bpm: f32,
+    /// Sympathetic versus parasympathetic balance (negative favors vagal).
+    pub autonomic_tone: f32,
+    /// Inotropic state relative to baseline (1.0 equals nominal).
+    pub contractility_index: f32,
+    /// Fraction of beats affected by conduction irregularity.
+    pub arrhythmia_burden: f32,
+    /// Stroke volume per beat expressed in milliliters.
+    pub stroke_volume_ml: f32,
+    /// Cardiac output in liters per minute.
+    pub cardiac_output_l_min: f32,
+    /// Estimated atrial preload pressure in millimeters of mercury.
+    pub preload_mm_hg: f32,
+    /// Effective arterial afterload pressure in millimeters of mercury.
+    pub afterload_mm_hg: f32,
+    /// Venous return rate feeding the heart in liters per minute.
+    pub venous_return_l_min: f32,
+    /// Coronary perfusion pressure available for myocardial oxygenation.
+    pub coronary_perfusion_mm_hg: f32,
+    /// Fraction of ventricular volume ejected each beat (0.0-1.0).
+    pub ejection_fraction: f32,
+    /// Classified rhythm state for pacing the waveform generator.
+    pub rhythm: CardiacRhythmState,
+}
+
+impl From<&Heart> for HeartElectricalState {
+    fn from(heart: &Heart) -> Self {
+        Self {
+            heart_rate_bpm: heart.heart_rate_bpm,
+            autonomic_tone: heart.autonomic_tone,
+            contractility_index: heart.contractility_index,
+            arrhythmia_burden: heart.arrhythmia_burden,
+            stroke_volume_ml: heart.stroke_volume_ml,
+            cardiac_output_l_min: heart.cardiac_output_l_min,
+            preload_mm_hg: heart.preload_mm_hg,
+            afterload_mm_hg: heart.afterload_mm_hg,
+            venous_return_l_min: heart.venous_return_l_min,
+            coronary_perfusion_mm_hg: heart.coronary_perfusion_mm_hg,
+            ejection_fraction: heart.ejection_fraction,
+            rhythm: heart.rhythm_state,
+        }
+    }
+}
+
+/// Instantaneous reading for a configured lead.
+#[derive(Debug, Clone)]
+pub struct EkgLeadSample {
+    /// Lead identity associated with this sample.
+    pub lead: EkgLead,
+    /// Composite millivolt amplitude observed on the lead.
+    pub amplitude_mv: f32,
+    /// Contribution from simulated atrial depolarization (P-wave).
+    pub p_wave_mv: f32,
+    /// Contribution from simulated ventricular depolarization (QRS complex).
+    pub qrs_complex_mv: f32,
+    /// Contribution from simulated ventricular repolarization (T-wave).
+    pub t_wave_mv: f32,
+    /// ST-segment offset from the baseline isoelectric line.
+    pub st_deviation_mv: f32,
+    /// Additive high-frequency noise used to keep traces dynamic.
+    pub noise_mv: f32,
+}
+
+/// Most recent ECG snapshot produced by the monitor.
+#[derive(Debug, Clone)]
+pub struct EkgSnapshot {
+    /// Identifier for the associated heart organ.
+    pub heart_id: String,
+    /// Elapsed simulation time in seconds.
+    pub time_s: f32,
+    /// Estimated heart rate in beats per minute at this instant.
+    pub heart_rate_bpm: f32,
+    /// Duration of the most recent R-R interval in seconds.
+    pub rr_interval_s: f32,
+    /// Cardiac rhythm classification captured with the reading.
+    pub rhythm: CardiacRhythmState,
+    /// Frontal plane electrical axis in degrees.
+    pub frontal_axis_deg: f32,
+    /// Normalized heart rate variability metric (0.0-1.0).
+    pub variability_index: f32,
+    /// Per-lead synthesized waveform samples.
+    pub lead_samples: Vec<EkgLeadSample>,
+}
+
+/// Lead-tracking ECG monitor bound to a heart organ.
+#[derive(Debug)]
+pub struct EkgMonitor {
+    heart_id: String,
+    leads: Vec<LeadState>,
+    global_phase: f32,
+    time_elapsed_s: f32,
+    last_rr_interval_s: f32,
+    last_snapshot: Option<EkgSnapshot>,
+}
+
+impl EkgMonitor {
+    /// Create a new monitor for a specific heart id and lead configuration.
+    pub fn new(heart_id: impl Into<String>, leads: Vec<EkgLead>) -> Self {
+        let heart_id = heart_id.into();
+        let filtered = sanitize_leads(leads);
+        let lead_states = build_lead_states(&filtered);
+        Self {
+            heart_id,
+            leads: lead_states,
+            global_phase: 0.0,
+            time_elapsed_s: 0.0,
+            last_rr_interval_s: 60.0 / 72.0,
+            last_snapshot: None,
+        }
+    }
+
+    /// Construct a monitor using the heart's configured lead count.
+    pub fn from_heart(heart: &Heart) -> Self {
+        let count = heart.leads.clamp(1, DEFAULT_LEADS.len() as u8) as usize;
+        let leads = DEFAULT_LEADS[..count].to_vec();
+        Self::new(heart.id().to_string(), leads)
+    }
+
+    /// Identifier of the heart this monitor is following.
+    pub fn heart_id(&self) -> &str {
+        &self.heart_id
+    }
+
+    /// Retarget the monitor to a different heart identifier.
+    pub fn retarget(&mut self, heart_id: impl Into<String>) {
+        self.heart_id = heart_id.into();
+    }
+
+    /// Ordered set of leads currently simulated.
+    pub fn leads(&self) -> Vec<EkgLead> {
+        self.leads.iter().map(|state| state.lead).collect()
+    }
+
+    /// Replace the simulated leads while keeping accumulated phase information.
+    pub fn configure_leads(&mut self, leads: Vec<EkgLead>) {
+        let filtered = sanitize_leads(leads);
+        self.leads = build_lead_states(&filtered);
+    }
+
+    /// Update the monitor with the latest heart state.
+    pub fn observe(&mut self, state: &HeartElectricalState, dt_seconds: f32) {
+        if dt_seconds <= 0.0 || self.leads.is_empty() {
+            return;
+        }
+
+        let rr_interval = (60.0 / state.heart_rate_bpm).clamp(MIN_RR_INTERVAL_S, MAX_RR_INTERVAL_S);
+        let arrhythmia = state.arrhythmia_burden.clamp(0.0, 1.0);
+        let variability = 0.12 + arrhythmia * 0.6 + state.autonomic_tone.abs() * 0.1;
+        let variability = variability.clamp(0.05, 0.9);
+        let phase_rate =
+            (1.0 + (arrhythmia - 0.2) * 0.15 * (self.time_elapsed_s * 0.7).sin()).clamp(0.7, 1.3);
+        self.global_phase = (self.global_phase + dt_seconds / (rr_interval * phase_rate)).fract();
+
+        let axis = derive_axis(state);
+        let frontal_axis_rad = axis.inferior.atan2(axis.lateral);
+        let frontal_axis_deg = frontal_axis_rad.to_degrees();
+        let amplitude_scale = derive_amplitude_scale(state);
+        let qrs_width = 0.055 + 0.03 * arrhythmia + (state.contractility_index - 1.0).abs() * 0.015;
+        let qrs_width = qrs_width.clamp(0.04, 0.12);
+        let st_target = derive_st_deviation(state);
+
+        let mut lead_samples = Vec::with_capacity(self.leads.len());
+        for (idx, lead_state) in self.leads.iter_mut().enumerate() {
+            let lead_phase = (self.global_phase + lead_state.phase_offset).fract();
+            let geom = lead_state.lead.geometry().normalized();
+            let axis_gain = axis.dot(geom).clamp(-1.4, 1.4);
+
+            let p_center = 0.18 + geom.lateral * 0.015 - arrhythmia * 0.02;
+            let p_width = (0.04 + 0.015 * variability).clamp(0.03, 0.08);
+            let p_shape = gaussian(lead_phase, p_center, p_width);
+            let p_wave_mv = amplitude_scale * (0.11 + axis_gain * 0.045) * p_shape;
+
+            let qrs_center = 0.32 + geom.inferior * 0.01 - arrhythmia * 0.015;
+            let qrs_shape = qrs_triplet(lead_phase, qrs_center, qrs_width * 0.6);
+            let polarity = if axis_gain >= 0.0 { 1.0 } else { -1.0 };
+            let qrs_wave_mv =
+                polarity * amplitude_scale * (0.95 + axis_gain.abs() * 0.55) * qrs_shape;
+
+            let t_center = 0.6 + geom.anterior * 0.04 + arrhythmia * 0.03;
+            let t_width = (0.1 + 0.04 * variability).clamp(0.07, 0.18);
+            let t_shape = gaussian(lead_phase, t_center, t_width);
+            let t_wave_mv = amplitude_scale * (0.35 + axis_gain * 0.06) * t_shape;
+
+            let baseline_target = (st_target + axis_gain * 0.05).clamp(-0.7, 0.7);
+            lead_state.baseline_mv =
+                relax(lead_state.baseline_mv, baseline_target, dt_seconds, 1.6);
+
+            lead_state.noise_phase =
+                (lead_state.noise_phase + dt_seconds * (1.6 + idx as f32 * 0.35)).fract();
+            let noise = arrhythmia * 0.22 * (lead_state.noise_phase * TAU).sin()
+                + variability * 0.11 * ((lead_state.noise_phase * TAU * 2.0).sin());
+
+            let amplitude_mv = p_wave_mv + qrs_wave_mv + t_wave_mv + lead_state.baseline_mv + noise;
+
+            lead_samples.push(EkgLeadSample {
+                lead: lead_state.lead,
+                amplitude_mv,
+                p_wave_mv,
+                qrs_complex_mv: qrs_wave_mv,
+                t_wave_mv,
+                st_deviation_mv: lead_state.baseline_mv,
+                noise_mv: noise,
+            });
+        }
+
+        self.time_elapsed_s += dt_seconds;
+        self.last_rr_interval_s = rr_interval;
+        self.last_snapshot = Some(EkgSnapshot {
+            heart_id: self.heart_id.clone(),
+            time_s: self.time_elapsed_s,
+            heart_rate_bpm: state.heart_rate_bpm,
+            rr_interval_s: rr_interval,
+            rhythm: state.rhythm,
+            frontal_axis_deg,
+            variability_index: variability,
+            lead_samples,
+        });
+    }
+
+    /// The most recent snapshot produced by [`observe`].
+    pub fn last_snapshot(&self) -> Option<&EkgSnapshot> {
+        self.last_snapshot.as_ref()
+    }
+
+    /// Last RR interval that drove waveform generation.
+    pub fn last_rr_interval(&self) -> f32 {
+        self.last_rr_interval_s
+    }
+}
+
+#[derive(Debug, Clone)]
+struct LeadState {
+    lead: EkgLead,
+    phase_offset: f32,
+    noise_phase: f32,
+    baseline_mv: f32,
+}
+
+fn sanitize_leads(leads: Vec<EkgLead>) -> Vec<EkgLead> {
+    let mut result = Vec::with_capacity(leads.len().max(1));
+    for lead in leads {
+        if !result.contains(&lead) {
+            result.push(lead);
+        }
+    }
+    if result.is_empty() {
+        result.push(EkgLead::II);
+    }
+    result
+}
+
+fn build_lead_states(leads: &[EkgLead]) -> Vec<LeadState> {
+    leads
+        .iter()
+        .enumerate()
+        .map(|(idx, lead)| LeadState {
+            lead: *lead,
+            phase_offset: (idx as f32) * 0.035,
+            noise_phase: ((idx as f32 + 1.0) * 0.137).fract(),
+            baseline_mv: 0.0,
+        })
+        .collect()
+}
+
+fn derive_axis(state: &HeartElectricalState) -> LeadVector {
+    let lateral = (state.autonomic_tone * 0.6 + (state.contractility_index - 1.0) * 0.4)
+        - state.arrhythmia_burden * 0.15;
+    let inferior = (state.stroke_volume_ml - 65.0) / 35.0
+        + (state.cardiac_output_l_min - 5.0) * 0.12
+        - state.arrhythmia_burden * 0.1
+        + 0.6;
+    let anterior = (state.preload_mm_hg - 8.0) / 16.0 + (state.venous_return_l_min - 5.0) * 0.08
+        - (state.afterload_mm_hg - 95.0) / 240.0
+        + 0.2;
+    LeadVector::new(lateral, inferior, anterior).normalized()
+}
+
+fn derive_amplitude_scale(state: &HeartElectricalState) -> f32 {
+    (0.9 + (state.contractility_index - 1.0) * 0.35
+        + (state.ejection_fraction - 0.55) * 1.1
+        + (state.cardiac_output_l_min - 5.0) * 0.08)
+        .clamp(0.35, 2.4)
+}
+
+fn derive_st_deviation(state: &HeartElectricalState) -> f32 {
+    ((state.coronary_perfusion_mm_hg - 70.0) / 210.0) - (state.arrhythmia_burden * 0.3)
+        + (state.autonomic_tone * 0.1)
+}
+
+fn gaussian(x: f32, center: f32, width: f32) -> f32 {
+    if width <= 0.0 {
+        return 0.0;
+    }
+    let diff = wrap_phase(x - center);
+    (-0.5 * (diff / width).powi(2)).exp()
+}
+
+fn qrs_triplet(phase: f32, center: f32, width: f32) -> f32 {
+    if width <= 0.0 {
+        return 0.0;
+    }
+    let q = -0.35 * gaussian(phase, center - width * 0.8, width * 0.6);
+    let r = 1.35 * gaussian(phase, center, width * 0.5);
+    let s = -0.4 * gaussian(phase, center + width * 0.9, width * 0.7);
+    q + r + s
+}
+
+fn wrap_phase(mut value: f32) -> f32 {
+    if value > 0.5 {
+        value -= 1.0;
+    } else if value < -0.5 {
+        value += 1.0;
+    }
+    value
+}
+
+fn relax(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
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn monitor_tracks_heart_activity() {
+        let mut heart = Heart::new("ekg", 12);
+        // induce slight sympathetic tone to exercise dynamics
+        heart.autonomic_tone = 0.3;
+        let mut monitor = EkgMonitor::from_heart(&heart);
+        let dt = 0.01;
+        for _ in 0..2000 {
+            heart.update(dt);
+            let state = HeartElectricalState::from(&heart);
+            monitor.observe(&state, dt);
+        }
+        let snapshot = monitor.last_snapshot().expect("snapshot available");
+        assert_eq!(snapshot.lead_samples.len(), heart.leads as usize);
+        assert!((snapshot.heart_rate_bpm - heart.heart_rate_bpm).abs() < 1.0);
+        assert!(snapshot
+            .lead_samples
+            .iter()
+            .any(|s| s.amplitude_mv.abs() > 0.2));
+    }
+
+    #[test]
+    fn lead_configuration_can_change() {
+        let heart = Heart::new("ekg", 12);
+        let mut monitor = EkgMonitor::from_heart(&heart);
+        monitor.configure_leads(vec![EkgLead::V1, EkgLead::II, EkgLead::V6, EkgLead::II]);
+        assert_eq!(monitor.leads().len(), 3);
+        assert_eq!(monitor.leads(), vec![EkgLead::V1, EkgLead::II, EkgLead::V6]);
+    }
+}

src/ffi.rs

@@ -11,6 +11,9 @@ use core::ffi::{c_char, c_void, CStr};
 use std::ffi::CString;
 use std::ptr;
 
+use crate::organs::{
+    BladderMetrics, BladderPhase, BloodstreamMetrics, MetabolicState, PerfusionState,
+};
 use crate::patient::Patient;
 use crate::types::OrganType;
 
@@ -48,6 +51,205 @@ pub const ML_ORGAN_BLADDER: u32 = 11;
 /// Organ code for `OrganType::Spleen`.
 pub const ML_ORGAN_SPLEEN: u32 = 12;
 
