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Biologically Inspired Model

In 2011, David M. D. Smith and colleagues described Network Automata, a computational framework in which the topological evolution of a network is coupled to its structure. To demonstrate Network Automata, they implemented a biologically inspired model of fungal growth.

The model consists of a number of agents related spatially via an underlying lattice. The agents accumulate resources through absorption from a resource layer, and the resources are moved between neighbours. Netomaton contains an implementation of the fungal growth model described by Smith et al., in the FungalGrowthModel class. The following is an example of how the FungalGrowthModel class can be used to model fungal growth:

import netomaton as ntm

R_E = 80000.0  # resource absorption rate
timesteps = 100
width = 200
height = 200
# for longer timeframes (e.g. 1000 timesteps) and more nodes, set this to True;
#  it will take a little longer, but the memory footprint will be greatly reduced
compression = False
# if the network over time is not of interest, then set this to False,
# and the network will not be persisted, reducing both the memory and running time footprint
persist_network = False

initial_conditions = ntm.init_simple2d(width, height, val=R_E, dtype=float)

model = ntm.FungalGrowthModel(R_E, width, height, initial_conditions, seed=20210408)

trajectory = ntm.evolve(network=model.network, initial_conditions=initial_conditions, timesteps=timesteps,
                        activity_rule=model.activity_rule, topology_rule=model.topology_rule,
                        update_order=model.update_order, copy_network=model.copy_network,
                        compression=compression, persist_network=persist_network)

ntm.animate_activities(trajectory, shape=(width, height), interval=200, colormap="jet")

The full source code for this example can be found here.

For more information, see:

Smith, David MD, et al. "Network automata: Coupling structure and function in dynamic networks." Advances in Complex Systems 14.03 (2011): 317-339.