Atlas Of Physarum Computing

Andrew Adamatzky

• Publisher: WSPC
• Year: 2015
• eBook ISBN: 9789814675338
• Topic: Biological Sciences
• Subtopic: Science General
• Index: Biological Sciences

The slime mould Physarum polycephalum is a large cell visible by the unaided eye. It behaves as an intelligent nonlinear spatially extended active medium encapsulated in an elastic membrane. The cell optimises its growth patterns in configurations of attractants and repellents. This behaviour is interpreted as computation. Numerous prototypes of slime mould computers were designed to solve problems of computational geometry, graphs and transport networks and to implement universal computing circuits.

In this unique set of scientific photographs and micrographs, the leading experts in computer science, biology, chemistry and material science illustrate in superb detail the nature of the slime mould computers and hybrid devices. Every photograph or micrograph in this book is of real scientific, theoretical or technological interest. Each entry includes a self-contained description of how the visualised phenomenon is used in the relevant slime mould computer.

This atlas is unique in providing the depth and breadth of knowledge in harnessing behaviour of the slime mould to perform computation. It will help readers to understand how exploitation of biological processes has sparked new ideas and spurred progress in many fields of science and engineering.

Contents:

• Slime Mould Gates, Roads and Sensors (Andrew Adamatzky)
• Multi-Agent Model of Slime Mould for Computing and Robotics (Jeff Jones)
• Slime Mould Biotechnology (Richard Mayne)
• Slime Mould Interactions with Chemicals and Materials (Benjamin De Lacy Costello)
• Basic Features of Slime Mould Motility (Tomohiro Shirakawa)
• Slime Mould Grown on Polymer Layers (Alice Dimonte, Tatiana Berzina and Victor Erokhin)
• Diversity of Slime Mould Circuits (Martin Grube)
• Slime Mould Fluids and Networks from an Artist's Point of View (Theresa Schubert)

Readership: Students and researchers interested in biological processes and computing.
Key Features:

• Full of interesting photos and illustrations, which appeal not only to experts but to laymen and general public
• The contents are of real scientific, theoretical, or technological interest — guaranteed to make every geek's heart pound a little faster
• A unique compilation of new knowledge and its integration with existing information
• The Atlas provides a concise review of each thematic unit, with spreads of color illustrations and accompanying text that allows for speedy comprehension of key concepts
• All topics related to the slime mould are not covered well in mass media (newspapers, TV, pop-sci films and documentaries); therefore, the publication of the Atlas will be met warmly and is expected to attract huge support of academic and public outreach communities

Chapter 1

Slime mould gates, roads and sensors

Andrew Adamatzky

Unconventional Computing Centre,
University of the West of England, Bristol, United Kingdom
[email protected]

The photographs present a wide range of problems solved by the slime mould P. polycephalum: imitation of human-made transport pathways,¹ realisation of Boolean logical gates,² fabrication of self-repairing routable biowires,³ implementation of delay elements in computing circuits,⁴ computational geometry,⁵ sensors^6,7,8 and a would-be nervous system.⁹

When inoculated on a substrate with scattered sources of nutrients Physarum propagates towards the sources and spans them with a network of protoplasmic tubes. The structure of the network may vary between experiments; however, statistically, the most common planar graphs approximated are proximity graphs.¹⁰ When the configuration of nutrients matches a configuration of major urban areas of a country, the slime mould approximates a human-made transport network, i.e. motorways and highways of the country. ¹

On a nutrient substrate Physarum expands as an omnidirectional wave, e.g. as a classical excitation wave in a two-dimensional excitable medium. ⁵ It shows a pronounced wave front, comprising a very dense network of protoplasmic tubes. There are several orders of tubes which are differentiable by their width. The density of the protoplasmic network decreases towards the inoculation site, the epicentre of the wave pattern. Morphological transitions of the slime mould’s networks during expansion, colonisation and development bear a remarkable resemblance to the Cosmic Web.¹¹ Web-like spatial arrangements of galaxies and masses into elongated filaments of the Cosmic Web¹² are represented by wave-fragment-like active growing zones and colonies of Physarum. Morphologies of sheet-like walls and dense compact clusters¹² are typical for the slime mould growing on a nutrient agar.