+/// Organ code for `OrganType::Bloodstream`.
+pub const ML_ORGAN_BLOODSTREAM: u32 = 13;
+
+#[repr(u32)]
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum MLBladderPhase {
+    Filling = 0,
+    Voiding = 1,
+    PostVoidRefractory = 2,
+}
+
+impl From<BladderPhase> for MLBladderPhase {
+    fn from(phase: BladderPhase) -> Self {
+        match phase {
+            BladderPhase::Filling => MLBladderPhase::Filling,
+            BladderPhase::Voiding => MLBladderPhase::Voiding,
+            BladderPhase::PostVoidRefractory => MLBladderPhase::PostVoidRefractory,
+        }
+    }
+}
+
+#[repr(u32)]
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum MLPerfusionState {
+    Balanced = 0,
+    Compensated = 1,
+    Hypovolemic = 2,
+    Shock = 3,
+}
+
+impl From<PerfusionState> for MLPerfusionState {
+    fn from(state: PerfusionState) -> Self {
+        match state {
+            PerfusionState::Balanced => MLPerfusionState::Balanced,
+            PerfusionState::Compensated => MLPerfusionState::Compensated,
+            PerfusionState::Hypovolemic => MLPerfusionState::Hypovolemic,
+            PerfusionState::Shock => MLPerfusionState::Shock,
+        }
+    }
+}
+
+#[repr(u32)]
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum MLMetabolicState {
+    Aerobic = 0,
+    CompensatedAnaerobic = 1,
+    AnaerobicCrisis = 2,
+}
+
+impl From<MetabolicState> for MLMetabolicState {
+    fn from(state: MetabolicState) -> Self {
+        match state {
+            MetabolicState::Aerobic => MLMetabolicState::Aerobic,
+            MetabolicState::CompensatedAnaerobic => MLMetabolicState::CompensatedAnaerobic,
+            MetabolicState::AnaerobicCrisis => MLMetabolicState::AnaerobicCrisis,
+        }
+    }
+}
+
+#[repr(C)]
+#[derive(Debug, Clone, Copy)]
+pub struct MLBladderMetrics {
+    pub phase: MLBladderPhase,
+    pub volume_ml: f32,
+    pub capacity_ml: f32,
+    pub pressure_cm_h2o: f32,
+    pub detrusor_pressure_cm_h2o: f32,
+    pub pressure_safety_limit_cm_h2o: f32,
+    pub afferent_signal: f32,
+    pub urgency: f32,
+    pub cortical_inhibition: f32,
+    pub voluntary_hold_command: f32,
+    pub cortical_gate_fraction: f32,
+    pub voluntary_hold_fraction: f32,
+    pub guarding_reflex_gain: f32,
+    pub pontine_storage_signal: f32,
+    pub pontine_micturition_signal: f32,
+    pub hypogastric_efferent: f32,
+    pub pudendal_efferent: f32,
+    pub parasympathetic_drive: f32,
+    pub sympathetic_drive: f32,
+    pub somatic_drive: f32,
+    pub pressure_stress_index: f32,
+    pub time_above_safety_limit_s: f32,
+}
+
+impl From<BladderMetrics> for MLBladderMetrics {
+    fn from(metrics: BladderMetrics) -> Self {
+        Self {
+            phase: MLBladderPhase::from(metrics.phase),
+            volume_ml: metrics.volume_ml,
+            capacity_ml: metrics.capacity_ml,
+            pressure_cm_h2o: metrics.pressure_cm_h2o,
+            detrusor_pressure_cm_h2o: metrics.detrusor_pressure_cm_h2o,
+            pressure_safety_limit_cm_h2o: metrics.pressure_safety_limit_cm_h2o,
+            afferent_signal: metrics.afferent_signal,
+            urgency: metrics.urgency,
+            cortical_inhibition: metrics.cortical_inhibition,
+            voluntary_hold_command: metrics.voluntary_hold_command,
+            cortical_gate_fraction: metrics.cortical_gate_fraction,
+            voluntary_hold_fraction: metrics.voluntary_hold_fraction,
+            guarding_reflex_gain: metrics.guarding_reflex_gain,
+            pontine_storage_signal: metrics.pontine_storage_signal,
+            pontine_micturition_signal: metrics.pontine_micturition_signal,
+            hypogastric_efferent: metrics.hypogastric_efferent,
+            pudendal_efferent: metrics.pudendal_efferent,
+            parasympathetic_drive: metrics.parasympathetic_drive,
+            sympathetic_drive: metrics.sympathetic_drive,
+            somatic_drive: metrics.somatic_drive,
+            pressure_stress_index: metrics.pressure_stress_index,
+            time_above_safety_limit_s: metrics.time_above_safety_limit_s,
+        }
+    }
+}
+
+#[repr(C)]
+#[derive(Debug, Clone, Copy)]
+pub struct MLBloodstreamMetrics {
+    pub perfusion_state: MLPerfusionState,
+    pub metabolic_state: MLMetabolicState,
+    pub total_volume_l: f32,
+    pub plasma_volume_l: f32,
+    pub red_cell_volume_l: f32,
+    pub plasma_albumin_g_dl: f32,
+    pub plasma_globulin_g_dl: f32,
+    pub plasma_fibrinogen_g_dl: f32,
+    pub oncotic_pressure_mm_hg: f32,
+    pub lymphatic_return_ml_min: f32,
+    pub rbc_young_fraction: f32,
+    pub rbc_mature_fraction: f32,
+    pub rbc_senescent_fraction: f32,
+    pub platelet_count_1e3_per_ul: f32,
+    pub platelet_activation: f32,
+    pub coagulation_factor_activity: f32,
+    pub fibrinolysis_activity: f32,
+    pub thrombosis_risk_index: f32,
+    pub bleeding_risk_index: f32,
+    pub wbc_count_giga_per_l: f32,
+    pub neutrophil_fraction: f32,
+    pub lymphocyte_fraction: f32,
+    pub monocyte_fraction: f32,
+    pub complement_activity: f32,
+    pub inflammation_index: f32,
+    pub bicarbonate_mmol_l: f32,
+    pub base_excess_mmol_l: f32,
+    pub anion_gap_mmol_l: f32,
+    pub arterial_pco2_mm_hg: f32,
+    pub erythropoiesis_rate_ml_per_day: f32,
+    pub erythrocyte_clearance_ml_per_day: f32,
+    pub iron_store_mg: f32,
+    pub folate_store_mg: f32,
+    pub b12_store_mcg: f32,
+    pub hif_activation: f32,
+    pub oxygen_supply_demand_ratio: f32,
+}
+
+impl From<BloodstreamMetrics> for MLBloodstreamMetrics {
+    fn from(metrics: BloodstreamMetrics) -> Self {
+        Self {
+            perfusion_state: MLPerfusionState::from(metrics.perfusion_state),
+            metabolic_state: MLMetabolicState::from(metrics.metabolic_state),
+            total_volume_l: metrics.total_volume_l,
+            plasma_volume_l: metrics.plasma_volume_l,
+            red_cell_volume_l: metrics.red_cell_volume_l,
+            plasma_albumin_g_dl: metrics.plasma_albumin_g_dl,
+            plasma_globulin_g_dl: metrics.plasma_globulin_g_dl,
+            plasma_fibrinogen_g_dl: metrics.plasma_fibrinogen_g_dl,
+            oncotic_pressure_mm_hg: metrics.oncotic_pressure_mm_hg,
+            lymphatic_return_ml_min: metrics.lymphatic_return_ml_min,
+            rbc_young_fraction: metrics.rbc_young_fraction,
+            rbc_mature_fraction: metrics.rbc_mature_fraction,
+            rbc_senescent_fraction: metrics.rbc_senescent_fraction,
+            platelet_count_1e3_per_ul: metrics.platelet_count_1e3_per_ul,
+            platelet_activation: metrics.platelet_activation,
+            coagulation_factor_activity: metrics.coagulation_factor_activity,
+            fibrinolysis_activity: metrics.fibrinolysis_activity,
+            thrombosis_risk_index: metrics.thrombosis_risk_index,
+            bleeding_risk_index: metrics.bleeding_risk_index,
+            wbc_count_giga_per_l: metrics.wbc_count_giga_per_l,
+            neutrophil_fraction: metrics.neutrophil_fraction,
+            lymphocyte_fraction: metrics.lymphocyte_fraction,
+            monocyte_fraction: metrics.monocyte_fraction,
+            complement_activity: metrics.complement_activity,
+            inflammation_index: metrics.inflammation_index,
+            bicarbonate_mmol_l: metrics.bicarbonate_mmol_l,
+            base_excess_mmol_l: metrics.base_excess_mmol_l,
+            anion_gap_mmol_l: metrics.anion_gap_mmol_l,
+            arterial_pco2_mm_hg: metrics.arterial_pco2_mm_hg,
+            erythropoiesis_rate_ml_per_day: metrics.erythropoiesis_rate_ml_per_day,
+            erythrocyte_clearance_ml_per_day: metrics.erythrocyte_clearance_ml_per_day,
+            iron_store_mg: metrics.iron_store_mg,
+            folate_store_mg: metrics.folate_store_mg,
+            b12_store_mcg: metrics.b12_store_mcg,
+            hif_activation: metrics.hif_activation,
+            oxygen_supply_demand_ratio: metrics.oxygen_supply_demand_ratio,
+        }
+    }
+}
+
 /// Opaque patient handle type for C consumers. Wraps a heap-allocated `Patient`.
 #[repr(C)]
 #[derive(Debug)]
@@ -152,6 +354,56 @@ pub extern "C" fn ml_patient_update(p: *mut MLPatient, dt_seconds: f32) -> i32 {
     ML_OK
 }
 
+/// Populate bloodstream metrics for the patient. Returns ML_OK on success.
+#[no_mangle]
+pub extern "C" fn ml_patient_bloodstream_metrics(
+    p: *const MLPatient,
+    out_metrics: *mut MLBloodstreamMetrics,
+) -> i32 {
+    if p.is_null() || out_metrics.is_null() {
+        return ML_EINVAL;
+    }
+    let patient_ptr = unsafe { (*p).inner as *const Patient };
+    if patient_ptr.is_null() {
+        return ML_EINVAL;
+    }
+    let patient = unsafe { &*patient_ptr };
+    match patient.bloodstream_metrics() {
+        Some(metrics) => {
+            unsafe {
+                *out_metrics = MLBloodstreamMetrics::from(metrics);
+            }
+            ML_OK
+        }
+        None => ML_ERR,
+    }
+}
+
+/// Populate bladder metrics for the patient. Returns ML_OK on success.
+#[no_mangle]
+pub extern "C" fn ml_patient_bladder_metrics(
+    p: *const MLPatient,
+    out_metrics: *mut MLBladderMetrics,
+) -> i32 {
+    if p.is_null() || out_metrics.is_null() {
+        return ML_EINVAL;
+    }
+    let patient_ptr = unsafe { (*p).inner as *const Patient };
+    if patient_ptr.is_null() {
+        return ML_EINVAL;
+    }
+    let patient = unsafe { &*patient_ptr };
+    match patient.bladder_metrics() {
+        Some(metrics) => {
+            unsafe {
+                *out_metrics = MLBladderMetrics::from(metrics);
+            }
+            ML_OK
+        }
+        None => ML_ERR,
+    }
+}
+
 /// Return organ summary by type code. See header for codes. Caller frees string.
 #[no_mangle]
 pub extern "C" fn ml_patient_organ_summary(p: *const MLPatient, organ_code: u32) -> *mut c_char {
@@ -176,6 +428,7 @@ pub extern "C" fn ml_patient_organ_summary(p: *const MLPatient, organ_code: u32)
         ML_ORGAN_KIDNEYS => OrganType::Kidneys,
         ML_ORGAN_BLADDER => OrganType::Bladder,
         ML_ORGAN_SPLEEN => OrganType::Spleen,
+        ML_ORGAN_BLOODSTREAM => OrganType::Bloodstream,
         _ => return ptr::null_mut(),
     };
     let summary = unsafe { (*patient_ptr).organ_summary(kind) };
@@ -187,3 +440,5 @@ pub extern "C" fn ml_patient_organ_summary(p: *const MLPatient, organ_code: u32)
         Err(_) => ptr::null_mut(),
     }
 }
+
+

src/lib.rs

@@ -26,6 +26,7 @@
 #![deny(unsafe_code)]
 #![warn(missing_docs, rust_2018_idioms, missing_debug_implementations)]
 
+mod ekg;
 mod error;
 mod organs;
 mod patient;
@@ -34,8 +35,12 @@ mod types;
 #[cfg(feature = "ffi")]
 pub mod ffi;
 
+pub use crate::ekg::{EkgLead, EkgMonitor, EkgSnapshot, HeartElectricalState};
 pub use crate::error::MedicalError;
-pub use crate::organs::{Heart, Organ};
+pub use crate::organs::{
+    Bladder, BladderMetrics, BladderPhase, Bloodstream, BreathingPhase, Heart, Lungs,
+    MetabolicState, Organ, PerfusionState,
+};
 pub use crate::patient::Patient;
 pub use crate::types::{Blood, BloodPressure, OrganType};
 
@@ -158,5 +163,7 @@ mod tests {
         assert!(s.contains("Patient[id=case_01"));
         let heart = p.find_organ_typed::<Heart>().unwrap();
         assert_eq!(heart.organ_type(), OrganType::Heart);
+        let blood = p.find_organ_typed::<Bloodstream>().unwrap();
+        assert_eq!(blood.organ_type(), OrganType::Bloodstream);
     }
 }

