Physarum machines: encapsulating reaction–diffusion to compute spanning tree

The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction–diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction–diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction–diffusion system is enclosed in a membrane with few ‘growth points’, sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction–diffusion computation by enriching it with ideas of slime mold computation.