Architecture Docs

ABIO biology

Molecules, reactions, pathways, containers, and their generators.

Generators

Base protocols for synthetic biology factories. - Generator - Base protocol for factories that produce synthetic biology components.

Atoms and Molecules

Chemical elements and compounds in the alien biology. - Atom - Chemical element with symbol, name, and atomic weight. Immutable value objects shared across molecules. - Molecule - Chemical compound composed of atoms. Has biosynthetic depth, derived formula (symbol), and molecular weight. - MoleculeGenerator - Factory that produces synthetic molecules with configurable properties.

Reactions (Rust)

Transformations between molecules. - Reaction - Transformation with reactants, products, effectors, and rate functions. - ReactionGenerator - Factory that produces synthetic reactions with configurable kinetics.

Chemistry

Container for molecules and reactions forming a chemical system. - Chemistry - Entity that groups molecules and reactions together. Provides validation, state management, and simulation support.

Pathways

Connected sequences of reactions (analytical abstraction). - Pathway - Connected subgraph forming a metabolic function: linear chains, branching paths, cycles, or signaling cascades. Used for understanding and generating coherent reaction networks, not directly in simulation.

Compartments (Rust)

Nestable biological structures from organelles to organisms. All are Entity subclasses. - Compartment - Nestable Entity for molecules, reactions, and child containers. Kind labels: organism, organ, cell, organelle. - ContainerGenerator - Composable factory for Compartments. Generators compose recursively: simple generators build complex ones.

Simulation

Multi-compartment simulation with reactions within compartments and flows across membranes. - WorldState - Dense concentration storage: [num_compartments × num_molecules] array. GPU-friendly, O(1) access. - CompartmentTree - Hierarchical topology of compartments. Stores parent-child relationships, separated from concentrations. - Flow - Membrane transport between compartments. Moves molecules across parent-child boundaries (diffusion, active transport). - WorldSimulator - Multi-compartment simulation engine. Applies reactions within compartments, flows across membranes. - Simulator - Legacy single-compartment simulator. See WorldSimulator for multi-compartment simulations. - State - Legacy single-compartment concentrations. See WorldState for multi-compartment storage.