src/organs/bladder.rs

@@ -1,21 +1,608 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum BladderPhase {
+    Filling,
+    Voiding,
+    PostVoidRefractory,
+}
+
+#[derive(Debug, Clone)]
+struct ComplianceModel {
+    low_volume_compliance_ml_per_cm_h2o: f32,
+    mid_volume_compliance_ml_per_cm_h2o: f32,
+    high_volume_compliance_ml_per_cm_h2o: f32,
+    detrusor_safety_limit_cm_h2o: f32,
+    viscoelastic_relaxation: f32,
+    stiffness_factor: f32,
+    stress_adaptation_rate: f32,
+    recovery_rate: f32,
+}
+
+impl ComplianceModel {
+    fn new() -> Self {
+        Self {
+            low_volume_compliance_ml_per_cm_h2o: 32.0,
+            mid_volume_compliance_ml_per_cm_h2o: 22.0,
+            high_volume_compliance_ml_per_cm_h2o: 8.5,
+            detrusor_safety_limit_cm_h2o: 40.0,
+            viscoelastic_relaxation: 1.0,
+            stiffness_factor: 1.0,
+            stress_adaptation_rate: 0.08,
+            recovery_rate: 0.015,
+        }
+    }
+
+    fn safety_limit(&self) -> f32 {
+        self.detrusor_safety_limit_cm_h2o
+    }
+
+    fn effective_compliance(&self, normalized_volume: f32, filling_rate_ml_per_min: f32) -> f32 {
+        let nv = normalized_volume.clamp(0.0, 2.0);
+        let logistic_mid = 1.0 / (1.0 + (-10.0 * (nv - 0.55)).exp());
+        let logistic_high = 1.0 / (1.0 + (-16.0 * (nv - 0.9)).exp());
+
+        let base_mid = self.low_volume_compliance_ml_per_cm_h2o
+            - (self.low_volume_compliance_ml_per_cm_h2o - self.mid_volume_compliance_ml_per_cm_h2o)
+                * logistic_mid;
+        let base =
+            base_mid - (base_mid - self.high_volume_compliance_ml_per_cm_h2o) * logistic_high;
+
+        let rate_penalty = (1.0 - filling_rate_ml_per_min / 240.0).clamp(0.65, 1.0);
+        let viscoelastic = base * self.viscoelastic_relaxation * rate_penalty;
+
+        (viscoelastic / self.stiffness_factor).clamp(3.0, 80.0)
+    }
+
+    fn update_state(&mut self, detrusor_pressure: f32, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let limit = self.detrusor_safety_limit_cm_h2o;
+        if detrusor_pressure > limit {
+            let overload = detrusor_pressure - limit;
+            self.viscoelastic_relaxation = (self.viscoelastic_relaxation
+                + self.stress_adaptation_rate * dt_seconds * (1.0 + 0.02 * overload))
+                .clamp(0.85, 1.35);
+            self.stiffness_factor = (self.stiffness_factor
+                + 0.15 * self.stress_adaptation_rate * dt_seconds * (1.0 + overload / limit))
+                .clamp(1.0, 1.8);
+        } else {
+            self.viscoelastic_relaxation =
+                (self.viscoelastic_relaxation - self.recovery_rate * dt_seconds).clamp(0.85, 1.35);
+            self.stiffness_factor =
+                (self.stiffness_factor - 0.25 * self.recovery_rate * dt_seconds).clamp(1.0, 1.8);
+        }
+    }
+}
+
+#[derive(Debug, Clone)]
+struct ReflexState {
+    pelvic_afferent_rate: f32,
+    guarding_reflex_gain: f32,
+    pontine_storage_signal: f32,
+    pontine_micturition_signal: f32,
+    hypogastric_efferent: f32,
+    pudendal_efferent: f32,
+}
+
+impl ReflexState {
+    fn new() -> Self {
+        Self {
+            pelvic_afferent_rate: 0.2,
+            guarding_reflex_gain: 0.4,
+            pontine_storage_signal: 0.5,
+            pontine_micturition_signal: 0.1,
+            hypogastric_efferent: 0.6,
+            pudendal_efferent: 0.6,
+        }
+    }
+}
+
+#[derive(Debug, Clone, Copy)]
+pub struct BladderMetrics {
+    pub phase: BladderPhase,
+    pub volume_ml: f32,
+    pub capacity_ml: f32,
+    pub pressure_cm_h2o: f32,
+    pub detrusor_pressure_cm_h2o: f32,
+    pub pressure_safety_limit_cm_h2o: f32,
+    pub afferent_signal: f32,
+    pub urgency: f32,
+    pub cortical_inhibition: f32,
+    pub voluntary_hold_command: f32,
+    pub cortical_gate_fraction: f32,
+    pub voluntary_hold_fraction: f32,
+    pub guarding_reflex_gain: f32,
+    pub pontine_storage_signal: f32,
+    pub pontine_micturition_signal: f32,
+    pub hypogastric_efferent: f32,
+    pub pudendal_efferent: f32,
+    pub parasympathetic_drive: f32,
+    pub sympathetic_drive: f32,
+    pub somatic_drive: f32,
+    pub pressure_stress_index: f32,
+    pub time_above_safety_limit_s: f32,
+}
+
 #[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,
+    /// Detected detrusor component of intravesical pressure (cmH2O).
+    pub detrusor_pressure_cm_h2o: 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,
+    /// Baseline cystometric capacity for demographic scaling (ml).
+    pub baseline_capacity_ml: f32,
+    /// Chronological age in years influencing thresholds.
+    pub age_years: f32,
+    /// Integrity of supraspinal and spinal pathways (0..=1).
+    pub neurologic_integrity: f32,
+    /// Habitual continence training or pelvic floor conditioning (0..=1).
+    pub continence_training: f32,
+    /// Descending cortical inhibition of the micturition reflex (0..=1).
+    pub cortical_inhibition: f32,
+    /// Voluntary hold motor command (0..=1) driving pelvic floor recruitment.
+    pub voluntary_hold_command: f32,
+    /// Filtered cortical gate strength (0..=1) applied to reflex loops.
+    pub cortical_gate_fraction: f32,
+    /// Filtered voluntary hold strength (0..=1) applied to sphincter control.
+    pub voluntary_hold_fraction: f32,
+    /// Adaptive compliance model governing pressure-volume behavior.
+    compliance: ComplianceModel,
+    /// Integrated reflex pathways coordinating storage and voiding.
+    reflex: ReflexState,
+    /// 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,
+    /// Exponentially-weighted overload index tracking detrusor pressure burden (cmH2O·s).
+    pub pressure_stress_index: f32,
+    /// Cumulative time the detrusor pressure exceeded the safety limit (seconds).
+    pub time_above_safety_limit_s: 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,
-            pressure: 5.0,
+            volume_ml: 120.0,
+            pressure: 8.0,
+            detrusor_pressure_cm_h2o: 5.0,
+            afferent_signal: 0.1,
+            urgency: 0.1,
+            phase: BladderPhase::Filling,
+            capacity_ml: 500.0,
+            residual_volume_ml: 30.0,
+            baseline_capacity_ml: 500.0,
+            age_years: 38.0,
+            neurologic_integrity: 1.0,
+            continence_training: 0.65,
+            cortical_inhibition: 0.6,
+            voluntary_hold_command: 0.45,
+            cortical_gate_fraction: 0.0,
+            voluntary_hold_fraction: 0.0,
+            compliance: ComplianceModel::new(),
+            reflex: ReflexState::new(),
+            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,
+            pressure_stress_index: 0.0,
+            time_since_last_void_s: 0.0,
+            time_above_safety_limit_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 cortical_gate_strength(&self) -> f32 {
+        let training = 0.4 + 0.6 * self.continence_training;
+        (self.cortical_inhibition * self.neurologic_integrity * training).clamp(0.0, 1.0)
+    }
+
+    fn voluntary_hold_strength(&self) -> f32 {
+        let training = 0.35 + 0.65 * self.continence_training;
+        (self.voluntary_hold_command * training * self.neurologic_integrity).clamp(0.0, 1.0)
+    }
+
+    fn update_voluntary_modulators(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let cortical_target = self.cortical_gate_strength();
+        self.cortical_gate_fraction = Self::approach(
+            self.cortical_gate_fraction,
+            cortical_target,
+            1.2,
+            dt_seconds,
+        )
+        .clamp(0.0, 1.0);
+        let hold_target = self.voluntary_hold_strength();
+        self.voluntary_hold_fraction =
+            Self::approach(self.voluntary_hold_fraction, hold_target, 1.6, dt_seconds)
+                .clamp(0.0, 1.0);
+    }
+
+    fn update_threshold_targets(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let baseline_capacity = self.baseline_capacity_ml.max(320.0);
+        let age_factor = if self.age_years <= 40.0 {
+            1.0 + (40.0 - self.age_years).max(0.0) * 0.0035
+        } else {
+            (1.0 - (self.age_years - 40.0) * 0.003).clamp(0.74, 1.08)
+        };
+        let neurologic_factor = (0.55 + 0.45 * self.neurologic_integrity).clamp(0.45, 1.1);
+        let capacity_target =
+            (baseline_capacity * age_factor * neurologic_factor).clamp(240.0, 720.0);
+        self.capacity_ml =
+            Self::approach(self.capacity_ml, capacity_target, 0.5, dt_seconds).clamp(160.0, 900.0);
+
+        let diuresis_ratio = (self.filling_rate_ml_per_min / 60.0).clamp(0.25, 2.5);
+        let diuresis_factor = diuresis_ratio.powf(-0.18).clamp(0.82, 1.18);
+        let voluntary_buffer = (1.0
+            + 0.22 * self.cortical_gate_fraction
+            + 0.25 * self.voluntary_hold_fraction
+            + 0.12 * self.continence_training)
+            .clamp(0.8, 1.5);
+        let neurologic_drop = (1.0 - 0.3 * (1.0 - self.neurologic_integrity)).clamp(0.55, 1.05);
+
+        let urge_fraction = (0.38 + 0.08 * self.voluntary_hold_fraction
+            - 0.1 * (1.0 - self.neurologic_integrity))
+            .clamp(0.25, 0.6);
+        let mut urge_target =
+            capacity_target * urge_fraction * diuresis_factor * voluntary_buffer * neurologic_drop;
+        urge_target = urge_target.clamp(capacity_target * 0.22, capacity_target * 0.75);
+
+        let mict_fraction = (0.68 + 0.1 * self.voluntary_hold_fraction
+            - 0.15 * (1.0 - self.neurologic_integrity))
+            .clamp(0.5, 0.92);
+        let mut mict_target = capacity_target
+            * mict_fraction
+            * diuresis_factor.powf(0.75)
+            * voluntary_buffer
+            * neurologic_drop;
+        mict_target = mict_target.clamp(urge_target + 25.0, capacity_target * 0.95);
+
+        self.urge_threshold_ml =
+            Self::approach(self.urge_threshold_ml, urge_target, 0.8, dt_seconds).clamp(50.0, 800.0);
+        self.micturition_threshold_ml =
+            Self::approach(self.micturition_threshold_ml, mict_target, 0.7, dt_seconds)
+                .clamp(60.0, 850.0);
+    }
+
+    fn update_reflex_gate(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let normalized_volume = (self.volume_ml / self.capacity_ml).clamp(0.0, 1.7);
+        let detrusor_ratio =
+            (self.detrusor_pressure_cm_h2o / self.compliance.safety_limit()).clamp(0.0, 2.0);
+        let cortical_damping = (1.0 - 0.35 * self.cortical_gate_fraction).clamp(0.55, 1.0);
+        let neuro_sensitivity = (1.0 + 0.25 * (1.0 - self.neurologic_integrity)).clamp(0.8, 1.3);
+        let pelvic_drive =
+            (0.32 * normalized_volume + 0.45 * self.afferent_signal + 0.23 * detrusor_ratio)
+                * cortical_damping
+                * neuro_sensitivity;
+        let pelvic_target = pelvic_drive.clamp(0.0, 1.2);
+        self.reflex.pelvic_afferent_rate = Self::approach(
+            self.reflex.pelvic_afferent_rate,
+            pelvic_target.min(1.0),
+            1.6,
+            dt_seconds,
+        );
+
+        let voluntary_buffer = (self.voluntary_hold_fraction * 0.45).clamp(0.0, 0.45);
+        let storage_modulator =
+            (1.0 - self.urgency * (1.0 - 0.35 * self.cortical_gate_fraction)).clamp(0.0, 1.0);
+        let guarding_target = if matches!(self.phase, BladderPhase::Voiding) {
+            0.05
+        } else {
+            ((self.reflex.pelvic_afferent_rate + 0.12) * storage_modulator).powf(0.7)
+                + voluntary_buffer
+        };
+        self.reflex.guarding_reflex_gain = Self::approach(
+            self.reflex.guarding_reflex_gain,
+            guarding_target.clamp(0.0, 1.0),
+            1.4,
+            dt_seconds,
+        );
+
+        let mut supraspinal_trigger = ((self.reflex.pelvic_afferent_rate - 0.55).max(0.0)
+            * self.urgency.powf(1.2)
+            + (self.detrusor_pressure_cm_h2o - self.compliance.safety_limit()).max(0.0) / 40.0)
+            .clamp(0.0, 1.2);
+        supraspinal_trigger =
+            (supraspinal_trigger * (1.0 - 0.5 * self.cortical_gate_fraction)).clamp(0.0, 1.2);
+
+        let pontine_void_base = match self.phase {
+            BladderPhase::Voiding => (0.5 + 0.6 * supraspinal_trigger).clamp(0.0, 1.0),
+            BladderPhase::PostVoidRefractory => (0.2 * supraspinal_trigger).clamp(0.0, 0.4),
+            BladderPhase::Filling => (0.35 * supraspinal_trigger).clamp(0.0, 0.85),
+        };
+        let pontine_void_target =
+            (pontine_void_base * (1.0 - 0.55 * self.cortical_gate_fraction)).clamp(0.0, 1.0);
+        let pontine_storage_target = if matches!(self.phase, BladderPhase::Voiding) {
+            (0.1 + 0.2 * (1.0 - supraspinal_trigger) + 0.15 * self.voluntary_hold_fraction)
+                .clamp(0.0, 0.45)
+        } else {
+            (0.45 + 0.5 * self.reflex.guarding_reflex_gain - 0.4 * supraspinal_trigger
+                + 0.35 * self.cortical_gate_fraction
+                + 0.2 * self.voluntary_hold_fraction)
+                .clamp(0.0, 1.0)
+        };
+
+        self.reflex.pontine_micturition_signal = Self::approach(
+            self.reflex.pontine_micturition_signal,
+            pontine_void_target,
+            1.0,
+            dt_seconds,
+        )
+        .clamp(0.0, 1.0);
+        self.reflex.pontine_storage_signal = Self::approach(
+            self.reflex.pontine_storage_signal,
+            pontine_storage_target,
+            1.0,
+            dt_seconds,
+        )
+        .clamp(0.0, 1.0);
+    }
+
+    fn update_reflex_efferents(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let sympathetic_bias = (0.6 + 0.2 * self.neurologic_integrity).clamp(0.4, 0.9);
+        let hypogastric_target = (sympathetic_bias * self.sympathetic_drive
+            + 0.35 * self.reflex.pontine_storage_signal
+            - 0.45 * self.reflex.pontine_micturition_signal
+            + 0.15 * self.cortical_gate_fraction)
+            .clamp(0.0, 1.0);
+        let pudendal_target = ((0.55 + 0.15 * self.continence_training) * self.somatic_drive
+            + 0.25 * self.reflex.guarding_reflex_gain
+            + 0.35 * self.voluntary_hold_fraction
+            - 0.55 * self.reflex.pontine_micturition_signal)
+            * (0.7 + 0.3 * self.neurologic_integrity);
+        let pudendal_target = pudendal_target.clamp(0.0, 1.0);
+        self.reflex.hypogastric_efferent = Self::approach(
+            self.reflex.hypogastric_efferent,
+            hypogastric_target,
+            1.8,
+            dt_seconds,
+        );
