Top

Published in:

2016 | OriginalPaper | Chapter

Biology of the Physarum polycephalum Plasmodium: Preliminaries for Unconventional Computing

Author : Richard Mayne

Published in: Advances in Physarum Machines

Publisher: Springer International Publishing

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Slime mould Physarum polycephalum is a macroscopic amoeba-like organism whose ability to ‘compute’ the solutions to complex problems ranging from logic to computational geometry has led to its extensive use as an unconventional computing substrate. In slime mould computing devices—‘Physarum machines’—data may be imparted to the organism via stimulation with chemical, optical, mechanical or electrical sources and outputs are generally behavioural, chemical or/and electrical. This chapter examines the biological basis of a slime mould’s ability to perceive and act upon input data and the mechanisms that contribute towards the output we interpret as computation. Furthermore, various research methods for slime mould cultivation, electrophysiological measurement and hybridisation with exogenous substances are discussed. The data presented here provides an essential foundation for the computer scientist wishing to fabricate their own Physarum machines.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

next chapter Physarum, Quo Vadis?

For the reader’s interest, Brown is credited with the discovery which was presented in 1831, but he graciously acknowledged the earlier observations of Bauer [13].

It is beyond the scope of this chapter to discuss the discrepancies between recent and historical results but we refer the reader to Refs. [7, 21, 22] for a deeper explanation.

Parenthetically, it is interesting to note that following the studies that pioneered slime mould—and indeed, human—electrophysiological measurements in the 1950s, researchers were surprised to note that the organism could not be electrically innervated in the same manner as neurons [58], although we now know this to result from P. polycephalum’s electrical oscillator being controlled principally by chemical factors.

Adamatzky, A.: Die Naturwissenschaften 94(12), 975 (2007). doi:10.1007/s00114-007-0276-5. http://www.ncbi.nlm.nih.gov/pubmed/17603779

Fiore-Donno, A.M., Nikolaev, S.I., Nelson, M., Pawlowski, J., Cavalier-Smith, T., Baldauf, S.L.: Protist 161(1), 55 (2010). doi:10.1016/j.protis.2009.05.002 CrossRef

Stephenson, S., Stempenson, H.: Myxomycetes: A handbook of slime moulds. Timber Press, Portland, Oregon, USA (1994)

Gray, W., Alexopoulos, C.: Biology of the Myxomycetes. Ronald Press, New York, USA (1968)

Alexopoulos, C.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 1, chap. 1: Morphology, Taxonomy and Phylogeny

Olive, L.: Bot. Rev. 36, 59 (1970)CrossRef

Alexopoulos, C.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 1, chap. 5: Plasmodial structure and motility

Dussutour, A., Latty, T., Beekman, M., Simpson, S.J.: Proc. Natl. Acad. Sci. USA 107(10), 4607 (2010). doi:10.1073/pnas.0912198107 CrossRef

Goodman, E.: J. Bacteriol. 111, 242 (1972)

10.

E. of Life. Physarales species distribution (2015). http://eol.org/pages/5756/maps. Accessed 08 July 2015

11.

M.W. Dictionary. Physarum definition. http://www.merriam-webster.com/dictionary/physarum (2015)

12.

Geroulanos, S., Panaretos, C., Lyberopoulou, E.: Medicine and Healing in the Ancient Mediterranean. Oxbow Books (2014), chap. 20: Surgery in Byzantium

13.

Wayne, R.: Plant Cell Biology. Elsevier (2009), chap. 16: The nucleus

14.

Persoon, C.: Neues Magazin fur die Botanik 1, 63 (1794)

15.

Adamatzky, A., Jones, J.: On electrical correlates of Physarum polycephalum spatial activity: can we see Physarum Machine in the dark? Biophys. Rev. Lett. 6(01n02), 29–57 (2011)

16.

Nakagaki, T., Yamada, H., Tóth, A.: Biophys. Chem. 92(1–2), 47 (2001). http://www.ncbi.nlm.nih.gov/pubmed/11527578

17.

Grebecki, A., Cieślawska, M.: Cytobiologie 17, 335 (1978)

18.

Cieślawska, M., Grebecki, A.: Current research on Physarum, vol. 120 (1979), chap. Synchronal pulsation in plasmodia of Physarum polycephalum, pp. 167–170

19.

