Chemical Organization Theory

# Chemical Organization Theory

**Category:** Phase 3 Core - Autopoietic Systems
**Status:** Skeleton Implementation
**Dependencies:** `categorical-composition` (reaction networks as categories)

## Overview

Implements Chemical Organization Theory (COT) for modeling self-maintaining autopoietic systems through reaction-diffusion dynamics, organizational closure detection, and self-maintenance verification.

## Capabilities

- **Reaction Networks**: Define chemical reaction systems
- **Organizational Closure**: Detect self-maintaining organizations
- **Reaction-Diffusion**: Spatial dynamics simulation
- **Autopoiesis**: Verify self-production and boundary maintenance

## Core Components

1. **Reaction Network Builder** (`reaction_network.jl`)
   - Define species and reactions
   - Stoichiometric matrices
   - Mass-action kinetics

2. **Organization Detection** (`organization_detection.jl`)
   - Closure detection (no external inputs required)
   - Self-maintenance verification
   - Organizational hierarchy

3. **Reaction-Diffusion Simulator** (`reaction_diffusion.jl`)
   - Spatial PDE integration
   - Pattern formation
   - Turing instabilities

4. **Autopoietic Analysis** (`autopoiesis.jl`)
   - Boundary formation detection
   - Self-production metrics
   - Organizational resilience

## Integration Points

- **Input from**: `categorical-composition` (reaction networks as categories)
- **Output to**: `emergent-role-assignment` (role stability as organizations)
- **Coordinates with**: `formal-verification-ai` (verify closure properties)

## Usage

```julia
using ChemicalOrganizationTheory

# Define reaction network
network = ReactionNetwork()
add_species!(network, [:A, :B, :C])
add_reaction!(network, [:A, :B] => [:C], rate=0.1)
add_reaction!(network, [:C] => [:A, :B], rate=0.05)

# Detect organizations
orgs = find_organizations(network)

# Simulate reaction-diffusion
grid = Grid2D(100, 100)
state = initialize_state(grid, network)
trajectory = simulate_rd(network, state, time=100.0)

# Check autopoiesis
is_autopoietic = check_autopoiesis(network, orgs[1])
```

## References

- Dittrich & Speroni di Fenizio "Chemical Organization Theory" (2007)
- Fontana & Buss "The Barrier of Objects" (1996)
- Varela et al. "Autopoiesis: The Organization of Living Systems" (1974)

## Implementation Status

- [x] Basic reaction network structures
- [x] Stoichiometric analysis
- [ ] Full organization detection algorithm
- [ ] Reaction-diffusion solver
- [ ] Autopoiesis verification metrics