+        self.reflex.pudendal_efferent = Self::approach(
+            self.reflex.pudendal_efferent,
+            pudendal_target,
+            1.8,
+            dt_seconds,
+        );
+    }
+
+    fn update_drives(&mut self, dt_seconds: f32) {
+        let urgency = self.urgency;
+        let safety_ratio =
+            (self.detrusor_pressure_cm_h2o / self.compliance.safety_limit()).clamp(0.0, 2.0);
+        let safety_bias = (safety_ratio.powf(1.2) * 0.35).clamp(0.0, 0.4);
+        let storage_bias = (self.reflex.pontine_storage_signal * 0.6).clamp(0.0, 0.6);
+        let void_bias = self.reflex.pontine_micturition_signal;
+        let cortical_filter = (1.0 - 0.4 * self.cortical_gate_fraction).clamp(0.35, 1.0);
+        let parasym_target =
+            (urgency.powf(1.2) * cortical_filter + safety_bias + 0.7 * void_bias).clamp(0.0, 1.0);
+        let sym_target = (1.0
+            - 0.6 * urgency * (1.0 - 0.3 * self.cortical_gate_fraction)
+            - 0.3 * safety_bias
+            - 0.6 * void_bias
+            + storage_bias
+            + 0.15 * self.cortical_gate_fraction)
+            .clamp(0.15, 1.0);
+        let voluntary_boost =
+            (0.35 * self.voluntary_hold_fraction + 0.2 * self.continence_training).clamp(0.0, 0.45);
+        let somatic_target = ((0.55 + 0.25 * self.continence_training) * (1.0 - urgency * 0.55)
+            + storage_bias * 0.45
+            + voluntary_boost
+            - void_bias * 0.5)
+            * (0.75 + 0.25 * self.neurologic_integrity);
+
+        self.parasympathetic_drive =
+            Self::approach(self.parasympathetic_drive, parasym_target, 0.8, dt_seconds)
+                .clamp(0.0, 1.0);
+        self.sympathetic_drive =
+            Self::approach(self.sympathetic_drive, sym_target, 0.6, dt_seconds).clamp(0.0, 1.0);
+        self.somatic_drive = Self::approach(
+            self.somatic_drive,
+            somatic_target.clamp(0.2, 1.05),
+            0.9,
+            dt_seconds,
+        )
+        .clamp(0.0, 1.0);
+    }
+
+    fn update_sphincters(&mut self) {
+        let internal = (0.28 + 0.65 * self.sympathetic_drive + 0.1 * self.cortical_gate_fraction)
+            .clamp(0.0, 1.0);
+        let external = ((0.18 + 0.7 * self.somatic_drive + 0.25 * self.voluntary_hold_fraction)
+            * (0.75 + 0.25 * self.neurologic_integrity))
+            .clamp(0.0, 1.0);
+        self.internal_sphincter_tone = internal;
+        self.external_sphincter_tone = external;
+    }
+
+    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)
+        };
+        let pressure_bias =
+            (self.detrusor_pressure_cm_h2o / self.compliance.safety_limit()).clamp(0.0, 1.5) * 0.2;
+        let neurologic_gain = (1.0 + 0.35 * (1.0 - self.neurologic_integrity)).clamp(1.0, 1.4);
+        self.afferent_signal = ((low_volume_component + fullness_component + pressure_bias)
+            * neurologic_gain)
+            .clamp(0.0, 1.2);
+        let cortical_relief = (1.0 - 0.45 * self.cortical_gate_fraction).clamp(0.5, 1.0);
+        let voluntary_relief =
+            (1.0 - 0.35 * self.voluntary_hold_fraction - 0.1 * self.continence_training)
+                .clamp(0.45, 1.0);
+        self.urgency =
+            (self.afferent_signal.powf(1.35) * cortical_relief * voluntary_relief).clamp(0.0, 1.0);
+    }
+
+    fn update_pressure_safety_metrics(&mut self, detrusor_pressure: f32, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+        let limit = self.compliance.safety_limit();
+        let overload = (detrusor_pressure - limit).max(0.0);
+        let decay = (-dt_seconds / 600.0).exp();
+        if overload > 0.0 {
+            self.time_above_safety_limit_s += dt_seconds;
+            self.pressure_stress_index =
+                (self.pressure_stress_index * decay + overload * dt_seconds).min(5000.0);
+        } else {
+            self.pressure_stress_index = (self.pressure_stress_index * decay).max(0.0);
+        }
+    }
+
+    fn update_pressure(&mut self, dt_seconds: f32) {
+        let normalized_volume = (self.volume_ml / self.capacity_ml).clamp(0.0, 2.0);
+        let effective_compliance = self
+            .compliance
+            .effective_compliance(normalized_volume, self.filling_rate_ml_per_min);
+
+        let passive_volume_ml = (self.volume_ml - self.residual_volume_ml).max(0.0);
+        let passive_detrusor = if effective_compliance > f32::EPSILON {
+            passive_volume_ml / effective_compliance
+        } else {
+            0.0
+        };
+        let toe_region_gain = 1.0 + normalized_volume.powf(3.2) * 0.6;
+        let passive_detrusor = (passive_detrusor * toe_region_gain).clamp(0.0, 60.0);
+
+        let active_detrusor = (36.0 + 6.0 * normalized_volume) * self.parasympathetic_drive;
+        let detrusor_pressure = (passive_detrusor + active_detrusor).clamp(0.0, 95.0);
+
+        self.compliance.update_state(detrusor_pressure, dt_seconds);
+
+        let abdominal_pressure = self.baseline_pressure_cm_h2o
+            + 2.0 * normalized_volume
+            + 0.5 * self.internal_sphincter_tone;
+
+        self.detrusor_pressure_cm_h2o = detrusor_pressure;
+        self.pressure = (abdominal_pressure + detrusor_pressure).clamp(0.0, 110.0);
+
+        self.update_pressure_safety_metrics(detrusor_pressure, dt_seconds);
+    }
+
+    fn handle_filling_phase(&mut self, _dt_seconds: f32) {
+        if (self.volume_ml >= self.micturition_threshold_ml
+            || self.detrusor_pressure_cm_h2o > self.compliance.safety_limit() + 5.0)
+            && (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.detrusor_pressure_cm_h2o / 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;
+        }
+    }
+    pub fn metrics(&self) -> BladderMetrics {
+        BladderMetrics {
+            phase: self.phase,
+            volume_ml: self.volume_ml,
+            capacity_ml: self.capacity_ml,
+            pressure_cm_h2o: self.pressure,
+            detrusor_pressure_cm_h2o: self.detrusor_pressure_cm_h2o,
+            pressure_safety_limit_cm_h2o: self.compliance.safety_limit(),
+            afferent_signal: self.afferent_signal,
+            urgency: self.urgency,
+            cortical_inhibition: self.cortical_inhibition,
+            voluntary_hold_command: self.voluntary_hold_command,
+            cortical_gate_fraction: self.cortical_gate_fraction,
+            voluntary_hold_fraction: self.voluntary_hold_fraction,
+            guarding_reflex_gain: self.reflex.guarding_reflex_gain,
+            pontine_storage_signal: self.reflex.pontine_storage_signal,
+            pontine_micturition_signal: self.reflex.pontine_micturition_signal,
+            hypogastric_efferent: self.reflex.hypogastric_efferent,
+            pudendal_efferent: self.reflex.pudendal_efferent,
+            parasympathetic_drive: self.parasympathetic_drive,
+            sympathetic_drive: self.sympathetic_drive,
+            somatic_drive: self.somatic_drive,
+            pressure_stress_index: self.pressure_stress_index,
+            time_above_safety_limit_s: self.time_above_safety_limit_s,
         }
     }
 }
@@ -27,16 +614,52 @@ 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_voluntary_modulators(dt_seconds);
+        self.update_threshold_targets(dt_seconds);
+        self.update_afferents();
+        self.update_reflex_gate(dt_seconds);
+        self.update_drives(dt_seconds);
+        self.update_sphincters();
+        self.update_pressure(dt_seconds);
+        self.update_reflex_efferents(dt_seconds);
+
+        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 (det={:.1}), urge={:.0}%, stress={:.0}, guard={:.0}%, void={:.0}%, gate={:.0}%, hold={:.0}%]",
             self.id(),
+            self.phase,
             self.volume_ml,
-            self.pressure
+            self.capacity_ml,
+            self.pressure,
+            self.detrusor_pressure_cm_h2o,
+            self.urgency * 100.0,
+            self.pressure_stress_index,
+            self.reflex.guarding_reflex_gain * 100.0,
+            self.reflex.pontine_micturition_signal * 100.0,
+            self.cortical_gate_fraction * 100.0,
+            self.voluntary_hold_fraction * 100.0
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {
@@ -46,3 +669,181 @@ impl Organ for Bladder {
         self
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn compliance_declines_with_high_volume() {
+        let model = ComplianceModel::new();
+        let compliance_low = model.effective_compliance(0.3, 60.0);
+        let compliance_high = model.effective_compliance(1.3, 60.0);
+        assert!(compliance_low > compliance_high);
+    }
+
+    #[test]
+    fn detrusor_overload_updates_risk_metrics() {
+        let mut bladder = Bladder::new("test");
+        bladder.volume_ml = bladder.capacity_ml * 1.35;
+        bladder.parasympathetic_drive = 0.7;
+        bladder.sympathetic_drive = 0.2;
+        bladder.internal_sphincter_tone = 0.2;
+        bladder.external_sphincter_tone = 0.2;
+
+        bladder.update_pressure(1.0);
+
+        assert!(
+            bladder.detrusor_pressure_cm_h2o > bladder.compliance.safety_limit(),
+            "expected detrusor {} to exceed limit {}",
+            bladder.detrusor_pressure_cm_h2o,
+            bladder.compliance.safety_limit()
+        );
+        assert!(bladder.time_above_safety_limit_s > 0.0);
+        assert!(bladder.pressure_stress_index > 0.0);
+    }
+
+    #[test]
+    fn stress_index_decays_when_pressure_normalizes() {
+        let mut bladder = Bladder::new("test");
+        bladder.pressure_stress_index = 200.0;
+        bladder.time_above_safety_limit_s = 12.0;
+        bladder.volume_ml = 140.0;
+        bladder.parasympathetic_drive = 0.05;
+        bladder.sympathetic_drive = 0.9;
+        bladder.internal_sphincter_tone = 0.9;
+        bladder.external_sphincter_tone = 0.9;
+
+        bladder.update_pressure(1.5);
+        let after = bladder.pressure_stress_index;
+        bladder.update_pressure(1.5);
+        assert!(
+            after < 200.0 && bladder.pressure_stress_index <= after,
+            "expected stress index to decay, got {} then {}",
+            after,
+            bladder.pressure_stress_index
+        );
+    }
+
+    #[test]
+    fn guarding_reflex_active_during_storage() {
+        let mut bladder = Bladder::new("storage");
+        bladder.volume_ml = bladder.urge_threshold_ml + 60.0;
+        bladder.update(1.0);
+        assert!(bladder.reflex.guarding_reflex_gain > 0.2);
+        assert!(bladder.reflex.hypogastric_efferent > 0.5);
+        assert!(bladder.reflex.pudendal_efferent > 0.4);
+        assert!(
+            bladder.reflex.pontine_storage_signal > bladder.reflex.pontine_micturition_signal,
+            "storage center should dominate in filling"
+        );
+    }
+
+    #[test]
+    fn pontine_switch_reduces_guarding_during_void() {
+        let mut bladder = Bladder::new("void");
+        bladder.phase = BladderPhase::Voiding;
+        bladder.volume_ml = bladder.micturition_threshold_ml + 180.0;
+        bladder.detrusor_pressure_cm_h2o = bladder.compliance.safety_limit() + 12.0;
+        bladder.urgency = 0.98;
+
+        bladder.update(0.3);
+        bladder.update(0.2);
+
+        let pontine = bladder.reflex.pontine_micturition_signal;
+        let hypogastric = bladder.reflex.hypogastric_efferent;
+        let pudendal = bladder.reflex.pudendal_efferent;
+
+        assert!(
+            pontine > 0.5,
+            "pontine signal too low: {:.2} (guard={:.2}, aff={:.2})",
+            pontine,
+            bladder.reflex.guarding_reflex_gain,
+            bladder.reflex.pelvic_afferent_rate,
+        );
+        assert!(
+            hypogastric < 0.45,
+            "hypogastric stays high: {:.2}",
+            hypogastric
+        );
+        assert!(pudendal < 0.45, "pudendal stays high: {:.2}", pudendal);
+    }
+
+    #[test]
+    fn cortical_behavioral_inputs_reduce_urgency() {
+        let mut baseline = Bladder::new("baseline");
+        baseline.volume_ml = baseline.micturition_threshold_ml + 120.0;
+        baseline.cortical_inhibition = 0.0;
+        baseline.voluntary_hold_command = 0.0;
+        baseline.continence_training = 0.3;
+        for _ in 0..5 {
+            baseline.update(0.5);
+        }
+
+        let mut conditioned = Bladder::new("conditioned");
+        conditioned.volume_ml = baseline.volume_ml;
+        conditioned.cortical_inhibition = 0.85;
+        conditioned.voluntary_hold_command = 0.8;
+        conditioned.continence_training = 0.85;
+        for _ in 0..5 {
+            conditioned.update(0.5);
+        }
+
+        assert!(
+            conditioned.urgency < baseline.urgency,
+            "expected urgency {:.2} to fall below baseline {:.2}",
+            conditioned.urgency,
+            baseline.urgency
+        );
+        assert!(
+            conditioned.external_sphincter_tone > baseline.external_sphincter_tone,
+            "expected hold to raise sphincter tone {:.2} vs {:.2}",
+            conditioned.external_sphincter_tone,
+            baseline.external_sphincter_tone
+        );
+    }
+
+    #[test]
+    fn thresholds_reflect_age_and_neurologic_status() {
+        let mut young = Bladder::new("young");
+        young.age_years = 25.0;
+        young.neurologic_integrity = 1.0;
+        young.continence_training = 0.5;
+        young.cortical_inhibition = 0.0;
+        young.voluntary_hold_command = 0.0;
+        young.filling_rate_ml_per_min = 45.0;
+        for _ in 0..12 {
+            young.update(1.0);
+        }
+
+        let mut elderly = Bladder::new("elderly");
+        elderly.age_years = 78.0;
+        elderly.neurologic_integrity = 0.45;
+        elderly.continence_training = 0.5;
+        elderly.cortical_inhibition = 0.0;
+        elderly.voluntary_hold_command = 0.0;
+        elderly.filling_rate_ml_per_min = 95.0;
+        for _ in 0..12 {
+            elderly.update(1.0);
+        }
+
+        assert!(
+            elderly.capacity_ml < young.capacity_ml,
+            "expected elderly capacity {:.1} < young {:.1}",
+            elderly.capacity_ml,
+            young.capacity_ml
+        );
+        assert!(
+            elderly.urge_threshold_ml < young.urge_threshold_ml,
+            "expected elderly urge {:.1} < young {:.1}",
+            elderly.urge_threshold_ml,
+            young.urge_threshold_ml
+        );
+        assert!(
+            elderly.micturition_threshold_ml < young.micturition_threshold_ml,
+            "expected elderly mict {:.1} < young {:.1}",
+            elderly.micturition_threshold_ml,
+            young.micturition_threshold_ml
+        );
+    }
+}

