FAIRImplementationABM
Welcome to the documentation for the FAIR_Implementation_ABM, a Julia-based agent-based model designed to simulate protein aggregation dynamics under intracellular-like conditions.
This model investigates how different environmental and molecular parameters — such as macromolecular crowding and conformational changes — influence the transition from native monomers to pathological amyloid structures.
Key Features
- Supports pathological aggregation scenarios
- Includes states:
- N: Native monomer
- A: Amyloid monomer
- O: Oligomer
- F: Fibril
- Integrates probabilistic reactions, movement logic, and crowding effects
- Built with an emphasis on FAIR (Findable, Accessible, Interoperable, Reusable) model design
API Reference
```@autodocs Modules = [FAIRImplementationABM]
Model Parameters
This section summarizes the main parameters used to control your agent-based model of protein aggregation.
| Parameter | Description | Example Value |
|---|---|---|
Lattice_Size | Size of the 3D FCC lattice | 30 |
MAX_NumberMovements | Number of time steps | 1000 |
Max_NumberMonomers_Native | Initial count of native monomers (N) | 50 |
Max_NumberMonomers_Amyloid | Initial count of amyloid-prone monomers (A) | 20 |
Native_to_Amyloid | Probability for N → A transition per timestep | 0.1 |
Amyloid_to_Native | Probability for A → N transition per timestep | 0.05 |
Oligomer_Formation | Probability of A + A → O | 0.5 |
Oligomer_Dissociation_rate | Probability of O → A + A | 0.1 |
Fibril_Formation | Probability of O + A → F | 0.8 |
Fibril_Growth | Probability of F + A → F(n) (elongation) | 0.9 |
Crowder_Concentration_Spheres | Volume fraction of crowders in lattice | 0.4 |
Obstacle_Radius | Radius of each spherical crowder | 1 |
Reaction Mechanisms
This model captures a simplified kinetic representation of protein aggregation pathways, driven by stochastic rules encoded in the agent-based framework.
1. Conformational Change
Reaction: N ⇌ A Native monomers can spontaneously convert into amyloid-prone conformations and vice versa, controlled by the probabilities Native_to_Amyloid and Amyloid_to_Native.
2. Oligomerization
Reaction: A + A ⇌ O Two amyloid monomers can associate to form a small oligomer. Oligomers can also dissociate into monomers.
3. Fibril Nucleation
Reaction: O + A → F Oligomers can convert into fibrils when interacting with an additional amyloid monomer, initiating fibril formation.
4. Fibril Elongation
Reaction: F + A → F(n) Fibrils grow through sequential addition of amyloid monomers, representing elongation.
Each of these reactions is probabilistic and depends on local lattice arrangement and spatial proximity of monomers.