Janmey, P.: Physiol. Rev. 78(3), 763 (1998)

20.

Mayne, R., Adamatzky, A., Jones, J.: Communicative Integr. Biol. 7(1), e32097 (2014)

21.

Alim, K., Amselem, G., Brenner, M.P., Pringle, A.: Proc. Natl. Acad. Sci. 110(33), 13306 (2013). doi:10.1073/pnas.1305049110/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1305049110 CrossRef

22.

Tyson, J.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 1, chap. 3: Periodic phenomena in Physarum

23.

Reid, C.R., Latty, T., Dussutour, A., Beekman, M.: Proc. Natl. Acad. Sci. USA 109(43), 17490 (2012). doi:10.1073/pnas.1215037109 CrossRef

24.

Rhea, R.: J. Ultrastruct. Res. 15, 349 (1966)CrossRef

25.

Olenhusen, K., Wohlfarth-Bottermann, K.: Cell Tissue Res. 196, 455 (1979)CrossRef

26.

Wohlfarth-Bottermann, K.: J. Cell Sci. 16(1), 23 (1974)

27.

Wohlfarth-Bottermann, K.E.: J. Exp. Biol. 81, 15 (1979)

28.

Mayne, R., Adamatzky, A.: Nano LIFE 5(1), 140007 (2015). doi:10.1142/S179398441450007X CrossRef

29.

Pierron, G.: Proceedings of a NATO Advanced Research Workshop on the Molecular Biology of Physarum Polycephalum. Plenum press (1985), chap. 4: Temporal order of replication and gene expression

30.

Adamatzky, A.: Physarum Machines: Making Computers from Slime Mould. World Scientific, Singapore (2010)CrossRef

31.

Fingerle, J., Gradmann, D.: Electrical properties of the plasma membraneof microplasmodia of Physarum polycephalum. J. Membr. Biol. 68, 67–77 (1982)

32.

Yoshiyama, S., Ishigami, M., Nakamura, A., Kohama, K.: Cell Biol. Int. 34(1), 35 (2010). doi:10.1042/CBI20090158

33.

Guttes, E., Guttes, S.: Exp. Cell Res. 20(1), 239 (1960). doi:10.1016/0014-4827(60)90248-2 CrossRef

34.

Nakagaki, T., Yamada, H., Ueda, T.: Biophys. Chem. 84(3), 195 (2000). doi:10.1016/S0301-4622(00)00108-3 CrossRef

35.

Adamatzky, A.: Mater. Sci. Eng.: C 30(8), 1211 (2010). doi:10.1016/j.msec.2010.06.020 CrossRef

36.

Mayne, R., Patton, D., Costello, B., Adamatzky, A., Patton, R.: Int. J. Nanotechnol. Mol. Comput. 3(3), 1 (2011). doi:10.4018/ijnmc.2011070101. http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/ijnmc.2011070101

37.

Anderson, O.: J. Eukaryot. Microbiol. 40(1), 67 (1993)CrossRef

38.

Githens, S., Karnovsky, M.L.: J. Cell Biol. 58(15), 536 (1973)CrossRef

39.

Adamatzky, A.: On attraction of slime mould Physarum polycephalum to plants with sedative properties. Nat. Proc. 10 (2011). doi:10.1038/npre.2011.5985.1

40.

Adamatzky, A., Costello, B.D.L.: Physarum attraction: why slime mold behaves as cats do? Communicative Integr. Biol. 5(3), 297–299 (2012)

41.

de Lacy Costello, B.P.J., Adamatzky, A.I.: Communicative Integr. Biol. 6(5), e25030 (2013). doi:10.4161/cib.25030

42.

Jones, J.: From Pattern Formation to Material Computation. Emergence, Complexity and Comutation, Springer (2015)

43.

Ueda, T., Hirose, T., Kobatake, Y.: Biophys. J. 11, 461 (1980)

44.

T. Ueda, Y. Kobatake.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 1, chap. 4: Chemotaxis in plasmodia of Physarum polycephalum

45.

Sauer, H.: Developmental Biology of Physarum. Developmental and Cell Biology Series. Cambridge University Press (1982)

46.