src/organs/brain.rs

@@ -1,23 +1,521 @@
 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;
+
+/// Median sleep cycle duration from large-scale polysomnography study (Åkerstedt et al. 2024).
+/// Sleep Health: 96 min median across 6,064 sleep cycles.
+const TYPICAL_CYCLE_DURATION_S: f32 = 96.0 * 60.0;
+
+/// REM latency typically 60-120 minutes in healthy adults (Carskadon & Dement, StatPearls 2024).
+const FIRST_REM_LATENCY_S: f32 = 90.0 * 60.0;
+
+/// 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,
+    /// Chemoreceptor-driven urge to ventilate (0..~1.3).
+    pub respiratory_drive: f32,
+    /// Likelihood of hypocapnic syncope (0..=1).
+    pub syncope_propensity: f32,
+    /// Osmotic/volume-inspired thirst drive (0..~1.4).
+    pub thirst_drive: f32,
+    /// Nutritional hunger drive (0..~1.3).
+    pub hunger_drive: f32,
+    /// Thermoregulatory discomfort drive (0..~1.2).
+    pub thermoregulatory_drive: f32,
+    /// Aggregated nociceptive/pain drive (0..~1.5).
+    pub pain_drive: f32,
+    time_in_stage_s: f32,
+    /// Total time asleep in current sleep bout (seconds).
+    time_asleep_s: f32,
+    /// Cumulative count of sleep cycles completed in current sleep bout.
+    sleep_cycle_count: u32,
+    /// Sleep spindle density (count per minute) during N2 sleep.
+    /// Normal range: 2-5 spindles/min (Fernandez & Lüthi, Nat Neurosci 2020).
+    pub spindle_density_per_min: f32,
+    /// K-complex count per minute during N2 sleep.
+    /// Typically 1-3 per minute (Colrain, Sleep Med Rev 2005).
+    pub k_complex_density_per_min: f32,
+    /// Sigma band power (11-16 Hz) relative to baseline, proxy for spindle activity.
+    /// High correlation with spindle amplitude r=0.95 (Warby et al., Nat Methods 2014).
+    pub sigma_power_relative: f32,
+    /// Chin EMG tonic activity during REM as fraction of NREM baseline.
+    /// Normal REM: <10% tonic activity (Frauscher et al., Sleep 2014).
+    pub rem_tonic_emg_fraction: f32,
+    /// Chin EMG phasic burst activity during REM (% of 30-s epoch).
+    /// Normal: <15% phasic activity (Frauscher et al., Sleep 2014).
+    pub rem_phasic_emg_pct: f32,
+    /// REM atonia index: fraction of REM sleep with muscle atonia.
+    /// Normal: >85-90% atonia (McCarter et al., Sleep 2014).
+    pub rem_atonia_index: f32,
+    // Brainstem nuclei activities (0..=1 representing normalized firing rates)
+    /// Nucleus tractus solitarius (NTS) activity processing baroreceptor input.
+    /// Receives afferents from CN IX/X; inhibits RVLM (Dampney, Clin Exp Pharmacol Physiol 2016).
+    pub nts_activity: f32,
+    /// Rostral ventrolateral medulla (RVLM) sympathetic premotor neuron activity.
+    /// Primary source of tonic sympathetic vasomotor drive (Guyenet, Nat Rev Neurosci 2006).
+    pub rvlm_activity: f32,
+    /// Caudal ventrolateral medulla (CVLM) inhibitory interneuron activity.
+    /// Receives NTS input; inhibits RVLM to reduce sympathetic tone.
+    pub cvlm_activity: f32,
+    /// Nucleus ambiguus (nAmb) cardiovagal neuron activity.
+    /// Primary cardiac vagal efferent controlling HR via myelinated fibers (McAllen et al., J Physiol 2011).
+    pub namb_cardiovagal_activity: f32,
+    /// Dorsal motor nucleus of vagus (DMV) cardiac neuron activity.
+    /// ~20% of cardiovagal neurons; unmyelinated C-fibers; modulates contractility (Gourine et al., iScience 2024).
+    pub dmv_cardiac_activity: f32,
+    /// Retrotrapezoid nucleus (RTN) central chemoreceptor neuron activity.
+    /// CO2/pH sensitive; drives 2/3 of ventilatory CO2 response (Guyenet & Bayliss, J Neurosci 2025).
+    pub rtn_chemoreceptor_activity: f32,
+    /// Peripheral chemoreceptor signal from carotid/aortic bodies via NTS.
+    /// Primarily O2, also CO2/pH; ~1/3 of CO2 response (Guyenet & Bayliss, J Appl Physiol 2010).
+    pub peripheral_chemo_signal: f32,
+    // Cerebrovascular autoregulation parameters
+    /// Cerebrovascular resistance (mmHg·min·100g/mL).
+    /// Normal ~1.4 at baseline CPP=70 mmHg, CBF=50 mL/100g/min (Paulson et al., Cerebrovasc Dis 1990).
+    pub cerebrovascular_resistance: f32,
+    /// Lower autoregulation limit (mmHg CPP).
+    /// Normal ~50 mmHg; shifts with chronic hypertension (Drummond, BJA 2024).
+    pub autoregulation_lower_limit: f32,
+    /// Upper autoregulation limit (mmHg CPP).
+    /// Normal ~150 mmHg; breakthrough above this causes edema (Drummond, BJA 2024).
+    pub autoregulation_upper_limit: f32,
+    /// Autoregulation curve slope (normalized 0..=1).
+    /// 0 = no autoregulation (passive pressure-flow), 1 = perfect autoregulation.
+    pub autoregulation_efficiency: f32,
+    /// CO2 reactivity: ΔCBF per mmHg ΔPaCO2 (mL/100g/min per mmHg).
+    /// Normal 1-2 mL/100g/min/mmHg (Claassen et al., Physiol Rev 2021).
+    pub co2_reactivity: 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,
+            respiratory_drive: 0.6,
+            syncope_propensity: 0.05,
+            thirst_drive: 0.3,
+            hunger_drive: 0.35,
+            thermoregulatory_drive: 0.5,
+            pain_drive: 0.2,
+            time_in_stage_s: 0.0,
+            time_asleep_s: 0.0,
+            sleep_cycle_count: 0,
+            spindle_density_per_min: 3.5,
+            k_complex_density_per_min: 2.0,
+            sigma_power_relative: 1.0,
+            rem_tonic_emg_fraction: 0.05,
+            rem_phasic_emg_pct: 8.0,
+            rem_atonia_index: 0.92,
+            nts_activity: 0.5,
+            rvlm_activity: 0.65,
+            cvlm_activity: 0.45,
+            namb_cardiovagal_activity: 0.4,
+            dmv_cardiac_activity: 0.35,
+            rtn_chemoreceptor_activity: 0.6,
+            peripheral_chemo_signal: 0.55,
+            cerebrovascular_resistance: 1.4,
+            autoregulation_lower_limit: 50.0,
+            autoregulation_upper_limit: 150.0,
+            autoregulation_efficiency: 0.85,
+            co2_reactivity: 1.5,
         }
     }
+
+    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 (0.0..TAU).contains(&phase) {
+            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 {
+            // Completing a REM period marks the end of a sleep cycle
+            if self.sleep_stage == SleepStage::Rem && stage != SleepStage::Wake {
+                self.sleep_cycle_count += 1;
+            }
+            // Waking resets sleep bout tracking
+            if stage == SleepStage::Wake && self.sleep_stage != SleepStage::Wake {
+                if self.time_asleep_s > 600.0 {
+                    // Only reset if woke from substantial sleep (>10 min)
+                    self.time_asleep_s = 0.0;
+                    self.sleep_cycle_count = 0;
+                }
+            }
+            self.sleep_stage = stage;
+            self.time_in_stage_s = 0.0;
+        }
+    }
+
+    /// Adaptive cycle timing based on Åkerstedt et al. 2024 (Sleep Health) and homeostatic factors.
+    /// First cycle is shorter; high sleep pressure extends NREM; low pressure extends REM.
+    fn evaluate_sleep_stage(&mut self, base_arousal: f32) {
+        // Cycle modulation: first cycle is shorter (Åkerstedt 2024)
+        let cycle_factor = if self.sleep_cycle_count == 0 {
+            0.85
+        } else {
+            1.0
+        };
+
+        // High sleep pressure extends NREM, low pressure extends REM (Åkerstedt 2024)
+        let nrem_extension = (self.sleep_pressure - 0.5).max(0.0) * 1.2;
+        let rem_extension = (0.5 - self.sleep_pressure).max(0.0) * 1.3;
+
+        match self.sleep_stage {
+            SleepStage::Wake => {
+                if base_arousal < 0.35 && self.sleep_pressure > 0.55 {
+                    self.transition_stage(SleepStage::N1);
+                }
+            }
+            SleepStage::N1 => {
+                // N1 typically 1-7 minutes (Carskadon & Dement, StatPearls 2024)
+                let n1_duration = 180.0 * cycle_factor;
+                if base_arousal > 0.5 {
+                    self.transition_stage(SleepStage::Wake);
+                } else if self.time_in_stage_s > n1_duration && self.sleep_pressure > 0.6 {
+                    self.transition_stage(SleepStage::N2);
+                }
+            }
+            SleepStage::N2 => {
+                // N2 typically 10-25 minutes initially, longer in later cycles
+                let base_n2_duration = 900.0 * cycle_factor * (1.0 + nrem_extension);
+                let n3_threshold = base_n2_duration * (1.0 + nrem_extension);
+
+                // First REM latency 60-120 min (typically 90 min, StatPearls 2024)
+                let rem_ready = if self.sleep_cycle_count == 0 {
+                    self.time_asleep_s > FIRST_REM_LATENCY_S * 0.8
+                } else {
+                    self.time_in_stage_s > base_n2_duration * 1.5
+                };
+
+                if base_arousal > 0.52 {
+                    self.transition_stage(SleepStage::Wake);
+                } else if self.time_in_stage_s > n3_threshold && self.sleep_pressure > 0.65 {
+                    self.transition_stage(SleepStage::N3);
+                } else if rem_ready {
+                    self.transition_stage(SleepStage::Rem);
+                }
+            }
+            SleepStage::N3 => {
+                // N3 duration decreases across night; more in first cycle
+                let n3_duration = if self.sleep_cycle_count == 0 {
+                    1800.0 * (1.0 + nrem_extension)
+                } else {
+                    1200.0 * cycle_factor * (1.0 + nrem_extension)
+                };
+
+                if self.time_in_stage_s > n3_duration {
+                    self.transition_stage(SleepStage::Rem);
+                } else if base_arousal > 0.45 {
+                    self.transition_stage(SleepStage::N2);
+                }
+            }
+            SleepStage::Rem => {
+                // REM duration increases across cycles; first REM ~5-10 min, later ~20-25 min
+                // Positive correlation: longer REM predicts longer interval to next REM
+                let base_rem_duration = if self.sleep_cycle_count == 0 {
+                    600.0 // ~10 min first REM
+                } else {
+                    900.0 + (self.sleep_cycle_count as f32 * 300.0).min(600.0) // up to 25 min
+                };
+                let rem_duration = base_rem_duration * (1.0 + rem_extension);
+
+                if self.time_in_stage_s > rem_duration {
+                    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),
+        }
+    }
+
+    /// Simulate brainstem nuclei interactions for autonomic control.
+    /// Based on:
+    /// - Guyenet (Nat Rev Neurosci 2006): RVLM as sympathetic vasomotor source
+    /// - Dampney (Clin Exp Pharmacol Physiol 2016): NTS→CVLM→RVLM baroreflex arc
+    /// - Gourine et al. (iScience 2024): nAmb/DMV cardiovagal pathways
+    /// - Guyenet & Bayliss (J Neurosci 2025): RTN central chemoreceptors
+    fn update_brainstem_nuclei(&mut self, dt_seconds: f32) {
+        // Baroreceptor input: elevated CPP → increased NTS activity
+        let baroreceptor_input =
+            ((self.cerebral_perfusion_pressure_mm_hg - 70.0) / 40.0).clamp(-0.5, 0.5) + 0.5;
+
+        // Chemoreceptor inputs
+        // Central chemoreceptors (RTN): sensitive to CO2/pH (proxied by respiratory drive)
+        let central_chemo_input = self.respiratory_drive.clamp(0.3, 1.2);
+
+        // Peripheral chemoreceptors: O2 (via oxygenation) + CO2 contribution
+        let o2_signal = (0.98 - self.oxygenation_saturation).max(0.0) * 3.0;
+        let co2_signal = (self.respiratory_drive - 0.6).max(0.0) * 0.4;
+        let peripheral_input = (0.5 + o2_signal + co2_signal).clamp(0.3, 1.3);
+
+        // NTS integrates baroreceptor and peripheral chemoreceptor inputs
+        // High baroreceptor → high NTS → inhibition of sympathetic tone
+        // Chemoreceptors also converge at NTS (interfere with baroreflex per 2024 study)
+        let nts_target =
+            (0.4 * baroreceptor_input + 0.35 * peripheral_input + 0.25 * central_chemo_input)
+                .clamp(0.2, 1.0);
+        self.nts_activity = Self::approach(self.nts_activity, nts_target, 1.5, dt_seconds);
+
+        // CVLM receives excitatory input from NTS and inhibits RVLM
+        let cvlm_target = (0.3 + 0.7 * self.nts_activity).clamp(0.2, 0.95);
+        self.cvlm_activity = Self::approach(self.cvlm_activity, cvlm_target, 1.2, dt_seconds);
+
+        // RVLM: tonic sympathetic drive, inhibited by CVLM
+        // Baseline drive adjusted by arousal and sleep stage
+        let arousal_drive = self.cortical_arousal * 0.4;
+        let sleep_suppression = match self.sleep_stage {
+            SleepStage::Wake => 0.0,
+            SleepStage::N1 => 0.05,
+            SleepStage::N2 => 0.1,
+            SleepStage::N3 => 0.18,
+            SleepStage::Rem => 0.08,
+        };
+        let rvlm_target = (0.65 + arousal_drive - 0.5 * self.cvlm_activity - sleep_suppression
+            + self.pain_drive * 0.15
+            + (self.respiratory_drive - 0.6) * 0.2)
+            .clamp(0.25, 1.1);
+        self.rvlm_activity = Self::approach(self.rvlm_activity, rvlm_target, 0.8, dt_seconds);
+
+        // Nucleus ambiguus cardiovagal neurons: primary HR control via myelinated vagal fibers
+        // High NTS activity (high BP) → high vagal tone → bradycardia
+        let vagal_excitation = self.nts_activity * 0.6;
+        let namb_target = (0.3 + vagal_excitation - self.cortical_arousal * 0.3
+            + match self.sleep_stage {
+                SleepStage::Wake => 0.0,
+                SleepStage::N1 => 0.05,
+                SleepStage::N2 => 0.1,
+                SleepStage::N3 => 0.15,
+                SleepStage::Rem => -0.05, // REM has more variable autonomic tone
+            })
+        .clamp(0.15, 0.85);
+        self.namb_cardiovagal_activity =
+            Self::approach(self.namb_cardiovagal_activity, namb_target, 1.0, dt_seconds);
+
+        // DMV cardiac neurons: ~20% of cardiovagal neurons, modulate contractility via C-fibers
+        let dmv_target = (0.25 + 0.5 * self.nts_activity - 0.2 * self.cortical_arousal
+            + match self.sleep_stage {
+                SleepStage::N2 | SleepStage::N3 => 0.12,
+                _ => 0.0,
+            })
+        .clamp(0.15, 0.75);
+        self.dmv_cardiac_activity =
+            Self::approach(self.dmv_cardiac_activity, dmv_target, 0.7, dt_seconds);
+
+        // RTN central chemoreceptors: CO2/pH drive (2/3 of ventilatory CO2 response)
+        let rtn_target = central_chemo_input.clamp(0.4, 1.1);
+        self.rtn_chemoreceptor_activity =
+            Self::approach(self.rtn_chemoreceptor_activity, rtn_target, 0.9, dt_seconds);
+
+        // Peripheral chemoreceptor signal (1/3 of CO2 response, primary O2 sensor)
+        self.peripheral_chemo_signal = Self::approach(
+            self.peripheral_chemo_signal,
+            peripheral_input,
+            1.2,
+            dt_seconds,
+        );
+
+        // Integrate brainstem outputs into autonomic drive and respiratory drive
+        // RVLM drives sympathetic tone → brainstem_autonomic_drive
+        // Combined vagal tone (nAmb + DMV) provides parasympathetic counterbalance
+        let sympathetic_component = self.rvlm_activity * 0.6;
+        let parasympathetic_component =
+            (self.namb_cardiovagal_activity * 0.8 + self.dmv_cardiac_activity * 0.2) * 0.4;
+        let net_autonomic =
+            (sympathetic_component + (1.0 - parasympathetic_component)).clamp(0.25, 1.1);
+
+        // Respiratory drive integrates RTN (central) and peripheral chemoreceptors
+        let chemo_drive = (self.rtn_chemoreceptor_activity * 0.65
+            + self.peripheral_chemo_signal * 0.35)
+            .clamp(0.4, 1.3);
+
+        // Blend computed autonomic/respiratory drives with existing targets
+        // (existing code uses these as feedback; brainstem provides mechanistic basis)
+        self.brainstem_autonomic_drive = Self::approach(
+            self.brainstem_autonomic_drive,
+            net_autonomic,
+            0.5,
+            dt_seconds,
+        )
+        .clamp(0.25, 1.1);
+
+        self.respiratory_drive =
+            Self::approach(self.respiratory_drive, chemo_drive, 0.4, dt_seconds).clamp(0.4, 1.3);
+    }
+
+    /// Cerebrovascular autoregulation model with myogenic, metabolic, and CO2 reactivity.
+    /// Based on:
+    /// - Paulson et al. (Cerebrovasc Dis 1990): CVR = CPP/CBF relationship
+    /// - Claassen et al. (Physiol Rev 2021): comprehensive autoregulation review
+    /// - Drummond (BJA 2024): monitoring and clinical implications
+    fn update_cerebrovascular_autoregulation(&mut self, dt_seconds: f32) {
+        let cpp = self.cerebral_perfusion_pressure_mm_hg;
+
+        // Within autoregulation range (50-150 mmHg): resistance adjusts to maintain CBF ~50 mL/100g/min
+        // Below lower limit: vasodilation exhausted, passive pressure-flow
+        // Above upper limit: forced vasodilation (breakthrough)
+        let in_autoregulation_range =
+            cpp >= self.autoregulation_lower_limit && cpp <= self.autoregulation_upper_limit;
+
+        let myogenic_resistance = if in_autoregulation_range {
+            // Active autoregulation: R = CPP / target_CBF
+            // Target CBF = 50 mL/100g/min baseline, modulated by metabolic demand
+            let target_cbf = 50.0 * self.metabolic_demand_fraction;
+            (cpp / target_cbf).clamp(0.8, 2.5)
+        } else if cpp < self.autoregulation_lower_limit {
+            // Below lower limit: vasodilation maximally exhausted, resistance low
+            let exhaustion_factor = (cpp / self.autoregulation_lower_limit).clamp(0.3, 1.0);
+            0.8 * exhaustion_factor
+        } else {
+            // Above upper limit: forced vasodilation (breakthrough), resistance collapses
+            let breakthrough_factor =
+                1.0 - ((cpp - self.autoregulation_upper_limit) / 50.0).clamp(0.0, 0.7);
+            0.6 * breakthrough_factor.max(0.3)
+        };
+
+        // Metabolic regulation: hypoxia, hypercapnia → vasodilation (decreased resistance)
+        let hypoxia_factor = (0.95 - self.oxygenation_saturation).max(0.0) * 2.0;
+        let metabolic_resistance_reduction = hypoxia_factor * 0.25;
+
+        // CO2 reactivity: 1-2 mL/100g/min per mmHg PaCO2 change (Claassen et al., Physiol Rev 2021)
+        // Proxy PaCO2 via respiratory drive: baseline ~40 mmHg at respiratory_drive=0.6
+        let estimated_paco2 = 30.0 + (self.respiratory_drive - 0.4) * 25.0; // rough estimate
+        let paco2_deviation = estimated_paco2 - 40.0;
+        // CBF increases ~4% per mmHg CO2 (1-2 mL/100g/min at baseline 50 mL/100g/min)
+        // Resistance inversely related: higher CO2 → lower resistance
+        let co2_resistance_factor =
+            1.0 - (paco2_deviation * self.co2_reactivity / 50.0).clamp(-0.3, 0.4);
+
+        // Neurogenic modulation: sympathetic tone can override autoregulation partially
+        let sympathetic_constriction = (self.rvlm_activity - 0.65) * 0.12;
+
+        // Combine factors
+        let target_resistance = (myogenic_resistance * co2_resistance_factor
+            - metabolic_resistance_reduction
+            + sympathetic_constriction)
+            .clamp(0.5, 3.0);
+
+        // Smooth resistance changes (myogenic response time constant ~5-15 sec)
+        self.cerebrovascular_resistance = Self::approach(
+            self.cerebrovascular_resistance,
+            target_resistance,
+            0.15,
+            dt_seconds,
+        )
+        .clamp(0.5, 3.5);
+
+        // Calculate CBF from CPP and resistance: CBF = CPP / CVR
+        let calculated_cbf = (cpp / self.cerebrovascular_resistance).clamp(25.0, 120.0);
+
+        self.cerebral_blood_flow_ml_per_100g_min = Self::approach(
+            self.cerebral_blood_flow_ml_per_100g_min,
+            calculated_cbf,
+            2.0,
+            dt_seconds,
+        )
+        .clamp(20.0, 130.0);
+    }
 }
 
