GMU:Habitats SS18/Physarum Polycephalum

Gallery

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Related Projects

Theresa Schubert

bodymetries, 2013

“In bodymetries visitors can experience virtual slime mould growth on their skin. Visitors enter a semi dark room with a bar table in the center. Some wobbling blobs appear on a small sections of the surface. Visitors are invited to lay their arms onto the desk. The system ‘scans’ it by taking and analysing a picture. The slime mould algorithm starts to grow from the darkest area it can find on the skin.”(http://theresaschubert.com/arts-experiments/art/bodymetries-mapping-the-human-body-through-amorphous-intelligence)

James Whiting, Ben De Lacy Costello, Andrew Adamatzky

Sonification

Towards slime mould chemical sensor: Mapping chemical inputs onto electrical potential dynamics of Physarum Polycephalum Sensors and Actuators B: Chemical. response to BenzylAlcohol https://www.youtube.com/watch?v=byTJEYHaIIM https://soundcloud.com/lessnullvoid/physarum-sonification

Toshiyuki Nakagaki

Experiments with Physarum polycefalum finding the shortest way to the food source through the maze

3-5 min @ Heather Barnett: What humans can learn from semi-intelligent slime https://www.youtube.com/watch?v=2UxGrde1NDA

Physarum Polycephalum

“Slime mold is an informal name given to several kinds of unrelated eukaryotic organisms that can live freely as single cells, but aggregate together to form multicellular reproductive structures.”(Wikipedia a) Slime molds belong to Protista, that is neither animal, nor fungi nor bacteria. They feed on microorganisms. “When food is in short supply, many of these single-celled organisms will congregate and start moving as a single body. In this state they are sensitive to airborne chemicals and can detect food sources. They can readily change the shape and function of parts and may form stalks that produce fruiting bodies, releasing countless spores”(Wikipedia a)

"Physarum polycephalum, literally the "many-headed slime", is a slime mold that inhabits shady, cool, moist areas, such as decaying leaves and logs. Like slime molds in general, it is sensitive to light; in particular, light can repel the slime mold and be a factor in triggering spore growth."(wikipedia b) It feeds on bacteria, spores and other microbial creatures.

chemotaxis

"..In the plasmodial phase of its life cycle consists of a large single celled mass of yellow plasmodium. The organism extends protoplasmic tubes which grow towards sources of food; flowing through these tubes is a cytoplasm, which oscillates back and forth by a process of protoplasmic streaming which forces the cytoplasm in the direction in which the organism is growing [1]. The movement and growth of P. polycephalum is predominantly controlled by favourable conditions, such as an abundance of food, warm temperature, darkness and moisture. It has been well documented that various substances trigger a chemotactic response in P. polycephalum, various carbohydrates such as glucose and maltose initiate positive chemotaxis while sucrose shows marginal but consistent negative chemotaxis [2, 3, 4, 5]." (Whiting 2013)

life cycle

• Vegetative phase: plasmodium (consists of networks of protoplasmic veins, and many nuclei)
• sclerotium (hardened multinucleated tissue)
• sporangia

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Medium

• 1,7% agar plate
• oat flakes

Medium replacement

Instead of oat flakes two other recipes: a) 2,5g agar, 200ml distilled water, 1,5g peptone (lactose) b) 1g agar, 5g cooked (for 2 min) oat flakes in 100ml water. Medium could be placed either on top of agar as droplets or instead of agar.

Unconventional Computing and Physarum Machine

"Unconventional computing is an interdisciplinary branch of science where computer scientists, physicists, mathematicians, apply principles of information processing in natural systems to design novel computer devices and architectures" (Adamatzky 2007)

“The plasmodium functions as a parallel amorphous computer with parallel inputs and parallel outputs. Data are represented by spatial configurations of sources of nutrients. A program of computation is coded via configurations of repellents and attractants. Results of computation are presented by the configuration of the protoplasmic network and the localisation of the plasmodium.”(Adamatzky 2010)

“.. plasmodium is unique biological substrate that mimics universal storage modification machines, namely the Kolmogorov-Uspensky machine. In the plasmodium implementation of the storage modification machine data are represented by sources of nutrients and memory structure by protoplasmic tubes connecting the sources. In laboratory experiments and simulation we demonstrate how the plasmodium-based storage modification machine can be programmed.”(Adamatzky & Jones 2009)

Implementations

• Implementation of a Kolmogorov–Uspensky machine on a biological substrate. (Adamatzky 2007)
• Programmable reconfiguration of Physarum machines (Adamatzky 2009)

References

• Whiting, J. (2013). "Towards slime mould chemical sensor: Mapping chemical inputs onto electrical potential dynamics of Physarum Polycephalum." Available at https://arxiv.org/pdf/1312.4189.pdf (Accessed: 25 April 2018)
• Wikipedia (a). Slime mold. Available at: https://en.wikipedia.org/wiki/Slime_mold (Accessed 6 December 2016).
• Wikipedia (b). Physarum polycephalum. Available at: https://en.wikipedia.org/wiki/Physarum_polycephalum (Accessed 8 December 2015).

Other References (Unconventional Computing and Physarum Machines)

• Andrew Adamatzky (2007). Adamatzky A. Physarum machine: implementation of a Kolmogorov–Uspensky machine on a biological substrate. Available at: http://arxiv.org/pdf/cs/0703128.pdf (Accessed 8 December 2015).
• Andrew Adamatzky and Jeff Jones (2009). Programmable reconfiguration of Physarum machines. Available at: http://arxiv.org/pdf/0901.4556.pdf (Accessed 8 December 2015).
• Andrew Adamatzky (2010). Physarum Machines: Computers from Slime Mould. World Scientific Publishing. Partly available at: https://books.google.de/books?id=Kbs_AIDbfU8C&printsec=frontcover (Accessed 8 December 2015).
• Yuri Gurevich (1988). On Kolmogorov Machines And Related Issues. Available at: http://research.microsoft.com/en-us/um/people/gurevich/opera/78.pdf (Accessed 8 December 2015).
• А. Н. Колмогоров и В. А. Успенский (1958). “К ОПРЕДЕЛЕНИЮ АЛГОРИТМА”, УСПЕХИ МАТЕМАТИЧЕСКИХ НАУК, т. XIII, вып. 4 (82). Available at http://lpcs.math.msu.su/~uspensky/bib/Uspensky_1958_UMN_Kolmogorov_Opredelenie_algoritma.pdf (Accessed 8 December 2015).
• Turing, A. M. (1936). “On computable numbers, with an application to the Entscheidungsproblem,” in Proceedings of the London mathematical society, 2(42), pp. 230-265. Available at: http://www.dna.caltech.edu/courses/cs129/caltech_restricted/Turing_1936_IBID.pdf (Accessed 8 December 2015).
• wikipedia (c). Markov chain. Available at: https://en.wikipedia.org/wiki/Markov_chain (Accessed 8 December 2015).