Four particle-based reaction-diffusion simulations showcasing
process-bigraph integration with ReaDDy's Brownian dynamics
engine. Configurations range from topology-based actin treadmilling and
living polymer equilibria to predator-prey oscillations and confined diffusion.
Topology-based polymerization and structural depolymerization
An actin-like filament grows at its barbed (head) end by recruiting diffusing substrate monomers via a spatial topology reaction, while simultaneously losing monomers at the pointed (tail) end through a structural reaction. This treadmilling produces a steady-state filament length that balances polymerization and depolymerization rates. Topological bonds enforce linear chain geometry with angular rigidity.
304 particles · Box: 20.0×20.0×20.0
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t = 0
Population & Energy Dynamics
Bigraph Architecture
Composite Document
2
Lotka-Volterra Predator-Prey
Predator-prey dynamics with spatial stochasticity
A spatial Lotka-Volterra predator-prey model: prey (A) reproduce by fission, predators (B) consume prey upon contact via enzymatic reaction (A + B -> B + B), and predators spontaneously decay. Spatial diffusion and stochastic reactions introduce noise and fluctuations around the classical oscillatory dynamics. This uses the ReaDDyProcess PBG wrapper for configuration-driven setup.
Initial40particles
Final0A: 0, B: 0
Species2
Reactions3reproduce: A -> A + A; eat: A + B -> B +...
Time50.0sim. units
Steps10,000
Runtime8.1s
3D Particle Viewer
0 particles · Box: 15.0×15.0×15.0
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t = 0
Population & Energy Dynamics
Bigraph Architecture
Composite Document
3
Growing Polymer
Rapid polymerization from a monomer pool into a stiff filament
A single seed filament (head-core-tail) recruits diffusing substrate monomers from a concentrated pool of 500 particles. Each monomer that contacts the head end undergoes a spatial topology reaction, extending the chain. Angular potentials enforce rigidity, producing a stiff polymer that snakes through the box as it grows from 3 to hundreds of monomers. The substrate count drops as monomers are consumed.
503 particles · Box: 15.0×15.0×15.0
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t = 0
Population & Energy Dynamics
Bigraph Architecture
Composite Document
4
Two-Species Phase Separation
Like-like attraction drives demixing into clusters
One hundred and twenty particles of two species (A and B) start randomly mixed. Like particles attract via a piecewise-harmonic well (depth 2.0 kBT) while unlike particles repel. Over time the system spontaneously demixes: A particles cluster together and B particles cluster together, forming distinct phases. The energy drops dramatically as favorable same-species contacts form. This models liquid-liquid phase separation (LLPS) relevant to membraneless organelles in cells.