 impl Organ for Brain {
@@ -27,15 +525,327 @@ 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;
+
+        // Track total time asleep for cycle calculations
+        let asleep = !matches!(self.sleep_stage, SleepStage::Wake);
+        if asleep {
+            self.time_asleep_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 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);
+        let thirst_component = (self.thirst_drive - 0.3).max(0.0) * 0.18;
+        let hunger_component = (self.hunger_drive - 0.35).max(0.0) * 0.15;
+        let thermo_component = (self.thermoregulatory_drive - 0.5).abs() * 0.12;
+        let pain_component = self.pain_drive * 0.2;
+        let drive_bonus = (self.respiratory_drive - 0.6).max(0.0) * 0.25
+            + thirst_component
+            + hunger_component
+            + thermo_component
+            + pain_component;
+        let syncope_penalty = self.syncope_propensity * 0.35;
+        let drive_weighted_arousal =
+            (base_arousal + drive_bonus - syncope_penalty).clamp(0.05, 1.0);
+        self.evaluate_sleep_stage(drive_weighted_arousal);
+
+        let arousal_target = self.stage_arousal_target(drive_weighted_arousal);
+        self.cortical_arousal =
+            Self::approach(self.cortical_arousal, arousal_target, 0.8, dt_seconds).clamp(0.05, 1.0);
+
+        // Update brainstem nuclei (baroreflex, chemoreflex, vagal pathways)
+        self.update_brainstem_nuclei(dt_seconds);
+
+        let (base_autonomic_target, base_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),
+        };
+        let drive_push = (self.respiratory_drive - 0.6) * 0.35;
+        let syncope_pull = self.syncope_propensity * 0.45;
+        let autonomic_target = (base_autonomic_target + drive_push - syncope_pull).clamp(0.25, 1.1);
+        let variability_target = (base_variability_target
+            + (self.respiratory_drive - 0.6).abs() * 0.15
+            + self.syncope_propensity * 0.1
+            + self.pain_drive * 0.12
+            + (self.thermoregulatory_drive - 0.5).abs() * 0.08)
+            .clamp(0.05, 0.95);
+        self.brainstem_autonomic_drive = Self::approach(
+            self.brainstem_autonomic_drive,
+            autonomic_target,
+            0.6,
+            dt_seconds,
+        )
+        .clamp(0.25, 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)
+            + 0.12 * (self.respiratory_drive - 0.6)
+            + 0.14 * (self.hunger_drive - 0.35)
+            + 0.06 * (self.thermoregulatory_drive - 0.5)
+            - 0.1 * self.syncope_propensity)
+            .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)
+            - 0.05 * self.syncope_propensity
+            + 0.02 * (self.respiratory_drive - 0.6))
+            .clamp(0.85, 0.99);
+        self.oxygenation_saturation =
+            Self::approach(self.oxygenation_saturation, oxygen_target, 0.4, dt_seconds)
+                .clamp(0.8, 1.0);
+
+        // Cerebrovascular autoregulation replaces static CBF calculation
+        self.update_cerebrovascular_autoregulation(dt_seconds);
+
+        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
+            + self.pain_drive * 0.08
+            + (self.thirst_drive + self.hunger_drive) * 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
+                + (self.respiratory_drive - 0.6) * 15.0
+                - self.syncope_propensity * 25.0
+                + self.pain_drive * 12.0
+                + (self.thirst_drive + self.hunger_drive) * 6.0
+                - (self.thermoregulatory_drive - 0.5).abs() * 10.0)
+                .clamp(0.0, 100.0);
+        self.consciousness = target_consciousness.round() as u8;
+
+        // Polysomnographic markers (Warby et al. 2014, Frauscher et al. 2014)
+        match self.sleep_stage {
+            SleepStage::N2 => {
+                // Sleep spindle density 2-5/min normal (Fernandez & Lüthi, Nat Neurosci 2020)
+                // Spindle density correlates with sleep pressure and cycle number
+                let spindle_base = 3.5 + (self.sleep_pressure - 0.5) * 1.5;
+                let cycle_modulation = if self.sleep_cycle_count == 0 {
+                    1.1
+                } else {
+                    0.95
+                };
+                let spindle_target = (spindle_base * cycle_modulation).clamp(2.0, 5.5);
+                self.spindle_density_per_min = Self::approach(
+                    self.spindle_density_per_min,
+                    spindle_target,
+                    0.3,
+                    dt_seconds,
+                );
+
+                // K-complex density 1-3/min (Colrain, Sleep Med Rev 2005)
+                let k_complex_target = (2.0 + (self.sleep_pressure - 0.6) * 1.0).clamp(1.0, 3.2);
+                self.k_complex_density_per_min = Self::approach(
+                    self.k_complex_density_per_min,
+                    k_complex_target,
+                    0.25,
+                    dt_seconds,
+                );
+
+                // Sigma power (11-16 Hz) correlates strongly with spindle amplitude r=0.95
+                let sigma_target =
+                    (1.0 + (self.spindle_density_per_min - 3.5) * 0.15).clamp(0.7, 1.4);
+                self.sigma_power_relative =
+                    Self::approach(self.sigma_power_relative, sigma_target, 0.2, dt_seconds);
+            }
+            SleepStage::Rem => {
+                // REM atonia: normal >85-90% atonia (McCarter et al., Sleep 2014)
+                // Tonic EMG <10%, phasic <15% in normal REM (Frauscher et al., Sleep 2014)
+
+                // Arousal and sleep pressure affect atonia integrity
+                let atonia_disruption = (self.cortical_arousal - 0.5).max(0.0) * 0.15
+                    + (0.4 - self.sleep_pressure).max(0.0) * 0.08
+                    + self.pain_drive * 0.05;
+
+                let atonia_target = (0.92 - atonia_disruption).clamp(0.75, 0.96);
+                self.rem_atonia_index =
+                    Self::approach(self.rem_atonia_index, atonia_target, 0.15, dt_seconds);
+
+                // Tonic EMG is inverse of atonia
+                let tonic_target = ((1.0 - self.rem_atonia_index) * 10.0).clamp(2.0, 18.0);
+                self.rem_tonic_emg_fraction =
+                    Self::approach(self.rem_tonic_emg_fraction, tonic_target, 0.12, dt_seconds);
+
+                // Phasic bursts: normal <15%, increase with arousal and dream intensity
+                let phasic_base = 8.0 + self.cortical_arousal * 6.0 + atonia_disruption * 12.0;
+                let phasic_target = phasic_base.clamp(5.0, 25.0);
+                self.rem_phasic_emg_pct =
+                    Self::approach(self.rem_phasic_emg_pct, phasic_target, 0.18, dt_seconds);
+            }
+            SleepStage::N1 | SleepStage::N3 => {
+                // Gradually return markers to baseline when not in N2 or REM
+                self.spindle_density_per_min =
+                    Self::approach(self.spindle_density_per_min, 3.5, 0.2, dt_seconds);
+                self.k_complex_density_per_min =
+                    Self::approach(self.k_complex_density_per_min, 2.0, 0.2, dt_seconds);
+                self.sigma_power_relative =
+                    Self::approach(self.sigma_power_relative, 1.0, 0.15, dt_seconds);
+                self.rem_tonic_emg_fraction =
+                    Self::approach(self.rem_tonic_emg_fraction, 0.05, 0.1, dt_seconds);
+                self.rem_phasic_emg_pct =
+                    Self::approach(self.rem_phasic_emg_pct, 8.0, 0.12, dt_seconds);
+                self.rem_atonia_index =
+                    Self::approach(self.rem_atonia_index, 0.92, 0.1, dt_seconds);
+            }
+            SleepStage::Wake => {
+                // Reset to wake baseline
+                self.spindle_density_per_min =
+                    Self::approach(self.spindle_density_per_min, 0.0, 0.5, dt_seconds);
+                self.k_complex_density_per_min =
+                    Self::approach(self.k_complex_density_per_min, 0.0, 0.5, dt_seconds);
+                self.sigma_power_relative =
+                    Self::approach(self.sigma_power_relative, 0.5, 0.3, dt_seconds);
+                self.rem_tonic_emg_fraction =
+                    Self::approach(self.rem_tonic_emg_fraction, 0.8, 0.15, dt_seconds);
+                self.rem_phasic_emg_pct =
+                    Self::approach(self.rem_phasic_emg_pct, 25.0, 0.2, dt_seconds);
+                self.rem_atonia_index =
+                    Self::approach(self.rem_atonia_index, 0.15, 0.15, dt_seconds);
+            }
+        }
+
+        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}, drives[r={:.2},th={:.2},hu={:.2},tmp={:.2},pain={:.2},syn={:.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.respiratory_drive,
+            self.thirst_drive,
+            self.hunger_drive,
+            self.thermoregulatory_drive,
+            self.pain_drive,
+            self.syncope_propensity,
+            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 +1,157 @@
 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 = 18.5;
+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,
+}
+
+/// Discrete cardiac cycle phases for phase-based state machine.
+/// Based on: Sengupta PP et al. "The Cardiac Cycle" (2008) PMC2390899
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum CardiacPhase {
+    /// Late diastole with atrial contraction completing ventricular filling
+    AtrialSystole,
+    /// Early systole with all valves closed, pressure rising without volume change
+    IsovolumetricContraction,
+    /// Mid-systole with semilunar valves open, blood ejection
+    Ejection,
+    /// Early diastole with all valves closed, pressure falling without volume change
+    IsovolumetricRelaxation,
+    /// Mid-to-late diastole with passive ventricular filling
+    PassiveFilling,
+}
+
+/// Valve states for discrete valve modeling.
+/// Based on: CV Physiology - Valvular function and hemodynamics
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum ValveState {
+    /// Fully closed, no flow
+    Closed,
+    /// Opening transition
+    Opening,
+    /// Fully open, forward flow
+    Open,
+    /// Closing transition
+    Closing,
+    /// Incompetent closure allowing regurgitant flow
+    Regurgitant,
+}
+
+/// 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,
+
+    // === NEW: Discrete atrial and valve modeling ===
+    /// Left atrial pressure (mmHg).
+    pub left_atrial_pressure_mm_hg: f32,
+    /// Left atrial volume (ml).
+    pub left_atrial_volume_ml: f32,
+    /// Right atrial pressure (mmHg).
+    pub right_atrial_pressure_mm_hg: f32,
+    /// Right atrial volume (ml).
+    pub right_atrial_volume_ml: f32,
+    /// Mitral valve state.
+    pub mitral_valve_state: ValveState,
+    /// Aortic valve state.
+    pub aortic_valve_state: ValveState,
+    /// Tricuspid valve state.
+    pub tricuspid_valve_state: ValveState,
+    /// Pulmonic valve state.
+    pub pulmonic_valve_state: ValveState,
+    /// Mitral regurgitant fraction (0..=1).
+    pub mitral_regurgitation_fraction: f32,
+    /// Aortic regurgitant fraction (0..=1).
+    pub aortic_regurgitation_fraction: f32,
+
+    // === NEW: Extended conduction system modeling ===
+    /// His bundle conduction velocity (m/s). Normal: 1.0-1.5 m/s.
+    pub his_bundle_velocity_m_s: f32,
+    /// Purkinje fiber conduction velocity (m/s). Normal: 2.0-4.0 m/s (fastest in heart).
+    pub purkinje_velocity_m_s: f32,
+    /// His-Purkinje effective refractory period (ms). Normal: 350-450 ms.
+    pub his_purkinje_erp_ms: f32,
+    /// Ventricular action potential duration at 90% repolarization (ms).
+    pub ventricular_apd90_ms: f32,
+    /// Time since last ventricular depolarization (ms).
+    pub time_since_depolarization_ms: f32,
+
+    // === NEW: Phase-based cardiac cycle state machine ===
+    /// Current phase of cardiac cycle.
+    pub cardiac_phase: CardiacPhase,
+    /// Time in current cardiac phase (s).
+    pub phase_time_s: f32,
+    /// Left ventricular pressure (mmHg).
+    pub left_ventricular_pressure_mm_hg: f32,
+    /// Aortic pressure (mmHg).
+    pub aortic_pressure_mm_hg: f32,
+
+    // === NEW: RAAS hormonal regulation ===
+    /// Plasma renin activity (ng/mL/hr). Normal: 0.5-3.5.
+    pub plasma_renin_activity: f32,
+    /// Angiotensin II level (pg/mL). Normal: 10-60.
+    pub angiotensin_ii_pg_ml: f32,
+    /// Plasma aldosterone (ng/dL). Normal: 4-31.
+    pub aldosterone_ng_dl: f32,
+    /// Effective circulating volume fraction (0..=1.2). 1.0 = euvolemic.
+    pub effective_circulating_volume: f32,
 }
 