Hato, M., Ueda, T., Kurihara, K., Kobatake, Y.: Cell Struct. Funct. 1, 269 (1976)CrossRef

47.

Mayne, R., Adamatzky, A.: Int. J. Gen. Syst. 44(3), 305 (2015). doi:10.1080/03081079.2014.997528 MathSciNetCrossRef

48.

Wormington, W., Weaver, R.: Proc. Natl. Acad. Sci. USA 73(11), 3896 (1976)CrossRef

49.

Barrantes, I., Glockner, G., Meyer, S., Marwan, W.: BMC Genomics 11, 115 (2010). doi:10.1186/1471-2164-11-115 CrossRef

50.

Adamatzky, A.: Steering plasmodium with light: Dynamical programming of Physarum machine, (2009). arXiv preprint arXiv:0908.0850

51.

Adamatzky, A.: arXiv preprint. arXiv:0908.0850 (2009)

52.

Adamatzky, A.: Org. Electron.: Phys. Mater. Appl. 14(12), 3355 (2013). doi:10.1016/j.orgel.2013.10.004 CrossRef

53.

Adamatzky, A.: Sens. Actuators B: Chem. 188(1), 38 (2013)CrossRef

54.

Mayne, R., Tsompanas, M.A., Sirakoulis, G.C., Adamatzky, A.: Biomed. Eng. Lett. 5(1), 51 (2015). doi:10.1007/s13534-015-0173-3. http://link.springer.com/10.1007/s13534-015-0173-3

55.

Adamatzky, A., Schubert, T.: Mater. Today 17(2), 86 (2014). doi:10.1016/j.mattod.2014.01.018 CrossRef

56.

Anderson, J.: J. Gen. Physiol. 35(1), 1 (1951)CrossRef

57.

Hato, S.: Integral Biomathics. Springer (2012), chap. Galvanotaxis of the plasmodium of Physarum polycephalum, pp. 57–62

58.

Tasaki, I., Kamiya, N.: Protoplasma 39(3), 333 (1950)CrossRef

59.

Adamatzky, A.: Biomed. Eng. Lett. 3, 232 (2013)CrossRef

60.

Whiting, J.G., de Lacy Costello, B.P., Adamatzky, A.: Biosystems 128, 48 (2015). doi:10.1016/j. biosystems.2015.01.009

61.

Shirakawa, T.: Soft Computing and Intelligent Systems (SCIS) and 13th International Symposium on Advanced Intelligent Systems (ISIS). IEEE Xplore (2012), pp. 296–300. doi:10.1109/SCIS-ISIS.2012.6505318

62.

Goodman, E., Greenebaum, B., Marron, M.: Radiat. Res. 78, 485 (1976)CrossRef

63.

McCullough, C., Dee, J.: J. Gen. Microbiol. 95(1), 151 (1976)CrossRef

64.

Daniel, J., Rusch, H.: J. Gen. Microbiol. 25, 47 (1961)CrossRef

65.

Mohburg, J.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 2, chap. 8: Preparation of Spherules

66.

Aldrich, H.: The Biology of Physarum and Didymium. Academic Press (1982), Cell Biology: A series of monographs, vol. 2, chap. 23: Culture Methods

67.

Ishigami, M., Kuroda, K., Hatano, S.: J. Cell Biol. 105, 321 (1987)CrossRef

68.

Iwamura, T.: Bot. Mag. 62, 126 (1949)CrossRef

69.

Ueda, T., Gotz Von Olenhusen, K.: Exp. Cell Res. 116, 55 (1978)CrossRef

70.

Mayne, R., Adamatzky, A.: On the Computing Potential of Intracellular Vesicles. Plos One. 10(10), e0139617 (2015). doi:10.1371/journal.pone.0139617

Title: Biology of the Physarum polycephalum Plasmodium: Preliminaries for Unconventional Computing
Author: Richard Mayne
Publisher: Springer International Publishing
Book: Advances in Physarum Machines
Print ISBN: 978-3-319-26661-9

Electronic ISBN: 978-3-319-26662-6

Copyright Year: 2016
DOI: https://doi.org/10.1007/978-3-319-26662-6_1

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Premium Partner