Physarum machines

A Physarum machine is a programmable amorphous biological computer experimentally implemented in the state of slime mould Physarum polycephalum. It comprises an amorphous yellowish mass with networks of protoplasmic tubes, programmed by spatial configurations of attracting and repelling gradients. It feeds on bacteria, spores and other microbial creatures. When foraging for its food the plasmodium propagates towards sources of food particles, surrounds them, secretes enzymes and digests the food. The plasmodium is considered as a parallel computing similar to existing massive parallel reaction diffusion chemical processors. Adamatzky (University of Bristol) and collaborators demonstrate how to create experimental Physarum machines for general purpose computation: plasmodium can implement the Kolmogorov-Uspensky (KUM) machine, a mathematical machine in which the storage structure is an irregular graph. KUM is defined on a labeled undirected graph with bounded degrees of nodes and bounded number of labels. KUM executes several operations on its storage structure: SELECT an active node (that is, occupied by an active zone) in the storage graph; SPECIFY the node´s neighborhood; MODIFY the active zone by ADDING a new node with the pair of edges, connecting the new node with the active node; DELETE a node with a pair of incident edges; ADD/DELETE the edge between the nodes. A program for KUM establishes how to REPLACE the neighborhood of an active node with a new neighborhood, depending on the labels of edges connected to the active node and the labels of the nodes placed in proximity of the active node. In Physarun machine, a node of the storage structure is represented by a source of nutrients, an edge connecting two nodes is a protoplasmic tubes linkink two sources of nutrients corresponding to the nodes. Finally, an active node is domain of space (which may include nutrient sources) occupied by a propagating pseudopodium. The computation is implemented by several active zones. It uses distributed local sensory behaviours, approximating phenomena observed in Physarum, like foraging for food stimuli, amoebic movement, network formation, network minimisation, surface area minimisation, shuttle streaming, spatially distributed oscillations or oscillation phase shifting. The emergent plasmodium behaviours are represented taking a multi-agent approach or based upon particles. In fact, movement and internal oscillations of the plasmodium reflect the collective behaviour of the particles population. The movement of agents correspons to the flux of sol within the plasmodium. Cohesion of the plasmodium arises due to the agent-agent interactions and movement of the plasmodium is generated by coupling the emergent mass behaviours with chemoattraction to local food source stimuli. Agents both secrete and sense approximations of chemical trails being the population represented on a two-dimensional discrete map. The strength of the projected food sources can be adjusted using parameters and when the plasmodium engulfs a food source the stimulus for diffusion is reduced by the encapsulation. The diffusion gradient corresponds to the quality of the nutrient and substrate of the plasmodium´s environment, and differences in the stimulus strength, stimulus area, affect both the steepness, and propagation distance of the diffusion gradient and affect the growth patterns of the virtual plasmodium.

The Physarum machine by Adamatzky is a very interesting example of a green computer, showing the necessity for simulating simple behaviours, in first place, as motivation for developing more complex simulations. It will be an excellent source of ideas for anyone who is inspired by emerging non-silicon computers.