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1 Adamatzky, A. (2010) Physarum machines: computers from slime mould. (74) World Scientific Publishing. ISBN We recommend you cite the published version. The publisher s URL is Refereed: No Physarum Machines: computers from slime mould, Andrew Adamatzky, Copyright? 2010 World Scientific Publishing Co. with permission from World Scientific Publishing Co. Pte. Ltd. Disclaimer UWE has obtained warranties from all depositors as to their title in the material deposited and as to their right to deposit such material. UWE makes no representation or warranties of commercial utility, title, or fitness for a particular purpose or any other warranty, express or implied in respect of any material deposited. UWE makes no representation that the use of the materials will not infringe any patent, copyright, trademark or other property or proprietary rights. UWE accepts no liability for any infringement of intellectual property rights in any material deposited but will remove such material from public view pending investigation in the event of an allegation of any such infringement. PLEASE SCROLL DOWN FOR TEXT.

2 Contents Preface Acknowledgments v ix 1. From reaction diffusion to Physarum computing Reaction diffusion computers Limitations of reaction diffusion computers Physarum polycephalum Physarum as encapsulated reaction diffusion computer Dawn of Physarum computing Experimenting with Physarum Where to get plasmodium of P. polycephalum Physarum farms Dishes and scanners Data input with food Substrates Nutrient-rich vs. non-nutrient substrates Sensing Modeling plasmodium Summary Physarum solves mazes Multiple-site start Single-site start Summary xi

3 xii Physarum machines 4. Plane tessellation The ubiquitous diagram Physarum construction of Voronoi diagram Summary Oregonator model of Physarum growing trees What a BZ medium could not do Physarum and Oregonator Building trees with Oregonator Validating simulation by experiments Summary Does the plasmodium follow Toussaint hierarchy? Proximity graphs Nearest-neighborhood graph Minimal spanning tree Relative neighborhood graph Gabriel graph Delaunay triangulation Toussaint hierarchy Plasmodium network and Toussaint hierarchy Preparing for graph growing Growing graph from a single point Growing from all points Physarum hierarchy Summary Complexity of plasmodium computation Halting problem Reusability Further studies Physarum gates xor gate anyone? Ballistics of Physarum localizations Physarum gates Simulation of Physarum gates Simulated one-bit half-adder Why do we use a non-nutrient substrate?

4 Contents xiii 7.7 Summary Kolmogorov Uspensky machine in plasmodium Physarum machines Materials for Physarum machine Nodes Edges Data, results and halting Active zone Bounded connectivity Addressing and labeling Basic operations Example of Physarum machine solving simple task On parallelism Summary Reconfiguring Physarum machines with attractants Fusion and multiplication of active zones Translating active zone Reconfiguration of Physarum machine Summary Programming Physarum machines with light Physarum and light Designing control domains Trees and waves Diverting plasmodium Inertia Multiplying plasmodium waves Foraging around obstacles Routing signals in Physarum machine Disobedience Summary Routing Physarum with repellents Avoiding repellents on nutrient-rich substrate Operating on non-nutrient substrate Operation deflect

5 xiv Physarum machines 11.4 Operation multiply Operation merge Summary Physarum manipulators Plasmodium on water surface Manipulating floating objects Summary Physarum boats Random wandering Sliding Pushing Anchoring Propelling Cellular automaton model Physarum tugboat On failures Summary Manipulating substances with Physarum machine Operations with colored substances Transfer of substances to specified location Mixing substances Superpositions of transfer and mix operations Summary Road planning with slime mould United Kingdom in a gel Development of transport links Weighted Physarum graphs Physarum vs. Department for Transport Proximity graphs and motorways Imitating disasters Summary Epilogue 247 Bibliography 249 Index 261

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