 impl Heart {
@@ -20,12 +159,515 @@ 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: BASE_SV_ML * 72.0 / 1000.0,
+            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: BASE_SVR_MMHG_MIN_PER_L * (BASE_SV_ML * 72.0 / 1000.0),
+            systemic_vascular_resistance: BASE_SVR_MMHG_MIN_PER_L,
+            venous_return_l_min: BASE_SV_ML * 72.0 / 1000.0,
+            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,
+            // Atrial compartments
+            left_atrial_pressure_mm_hg: 8.0,
+            left_atrial_volume_ml: 55.0,
+            right_atrial_pressure_mm_hg: 4.0,
+            right_atrial_volume_ml: 50.0,
+            // Valve states
+            mitral_valve_state: ValveState::Open,
+            aortic_valve_state: ValveState::Closed,
+            tricuspid_valve_state: ValveState::Open,
+            pulmonic_valve_state: ValveState::Closed,
+            mitral_regurgitation_fraction: 0.0,
+            aortic_regurgitation_fraction: 0.0,
+            // Conduction system
+            his_bundle_velocity_m_s: 1.2,
+            purkinje_velocity_m_s: 3.0,
+            his_purkinje_erp_ms: 400.0,
+            ventricular_apd90_ms: 280.0,
+            time_since_depolarization_ms: 0.0,
+            // Cardiac cycle phase
+            cardiac_phase: CardiacPhase::PassiveFilling,
+            phase_time_s: 0.0,
+            left_ventricular_pressure_mm_hg: 8.0,
+            aortic_pressure_mm_hg: 80.0,
+            // RAAS
+            plasma_renin_activity: 1.5,
+            angiotensin_ii_pg_ml: 30.0,
+            aldosterone_ng_dl: 12.0,
+            effective_circulating_volume: 1.0,
         }
     }
+
+    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 raw_diastolic = map_target - pulse_pressure / 3.0;
+        let raw_systolic = raw_diastolic + pulse_pressure;
+        let systolic = raw_systolic.clamp(80.0, 220.0);
+        let diastolic = raw_diastolic.clamp(40.0, (systolic - 5.0).max(40.0));
+        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);
+    }
+
+    /// Update RAAS hormonal cascade.
+    /// Based on: Fountain JH, Lappin SL. Physiology, Renin Angiotensin System. StatPearls 2024.
+    fn update_raas(&mut self, dt_seconds: f32) {
+        // Renin release triggered by:
+        // 1. Reduced renal perfusion (low MAP)
+        // 2. Sympathetic stimulation
+        // 3. Hypovolemia
+        let map_current = self.mean_arterial_pressure();
+        let perfusion_deficit = ((85.0 - map_current) / 30.0).clamp(0.0, 1.0);
+        let sympathetic_drive = (self.autonomic_tone.max(0.0) * 0.6).clamp(0.0, 1.0);
+        let volume_deficit = ((1.0 - self.effective_circulating_volume) * 1.2).clamp(0.0, 1.0);
+
+        let renin_stimulus = perfusion_deficit + sympathetic_drive + volume_deficit;
+        let renin_target = (0.5 + 3.0 * renin_stimulus).clamp(0.2, 5.0);
+        self.plasma_renin_activity =
+            Self::approach(self.plasma_renin_activity, renin_target, 0.15, dt_seconds);
+
+        // Angiotensin II production via ACE in pulmonary circulation
+        // Proportional to renin with enzymatic conversion delay
+        let ang_ii_target = (10.0 + 45.0 * (self.plasma_renin_activity / 3.5)).clamp(5.0, 120.0);
+        self.angiotensin_ii_pg_ml =
+            Self::approach(self.angiotensin_ii_pg_ml, ang_ii_target, 0.4, dt_seconds);
+
+        // Aldosterone secretion from adrenal cortex
+        // Driven by angiotensin II and hyperkalemia (not modeled)
+        let aldo_target =
+            (4.0 + 30.0 * (self.angiotensin_ii_pg_ml / 60.0).powf(1.2)).clamp(2.0, 50.0);
+        self.aldosterone_ng_dl =
+            Self::approach(self.aldosterone_ng_dl, aldo_target, 0.25, dt_seconds);
+
+        // Angiotensin II effects on SVR (vasoconstriction)
+        // Normal Ang II ~ 30 pg/mL; elevated levels increase SVR
+        let ang_ii_vasoconstriction = ((self.angiotensin_ii_pg_ml - 30.0) / 30.0).clamp(-0.3, 1.5);
+        let svr_raas_component = 2.0 * ang_ii_vasoconstriction;
+
+        // Aldosterone effects on volume (increase preload over hours, simplified here)
+        let volume_retention_rate = (self.aldosterone_ng_dl - 12.0) / 40.0;
+        self.effective_circulating_volume = (self.effective_circulating_volume
+            + volume_retention_rate * dt_seconds / 3600.0)
+            .clamp(0.7, 1.3);
+
+        // Apply RAAS-mediated SVR adjustment
+        let base_svr = BASE_SVR_MMHG_MIN_PER_L + 5.5 * self.autonomic_tone;
+        let raas_svr_target = (base_svr + svr_raas_component).clamp(10.0, 28.0);
+        self.systemic_vascular_resistance = Self::approach(
+            self.systemic_vascular_resistance,
+            raas_svr_target,
+            0.3,
+            dt_seconds,
+        );
+    }
+
+    /// Update conduction system properties including His-Purkinje pathways and refractoriness.
+    /// Based on: Cardiac electrophysiology, refractory periods, and APD dynamics.
+    fn update_conduction_system(&mut self, dt_seconds: f32) {
+        let dt_ms = dt_seconds * 1000.0;
+        self.time_since_depolarization_ms += dt_ms;
+
+        // His-Purkinje conduction velocity modulated by:
+        // - Sympathetic tone (increased catecholamines increase velocity)
+        // - Ischemia/hypoxia (decreases velocity)
+        let supply_demand_ratio = self.myocardial_oxygen_supply / self.myocardial_oxygen_demand;
+        let ischemia_factor = supply_demand_ratio.clamp(0.6, 1.2);
+        let sympathetic_boost = 1.0 + 0.15 * self.autonomic_tone.max(0.0);
+
+        let his_target = (1.2 * ischemia_factor * sympathetic_boost).clamp(0.5, 1.8);
+        let purkinje_target = (3.0 * ischemia_factor * sympathetic_boost).clamp(1.2, 4.5);
+
+        self.his_bundle_velocity_m_s =
+            Self::approach(self.his_bundle_velocity_m_s, his_target, 0.08, dt_seconds);
+        self.purkinje_velocity_m_s = Self::approach(
+            self.purkinje_velocity_m_s,
+            purkinje_target,
+            0.15,
+            dt_seconds,
+        );
+
+        // APD and ERP modulated by rate, autonomic tone, and ischemia
+        // Rate adaptation: faster HR → shorter APD (protective against reentry)
+        let rate_adaptation_factor = 1.0 - 0.0015 * (self.heart_rate_bpm - 72.0);
+        let sympathetic_shortening = 1.0 - 0.12 * self.autonomic_tone.max(0.0);
+        let ischemia_prolongation = 1.0 + 0.15 * (1.0 - ischemia_factor);
+
+        let apd_target =
+            (280.0 * rate_adaptation_factor * sympathetic_shortening * ischemia_prolongation)
+                .clamp(200.0, 360.0);
+        self.ventricular_apd90_ms =
+            Self::approach(self.ventricular_apd90_ms, apd_target, 5.0, dt_seconds);
+
+        // ERP typically 90-95% of APD90, plus relative refractory period
+        let erp_target = (self.ventricular_apd90_ms * 1.1 + 80.0).clamp(280.0, 500.0);
+        self.his_purkinje_erp_ms =
+            Self::approach(self.his_purkinje_erp_ms, erp_target, 4.0, dt_seconds);
+
+        // Reset depolarization timer on each ventricular beat
+        let cycle_duration_ms = 60000.0 / self.heart_rate_bpm.max(30.0);
+        if self.time_since_depolarization_ms >= cycle_duration_ms {
+            self.time_since_depolarization_ms = 0.0;
+        }
+    }
+
+    /// Update cardiac cycle phase state machine and valve states.
+    /// Based on: Sengupta PP et al. PMC2390899 and Wiggers diagram.
+    fn update_cardiac_phase(&mut self, dt_seconds: f32) {
+        self.phase_time_s += dt_seconds;
+        let cycle_duration_s = 60.0 / self.heart_rate_bpm.max(30.0);
+
+        // Phase durations as fractions of cardiac cycle
+        // At 72 bpm (0.833s cycle): atrial systole ~0.1s, isovol contract ~0.05s,
+        // ejection ~0.3s, isovol relax ~0.08s, passive fill ~0.3s
+        let diastole_fraction = 0.6 - 0.15 * ((self.heart_rate_bpm - 72.0) / 60.0).clamp(-0.5, 1.0);
+        let systole_fraction = 1.0 - diastole_fraction;
+
+        let atrial_systole_duration = 0.1 * cycle_duration_s;
+        let isovol_contract_duration = 0.05 * cycle_duration_s;
+        let ejection_duration = (systole_fraction - 0.05) * cycle_duration_s;
+        let isovol_relax_duration = 0.08 * cycle_duration_s;
+
+        // State transitions
+        match self.cardiac_phase {
+            CardiacPhase::PassiveFilling => {
+                if self.phase_time_s >= (diastole_fraction - 0.1) * cycle_duration_s {
+                    self.cardiac_phase = CardiacPhase::AtrialSystole;
+                    self.phase_time_s = 0.0;
+                    self.mitral_valve_state = ValveState::Open;
+                    self.tricuspid_valve_state = ValveState::Open;
+                }
+            }
+            CardiacPhase::AtrialSystole => {
+                // Atrial contraction increases atrial and ventricular pressures
+                let atrial_kick_boost =
+                    1.0 + 0.2 * (self.phase_time_s / atrial_systole_duration).min(1.0);
+                self.left_atrial_pressure_mm_hg = 8.0 + 4.0 * atrial_kick_boost;
+                self.left_ventricular_pressure_mm_hg = Self::approach(
+                    self.left_ventricular_pressure_mm_hg,
+                    self.preload_mm_hg * 1.15,
+                    10.0,
+                    dt_seconds,
+                );
+
+                if self.phase_time_s >= atrial_systole_duration {
+                    self.cardiac_phase = CardiacPhase::IsovolumetricContraction;
+                    self.phase_time_s = 0.0;
+                    self.mitral_valve_state = ValveState::Closing;
+                    self.tricuspid_valve_state = ValveState::Closing;
+                }
+            }
+            CardiacPhase::IsovolumetricContraction => {
+                // All valves closed, LV pressure rises rapidly
+                self.mitral_valve_state = ValveState::Closed;
+                self.tricuspid_valve_state = ValveState::Closed;
+                self.aortic_valve_state = ValveState::Closed;
+                self.pulmonic_valve_state = ValveState::Closed;
+
+                let pressure_rise_rate = 1200.0 * self.contractility_index;
+                self.left_ventricular_pressure_mm_hg += pressure_rise_rate * dt_seconds;
+
+                // Transition when LV pressure exceeds aortic pressure
+                if self.left_ventricular_pressure_mm_hg >= self.aortic_pressure_mm_hg
+                    || self.phase_time_s >= isovol_contract_duration
+                {
+                    self.cardiac_phase = CardiacPhase::Ejection;
+                    self.phase_time_s = 0.0;
+                    self.aortic_valve_state = ValveState::Opening;
+                    self.pulmonic_valve_state = ValveState::Opening;
+                }
+            }
+            CardiacPhase::Ejection => {
+                self.aortic_valve_state = ValveState::Open;
+                self.pulmonic_valve_state = ValveState::Open;
+
+                // LV pressure tracks aortic pressure during ejection
+                let systolic_peak = self.arterial_bp.systolic as f32;
+                self.left_ventricular_pressure_mm_hg = Self::approach(
+                    self.left_ventricular_pressure_mm_hg,
+                    systolic_peak * 0.98,
+                    80.0,
+                    dt_seconds,
+                );
+                self.aortic_pressure_mm_hg =
+                    Self::approach(self.aortic_pressure_mm_hg, systolic_peak, 100.0, dt_seconds);
+
+                if self.phase_time_s >= ejection_duration {
+                    self.cardiac_phase = CardiacPhase::IsovolumetricRelaxation;
+                    self.phase_time_s = 0.0;
+                    self.aortic_valve_state = ValveState::Closing;
+                    self.pulmonic_valve_state = ValveState::Closing;
+                }
+            }
+            CardiacPhase::IsovolumetricRelaxation => {
+                self.mitral_valve_state = ValveState::Closed;
+                self.tricuspid_valve_state = ValveState::Closed;
+                self.aortic_valve_state = ValveState::Closed;
+                self.pulmonic_valve_state = ValveState::Closed;
+
+                // Rapid pressure drop with lusitropy
+                let relaxation_rate = -800.0;
+                self.left_ventricular_pressure_mm_hg += relaxation_rate * dt_seconds;
+                self.left_ventricular_pressure_mm_hg =
+                    self.left_ventricular_pressure_mm_hg.max(0.0);
+
+                // Aortic pressure decays toward diastolic
+                self.aortic_pressure_mm_hg = Self::approach(
+                    self.aortic_pressure_mm_hg,
+                    self.arterial_bp.diastolic as f32,
+                    150.0,
+                    dt_seconds,
+                );
+
+                // Transition when LV pressure drops below atrial pressure
+                if self.left_ventricular_pressure_mm_hg <= self.left_atrial_pressure_mm_hg
+                    || self.phase_time_s >= isovol_relax_duration
+                {
+                    self.cardiac_phase = CardiacPhase::PassiveFilling;
+                    self.phase_time_s = 0.0;
+                    self.mitral_valve_state = ValveState::Opening;
+                    self.tricuspid_valve_state = ValveState::Opening;
+                }
+            }
+        }
+
+        // Update regurgitant valve states
+        if self.mitral_regurgitation_fraction > 0.05
+            && self.mitral_valve_state == ValveState::Closed
+        {
+            self.mitral_valve_state = ValveState::Regurgitant;
+        }
+        if self.aortic_regurgitation_fraction > 0.05
+            && self.aortic_valve_state == ValveState::Closed
+        {
+            self.aortic_valve_state = ValveState::Regurgitant;
+        }
+
+        // Atrial filling from venous return
+        let filling_rate = self.venous_return_l_min * 1000.0 / 60.0;
+        self.left_atrial_volume_ml += filling_rate * dt_seconds;
+        self.right_atrial_volume_ml += filling_rate * dt_seconds * 0.95;
+
+        // Atrial emptying during open mitral valve
+        if matches!(
+            self.mitral_valve_state,
+            ValveState::Open | ValveState::Opening
+        ) {
+            let emptying_rate = filling_rate * 1.8;
+            self.left_atrial_volume_ml -= emptying_rate * dt_seconds;
+        }
+
+        // Clamp atrial volumes
+        self.left_atrial_volume_ml = self.left_atrial_volume_ml.clamp(30.0, 120.0);
+        self.right_atrial_volume_ml = self.right_atrial_volume_ml.clamp(28.0, 110.0);
+
+        // Update atrial pressures from volumes (compliance ~5 mL/mmHg)
+        self.left_atrial_pressure_mm_hg =
+            (4.0 + (self.left_atrial_volume_ml - 50.0) / 5.0).clamp(2.0, 25.0);
+        self.right_atrial_pressure_mm_hg =
+            (2.0 + (self.right_atrial_volume_ml - 45.0) / 6.0).clamp(1.0, 20.0);
+    }
+
+    /// Improve coronary perfusion model to emphasize diastolic flow.
+    /// Based on: Duncker DJ, Bache RJ. JACC 2021; coronary autoregulation research.
+    fn update_coronary_perfusion(&mut self) {
+        // CPP = Aortic Diastolic Pressure - LVEDP
+        // Most LV coronary flow occurs during diastole due to systolic compression
+        let diastolic_bp = self.arterial_bp.diastolic as f32;
+        let lvedp = self.preload_mm_hg;
+        self.coronary_perfusion_mm_hg = (diastolic_bp - lvedp).clamp(20.0, 140.0);
+
+        // Diastolic time fraction decreases with tachycardia
+        let cycle_duration_s = 60.0 / self.heart_rate_bpm.max(30.0);
+        let diastolic_fraction =
+            (0.6 - 0.15 * ((self.heart_rate_bpm - 72.0) / 60.0)).clamp(0.3, 0.7);
+        let diastolic_time_s = cycle_duration_s * diastolic_fraction;
+
+        // Coronary flow autoregulation maintains flow across CPP 60-180 mmHg
+        // Below 60 mmHg, flow becomes pressure-dependent
+        let autoregulation_factor = if self.coronary_perfusion_mm_hg < 60.0 {
+            self.coronary_perfusion_mm_hg / 60.0
+        } else {
+            1.0 + 0.1 * ((self.coronary_perfusion_mm_hg - 90.0) / 60.0).clamp(-0.5, 1.0)
+        };
+
+        // Metabolic vasodilation in response to increased demand
+        let demand_factor = (self.myocardial_oxygen_demand / 9.0).clamp(0.6, 1.8);
+
+        // Tachycardia penalty: reduced diastolic time → reduced perfusion opportunity
+        let time_penalty = (diastolic_time_s / 0.5).clamp(0.6, 1.2);
+
+        // Myocardial O2 supply now depends on CPP, autoregulation, and diastolic time
+        self.myocardial_oxygen_supply = (9.5 + 0.12 * self.coronary_perfusion_mm_hg
+            - 0.8 * (1.0 - autoregulation_factor)
+            + 1.5 * (autoregulation_factor - 1.0).max(0.0)
+            - 2.0 * (1.0 - time_penalty))
+            .clamp(3.0, 22.0)
+            * demand_factor.min(1.2);
+    }
 }
 
 impl Organ for Heart {
@@ -36,26 +678,39 @@ 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;
+
+        // Core hemodynamic control
+        self.update_autonomic_state(dt_seconds);
+        self.update_raas(dt_seconds); // NEW: RAAS hormonal regulation
+        self.determine_rhythm_state();
+        self.update_rate_and_contractility(dt_seconds);
+        self.update_volumes_and_output(dt_seconds);
+
+        // NEW: Phase-based cardiac cycle with discrete valves
+        self.update_cardiac_phase(dt_seconds);
+
+        // NEW: Extended conduction system modeling
+        self.update_conduction_system(dt_seconds);
+
+        // NEW: Improved coronary perfusion with diastolic emphasis
+        self.update_coronary_perfusion();
+
+        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
         )
@@ -67,3 +722,45 @@ impl Organ for Heart {
         self
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn resting_state_stays_stable() {
+        let mut heart = Heart::new("test-heart", 12);
+        for _ in 0..600 {
+            heart.update(1.0);
+        }
+        let baseline_hr = heart.heart_rate_bpm;
+        let baseline_map = heart.mean_arterial_pressure();
+        for _ in 0..600 {
+            heart.update(1.0);
+        }
+        let later_hr = heart.heart_rate_bpm;
+        let later_map = heart.mean_arterial_pressure();
+        assert!(
+            (60.0..=90.0).contains(&baseline_hr),
+            "baseline heart rate out of expected range: {baseline_hr}"
+        );
+        assert!(
+            (68.0..=78.0).contains(&later_hr),
+            "resting heart rate failed to settle: initial {baseline_hr}, later {later_hr}"
+        );
+        assert!(
+            (90.0..=96.0).contains(&baseline_map) && (90.0..=96.0).contains(&later_map),
+            "mean arterial pressure unstable: baseline {baseline_map}, later {later_map}"
+        );
+        assert!(
+            heart.autonomic_tone.abs() <= 0.2,
+            "autonomic tone should remain near neutral, found {} (hr={later_hr}, map={later_map})",
+            heart.autonomic_tone
+        );
+        assert!(
+            (18.0..=20.5).contains(&heart.systemic_vascular_resistance),
+            "systemic vascular resistance drifted to {}",
+            heart.systemic_vascular_resistance
+        );
+    }
+}

src/organs/intestines.rs

@@ -1,22 +1,337 @@
 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,
+    /// Iron absorbed into portal circulation per day (mg).
+    pub iron_absorption_mg_per_day: f32,
+    /// Folate absorbed per day (mg).
+    pub folate_absorption_mg_per_day: f32,
+    /// Vitamin B12 absorbed per day (mcg).
+    pub b12_absorption_mcg_per_day: 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,
+            iron_absorption_mg_per_day: 1.6,
+            folate_absorption_mg_per_day: 0.45,
+            b12_absorption_mcg_per_day: 5.2,
+            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 micronutrient_drive = (available / 400.0).clamp(0.0, 2.0);
+        let mucosal_factor = self.mucosal_integrity.clamp(0.3, 1.1);
+        let inflammation_penalty = (self.inflammation_index * 0.5).clamp(0.0, 0.6);
+
+        let iron_target = ((1.3 + 1.4 * micronutrient_drive) * mucosal_factor
+            - inflammation_penalty)
+            .clamp(0.3, 5.5);
+        self.iron_absorption_mg_per_day = Self::approach(
+            self.iron_absorption_mg_per_day,
+            iron_target,
+            0.03,
+            dt_seconds,
+        );
+
+        let folate_target = ((0.32 + 0.3 * micronutrient_drive) * mucosal_factor
+            - inflammation_penalty * 0.25)
+            .clamp(0.1, 1.4);
+        self.folate_absorption_mg_per_day = Self::approach(
+            self.folate_absorption_mg_per_day,
+            folate_target,
+            0.03,
+            dt_seconds,
+        );
+
+        let b12_target = ((4.2 + 3.4 * micronutrient_drive) * mucosal_factor
+            - inflammation_penalty * 3.0)
+            .clamp(0.5, 15.0);
+        self.b12_absorption_mcg_per_day = Self::approach(
+            self.b12_absorption_mcg_per_day,
+            b12_target,
+            0.03,
+            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 +342,28 @@ 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 +1,28 @@
 use super::{Organ, OrganInfo};
 use crate::types::OrganType;
 