Maze solving is a classical task of bionics, cybernetics and unconventional computing. A typical strategy for maze solving with a single device is to explore all possible passages, while marking visited parts, till the exit or a central chamber is found. Several attempts have been made to outperform Shannon’s electronic mouse Theseus¹³ using propagation of disturbances in unusual computing substrates, including excitable chemical systems, gas discharge and crystallisation. Most experimental prototypes were successful yet suffered from the computing substrate’s specific drawbacks. One of the entries of the chapter illustrates our laboratory experiment on path finding with Physarum guided by diffusion of an attractant placed in the target site.¹⁴

Given a cross-junction of agar channels and plasmodium inoculated in one of the channels, the plasmodium propagates straight through the junction;² the speed of propagation may increase if sources of chemoattractants are present (however, the presence of nutrients does not affect the direction of propagation). An active zone, or a growing tip, of plasmodium propagates in the initially chosen direction, as if it has some kind of inertia. Based on this phenomenon we designed two ballistic Boolean gates with two inputs and two outputs. ² In these gates input variables are x and y and outputs are p and q. Presence of a plasmodium in a given channel indicates TRUTH and absence indicates FALSE. Each gate implements a transformation 〈x, y〉 → 〈p, q〉.

A growing slime mould can develop conductive pathways, or wires, with its protoplasmic tubes.³ Given two pins to be connected by a wire, we place a piece of slime mould on one pin and an attractant on the other pin. Physarum propagates towards the attractant and thus connects the pins with a protoplasmic tube. A protoplasmic tube is conductive, can survive substantial over-voltage and can be used to transfer electrical current to lighting and actuating devices. In experiments we show how to route Physarum wires with chemoattractants and electrical fields. We demonstrate that a Physarum wire can be grown on almost bare breadboards and on top of electronic circuits. The Physarum wires can be insulated with a silicone oil without loss of functionality. A Physarum wire self-heals: the ends of a cut wire merge together and restore the conductive pathway in several hours after being cut. The slime mould wires will be used in future designs of self-growing wetware circuits and devices, and integration of slime mould electronics into unconventional biohybrid systems. ³

The slime mould is capable of sensing tactile,^6,8 chemical⁷ and optical¹⁵ stimuli and converting the stimuli to characteristic patterns of its electrical potential oscillations. The electrical responses to stimuli may propagate along protoplasmic tubes for distances exceeding tens of centimetres, like impulses in neural pathways do. A slime mould makes a decision about the propagation direction of its protoplasmic network based on information fusion from thousands of spatially extended protoplasmic loci, similarly to a neuron collecting information from its dendritic tree.^5,16 The analogy is distant yet inspiring. We speculate on whether an alternative —- would-be — nervous system can be developed and practically implemented from the slime mould.⁹ Based on the analogies between the slime mould and neurons, we demonstrate that the slime mould can play a role of primitive mechanoreceptors, photoreceptors and chemoreceptors; we also show how the Physarum neural pathways develop.

Physarum galaxy. ©2014 Andrew Adamatzky.

Physarum propagating on an artistic impression of a galaxy. See original picture in public domain, NASA/JPL–Caltech.¹⁷ The biological mechanisms underlying the optimal network formation in Physarum machines could be employed in design of large-scale transportation and communication networks in space, where paths between clusters, stars and matter formations are represented by growing protoplasmic tubes.¹¹

Physarum imitates development of Roman roads in the Balkans. ©2014 Andrew Adamatzky.

We placed oat flakes in the 17 most populated settlement are...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• Contents
• Preface
• Acknowledgements
• 1. Slime mould gates, roads and sensors
• 2. Multi-agent model of slime mould for computing and robotics
• 3. Slime mould biotechnology
• 4. Slime mould interactions with chemicals and materials
• 5. Basic features of slime mould motility
• 6. Slime mould grown on polymer layers
• 7. Diversity of slime mould circuits
• 8. Slime mould fluids and networks from an artist’s point of view
• Bibliography
• Index