-/// Pulmonary model tracking respiratory rate and oxygen saturation.
+/// High-level breathing cycle state.
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum BreathingPhase {
+    /// Active inspiration with diaphragmatic contraction.
+    Inhalation,
+    /// Passive expiration and recoil.
+    Exhalation,
+    /// Brief end-expiratory pause before the next breath.
+    Pause,
+}
+
+/// 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,
@@ -9,20 +30,425 @@ 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,
+    /// Current respiratory cycle phase.
+    pub breathing_phase: BreathingPhase,
+    phase_elapsed_s: f32,
+    current_phase_duration_s: f32,
+    breath_period_s: f32,
+    /// Diaphragm displacement fraction (0 relaxed, 1 fully contracted).
+    pub diaphragm_position: f32,
+    /// Rate of diaphragm displacement change per second.
+    pub diaphragm_velocity: f32,
 }
 
 impl Lungs {
     /// Construct lungs with a given id.
     pub fn new(id: impl Into<String>) -> Self {
+        let respiratory_rate_bpm = 14.0_f32;
+        let breath_period_s = (60.0_f32 / respiratory_rate_bpm).clamp(0.5, 12.0);
+        let inhale_fraction = 0.42;
+        let inhale_duration = breath_period_s * inhale_fraction;
         Self {
             info: OrganInfo::new(id, OrganType::Lungs),
-            respiratory_rate_bpm: 14.0,
+            respiratory_rate_bpm,
             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,
+            breathing_phase: BreathingPhase::Inhalation,
+            phase_elapsed_s: 0.0,
+            current_phase_duration_s: inhale_duration.max(0.1),
+            breath_period_s,
+            diaphragm_position: 0.0,
+            diaphragm_velocity: 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_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 breath_phase_fractions(&self) -> (f32, f32, f32) {
+        let base_inhale = match self.state {
+            VentilatoryState::Resting => 0.42,
+            VentilatoryState::HypercapnicResponse => 0.36,
+            VentilatoryState::HypoxicResponse => 0.38,
+            VentilatoryState::ExerciseAugmented => 0.46,
+            VentilatoryState::MechanicalDistress => 0.32,
+        };
+        let base_pause = match self.state {
+            VentilatoryState::Resting => 0.06,
+            VentilatoryState::HypercapnicResponse => 0.03,
+            VentilatoryState::HypoxicResponse => 0.04,
+            VentilatoryState::ExerciseAugmented => 0.0,
+            VentilatoryState::MechanicalDistress => 0.02,
+        };
+        let drive_adjust = (self.muscle_drive - 0.5).clamp(-0.5, 0.5);
+        let inhale = (base_inhale + 0.1 * drive_adjust).clamp(0.25, 0.55);
+        let pause = (base_pause - 0.05 * drive_adjust.max(0.0)).clamp(0.0, 0.1);
+        let exhale = (1.0 - inhale - pause).clamp(0.25, 0.7);
+        let total = inhale + exhale + pause;
+        if (total - 1.0).abs() < 1e-4 {
+            (inhale, exhale, pause)
+        } else {
+            let norm = if total <= 0.0 { 1.0 } else { total };
+            (inhale / norm, exhale / norm, pause / norm)
+        }
+    }
+
+    fn phase_durations(&self) -> (f32, f32, f32) {
+        let rate = self.respiratory_rate_bpm.clamp(4.0, 45.0);
+        let period = (60.0 / rate).clamp(0.6, 15.0);
+        let (inhale_frac, _exhale_frac, pause_frac) = self.breath_phase_fractions();
+        let mut inhale = (period * inhale_frac).max(0.12);
+        let mut pause = (period * pause_frac).max(0.0);
+        let mut exhale = (period - inhale - pause).max(0.2);
+        let total = inhale + exhale + pause;
+        let scale = if total > 0.0 { period / total } else { 1.0 };
+        inhale *= scale;
+        exhale *= scale;
+        pause *= scale;
+        (inhale, exhale, pause)
+    }
+
+    fn advance_phase(&mut self, pause_duration: f32) {
+        self.breathing_phase = match self.breathing_phase {
+            BreathingPhase::Inhalation => BreathingPhase::Exhalation,
+            BreathingPhase::Exhalation => {
+                if pause_duration <= 1e-3 {
+                    BreathingPhase::Inhalation
+                } else {
+                    BreathingPhase::Pause
+                }
+            }
+            BreathingPhase::Pause => BreathingPhase::Inhalation,
+        };
+        self.phase_elapsed_s = 0.0;
+    }
+
+    fn easing(progress: f32) -> f32 {
+        let p = progress.clamp(0.0, 1.0);
+        p * p * (3.0 - 2.0 * p)
+    }
+
+    fn update_breath_cycle(&mut self, dt_seconds: f32) {
+        if dt_seconds <= 0.0 {
+            return;
+        }
+
+        let total_dt = dt_seconds;
+        let (inhale_duration, exhale_duration, pause_duration) = self.phase_durations();
+        self.breath_period_s = inhale_duration + exhale_duration + pause_duration;
+
+        let previous_duration = self.current_phase_duration_s.max(1e-6);
+        let mut phase_progress = (self.phase_elapsed_s / previous_duration).clamp(0.0, 1.0);
+
+        let mut current_duration = match self.breathing_phase {
+            BreathingPhase::Inhalation => inhale_duration,
+            BreathingPhase::Exhalation => exhale_duration,
+            BreathingPhase::Pause => pause_duration.max(1e-3),
+        };
+        if current_duration <= 0.0 {
+            current_duration = 1e-3;
+        }
+        self.current_phase_duration_s = current_duration;
+        self.phase_elapsed_s = phase_progress * current_duration;
+
+        let mut remaining = dt_seconds;
+        while remaining > 0.0 {
+            let duration = self.current_phase_duration_s.max(1e-3);
+            let time_left = (duration - self.phase_elapsed_s).max(0.0);
+            if remaining < time_left {
+                self.phase_elapsed_s += remaining;
+                remaining = 0.0;
+            } else {
+                remaining -= time_left;
+                self.advance_phase(pause_duration);
+                let new_duration = match self.breathing_phase {
+                    BreathingPhase::Inhalation => inhale_duration,
+                    BreathingPhase::Exhalation => exhale_duration,
+                    BreathingPhase::Pause => pause_duration.max(1e-3),
+                }
+                .max(1e-3);
+                self.current_phase_duration_s = new_duration;
+            }
+        }
+
+        let current_duration = self.current_phase_duration_s.max(1e-3);
+        phase_progress = (self.phase_elapsed_s / current_duration).clamp(0.0, 1.0);
+        let start_position = self.diaphragm_position;
+        let target_position = match self.breathing_phase {
+            BreathingPhase::Inhalation => Self::easing(phase_progress),
+            BreathingPhase::Exhalation => 1.0 - Self::easing(phase_progress),
+            BreathingPhase::Pause => {
+                if pause_duration <= 1e-3 {
+                    0.0
+                } else {
+                    0.0
+                }
+            }
+        };
+        self.diaphragm_position = target_position.clamp(0.0, 1.0);
+        self.diaphragm_velocity = (self.diaphragm_position - start_position) / total_dt;
+    }
+
+    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 +459,29 @@ 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_breath_cycle(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={:?}, phase={:?}, RR={:.0}, diaphragm={:.2}, VT={:.0} ml, SpO2={:.0}%, PaO2~{:.0}]",
             self.id(),
+            self.state,
+            self.breathing_phase,
             self.respiratory_rate_bpm,
-            self.spo2_pct
+            self.diaphragm_position,
+            self.tidal_volume_ml,
+            self.spo2_pct,
+            self.alveolar_po2_mm_hg
         )
     }
     fn as_any(&self) -> &dyn core::any::Any {
@@ -58,3 +491,45 @@ impl Organ for Lungs {
         self
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn breathing_cycle_advances_and_moves_diaphragm() {
+        let mut lungs = Lungs::new("test-lungs");
+        assert_eq!(lungs.breathing_phase, BreathingPhase::Inhalation);
+
+        let mut seen_exhalation = false;
+        let mut seen_pause = false;
+        let mut min_position = f32::MAX;
+        let mut max_position = f32::MIN;
+        let mut max_velocity: f32 = 0.0;
+
+        for _ in 0..20 {
+            lungs.update(0.5);
+            min_position = min_position.min(lungs.diaphragm_position);
+            max_position = max_position.max(lungs.diaphragm_position);
+            max_velocity = max_velocity.max(lungs.diaphragm_velocity.abs());
+            match lungs.breathing_phase {
+                BreathingPhase::Exhalation => seen_exhalation = true,
+                BreathingPhase::Pause => seen_pause = true,
+                BreathingPhase::Inhalation => {}
+            }
+        }
+
+        assert!(seen_exhalation, "expected cycle to reach exhalation phase");
+        assert!(seen_pause, "expected cycle to reach post-breath pause");
+        assert!(max_position <= 1.0 + 1e-3, "diaphragm position upper bound");
+        assert!(min_position >= -1e-3, "diaphragm position lower bound");
+        assert!(
+            max_position - min_position > 0.3,
+            "diaphragm should sweep a meaningful range"
+        );
+        assert!(
+            max_velocity > 0.05,
+            "diaphragm velocity should become non-zero"
+        );
+    }
+}

src/organs/mod.rs

@@ -42,6 +42,7 @@ pub trait Organ: Debug + Send {
 }
 
 mod bladder;
+mod bloodstream;
 mod brain;
 mod esophagus;
 mod gallbladder;
@@ -55,15 +56,16 @@ mod spinal_cord;
 mod spleen;
 mod stomach;
 
-pub use bladder::Bladder;
-pub use brain::Brain;
-pub use esophagus::Esophagus;
+pub use bladder::{Bladder, BladderMetrics, BladderPhase};
+pub use bloodstream::{Bloodstream, BloodstreamMetrics, MetabolicState, PerfusionState};
+pub use brain::{Brain, SleepStage};
+pub use esophagus::{EsophagealStage, Esophagus};
 pub use gallbladder::Gallbladder;
-pub use heart::Heart;
+pub use heart::{CardiacRhythmState, Heart};
 pub use intestines::Intestines;
 pub use kidneys::Kidneys;
 pub use liver::Liver;
-pub use lungs::Lungs;
+pub use lungs::{BreathingPhase, Lungs};
 pub use pancreas::Pancreas;
 pub use spinal_cord::SpinalCord;
 pub use spleen::Spleen;

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/types.rs

@@ -10,6 +10,8 @@ pub enum OrganType {
     Heart,
     /// Lungs
     Lungs,
+    /// Circulating blood volume and transport network
+    Bloodstream,
     /// Brain
     Brain,
     /// Spinal cord

tests/bladder_metrics.rs

@@ -0,0 +1,70 @@
+use medicallib_rust::{Bladder, Organ, OrganType, Patient};
+
+#[test]
+fn bladder_metrics_match_patient_api() {
+    let patient = Patient::new("metrics")
+        .unwrap()
+        .initialize_default()
+        .with_organ(OrganType::Bladder);
+    let metrics_via_patient = patient.bladder_metrics().expect("bladder present");
+    let bladder = patient.find_organ_typed::<Bladder>().unwrap();
+    let direct = bladder.metrics();
+    assert!((metrics_via_patient.urgency - direct.urgency).abs() < 1e-6);
+    assert_eq!(metrics_via_patient.phase, direct.phase);
+    assert_eq!(metrics_via_patient.capacity_ml, direct.capacity_ml);
+}
+
+#[test]
+fn voluntary_hold_updates_metrics() {
+    let mut patient = Patient::new("hold")
+        .unwrap()
+        .initialize_default()
+        .with_organ(OrganType::Bladder);
+
+    {
+        let bladder = patient.find_organ_typed_mut::<Bladder>().unwrap();
+        bladder.volume_ml = bladder.micturition_threshold_ml + 140.0;
+        bladder.urgency = 0.82;
+        bladder.cortical_inhibition = 0.1;
+        bladder.voluntary_hold_command = 0.1;
+        bladder.continence_training = 0.45;
+        bladder.update(0.5);
+    }
+    let baseline = patient.bladder_metrics().unwrap();
+
+    {
+        let bladder = patient.find_organ_typed_mut::<Bladder>().unwrap();
+        bladder.cortical_inhibition = 0.9;
+        bladder.voluntary_hold_command = 0.9;
+        bladder.continence_training = 0.9;
+        bladder.update(0.5);
+    }
+    let hold = patient.bladder_metrics().unwrap();
+
+    assert!(hold.voluntary_hold_fraction > baseline.voluntary_hold_fraction);
+    assert!(hold.cortical_gate_fraction > baseline.cortical_gate_fraction);
+    assert!(hold.cortical_gate_fraction <= 1.0);
+    assert!(hold.voluntary_hold_fraction <= 1.0);
+}
+
+#[cfg(feature = "ffi")]
+#[test]
+fn ffi_exposes_bladder_metrics() {
+    use core::mem::MaybeUninit;
+    use medicallib_rust::ffi::{
+        ml_patient_bladder_metrics, ml_patient_free, ml_patient_new, ml_patient_update,
+        MLBladderMetrics, MLPatient, ML_ERR, ML_OK,
+    };
+    use std::ffi::CString;
+
+    unsafe {
+        let id = CString::new("ffi-metrics").unwrap();
+        let patient: *mut MLPatient = ml_patient_new(id.as_ptr());
+        assert!(!patient.is_null());
+        assert_eq!(ml_patient_update(patient, 0.5), ML_OK);
+        let mut metrics = MaybeUninit::<MLBladderMetrics>::zeroed();
+        let status = ml_patient_bladder_metrics(patient as *const MLPatient, metrics.as_mut_ptr());
+        assert_eq!(status, ML_ERR);
+        ml_patient_free(patient);
+    }
+}

tests/ffi.rs

@@ -29,3 +29,24 @@ fn ffi_errors() {
     let s = medicallib_rust::ffi::ml_patient_summary(std::ptr::null());
     assert!(s.is_null());
 }
+
+#[cfg(feature = "ffi")]
+#[test]
+fn ffi_bloodstream_metrics() {
+    use medicallib_rust::ffi::*;
+    use std::ffi::CString;
+
+    let id = CString::new("ffi-blood").unwrap();
+    let p = ml_patient_new(id.as_ptr());
+    assert!(!p.is_null());
+
+    let mut metrics = std::mem::MaybeUninit::<MLBloodstreamMetrics>::uninit();
+    assert_eq!(ml_patient_update(p, 0.5), ML_OK);
+    let rc = ml_patient_bloodstream_metrics(p, metrics.as_mut_ptr());
+    assert_eq!(rc, ML_OK);
+    let metrics = unsafe { metrics.assume_init() };
+    assert!(metrics.oncotic_pressure_mm_hg > 15.0);
+    assert!(metrics.rbc_mature_fraction > 0.4);
+    ml_patient_free(p);
+}
+

tests/patient.rs

@@ -6,4 +6,8 @@ fn default_patient_heart() {
     p.update(0.1);
     let s = p.patient_summary();
     assert!(s.contains("Heart"));
+    assert!(p
+        .organ_summary(medicallib_rust::OrganType::Bloodstream)
+        .unwrap()
+        .contains("Bloodstream"));
 }