An adaptive and robust biological network based on the vacant-particle transportation model

Yukio Gunji, Tomohiro Shirakawa, Takayuki Niizato, Masaki Yamachiyo, Iori Tani

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

A living system reveals local computing by referring to a whole system beyond the exploration-exploitation dilemma. The slime mold, Physarum polycephalum, uses protoplasmic flow to change its own outer shape, which yields the boundary condition and forms an adaptive and robust network. This observation suggests that the whole Physarum can be represented as a local protoplasmic flow system. Here, we show that a system composed of particles, which move and are modified based upon the particle transformation that contains the relationship between the parts and the whole, can emulate the network formed by Physarum. This system balances the exploration-exploitation trade-off and shows a scale-free sub-domain. By decreasing the number of particles, our model, VP-S, can emulate the Physarum adaptive network as it is attracted to a food stimulus. By increasing the number of particles, our model, VP-D, can emulate the pattern of a growing Physarum. The patterns produced by our model were compared with those of the Physarum pattern quantitatively, which showed that both patterns balance exploration with exploitation. This model should have a wide applicability to study biological collective phenomena in general.

Original languageEnglish
Pages (from-to)187-200
Number of pages14
JournalJournal of Theoretical Biology
Volume272
Issue number1
DOIs
Publication statusPublished - 2011 Mar 7
Externally publishedYes

Fingerprint

Physarum
Biological Networks
Exploitation
Living Systems
Dilemma
Physarum polycephalum
Biological Phenomena
Fungi
Model
Trade-offs
Boundary conditions
Computing
Food

Keywords

  • Asynchronous automata
  • Exploration-exploitation dilemma
  • Flock
  • Physarum
  • Unconventional computing

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Modelling and Simulation
  • Statistics and Probability
  • Applied Mathematics

Cite this

An adaptive and robust biological network based on the vacant-particle transportation model. / Gunji, Yukio; Shirakawa, Tomohiro; Niizato, Takayuki; Yamachiyo, Masaki; Tani, Iori.

In: Journal of Theoretical Biology, Vol. 272, No. 1, 07.03.2011, p. 187-200.

Research output: Contribution to journalArticle

Gunji, Yukio ; Shirakawa, Tomohiro ; Niizato, Takayuki ; Yamachiyo, Masaki ; Tani, Iori. / An adaptive and robust biological network based on the vacant-particle transportation model. In: Journal of Theoretical Biology. 2011 ; Vol. 272, No. 1. pp. 187-200.
@article{ecc3a252f59548f18cfc0242ab034076,
title = "An adaptive and robust biological network based on the vacant-particle transportation model",
abstract = "A living system reveals local computing by referring to a whole system beyond the exploration-exploitation dilemma. The slime mold, Physarum polycephalum, uses protoplasmic flow to change its own outer shape, which yields the boundary condition and forms an adaptive and robust network. This observation suggests that the whole Physarum can be represented as a local protoplasmic flow system. Here, we show that a system composed of particles, which move and are modified based upon the particle transformation that contains the relationship between the parts and the whole, can emulate the network formed by Physarum. This system balances the exploration-exploitation trade-off and shows a scale-free sub-domain. By decreasing the number of particles, our model, VP-S, can emulate the Physarum adaptive network as it is attracted to a food stimulus. By increasing the number of particles, our model, VP-D, can emulate the pattern of a growing Physarum. The patterns produced by our model were compared with those of the Physarum pattern quantitatively, which showed that both patterns balance exploration with exploitation. This model should have a wide applicability to study biological collective phenomena in general.",
keywords = "Asynchronous automata, Exploration-exploitation dilemma, Flock, Physarum, Unconventional computing",
author = "Yukio Gunji and Tomohiro Shirakawa and Takayuki Niizato and Masaki Yamachiyo and Iori Tani",
year = "2011",
month = "3",
day = "7",
doi = "10.1016/j.jtbi.2010.12.013",
language = "English",
volume = "272",
pages = "187--200",
journal = "Journal of Theoretical Biology",
issn = "0022-5193",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - An adaptive and robust biological network based on the vacant-particle transportation model

AU - Gunji, Yukio

AU - Shirakawa, Tomohiro

AU - Niizato, Takayuki

AU - Yamachiyo, Masaki

AU - Tani, Iori

PY - 2011/3/7

Y1 - 2011/3/7

N2 - A living system reveals local computing by referring to a whole system beyond the exploration-exploitation dilemma. The slime mold, Physarum polycephalum, uses protoplasmic flow to change its own outer shape, which yields the boundary condition and forms an adaptive and robust network. This observation suggests that the whole Physarum can be represented as a local protoplasmic flow system. Here, we show that a system composed of particles, which move and are modified based upon the particle transformation that contains the relationship between the parts and the whole, can emulate the network formed by Physarum. This system balances the exploration-exploitation trade-off and shows a scale-free sub-domain. By decreasing the number of particles, our model, VP-S, can emulate the Physarum adaptive network as it is attracted to a food stimulus. By increasing the number of particles, our model, VP-D, can emulate the pattern of a growing Physarum. The patterns produced by our model were compared with those of the Physarum pattern quantitatively, which showed that both patterns balance exploration with exploitation. This model should have a wide applicability to study biological collective phenomena in general.

AB - A living system reveals local computing by referring to a whole system beyond the exploration-exploitation dilemma. The slime mold, Physarum polycephalum, uses protoplasmic flow to change its own outer shape, which yields the boundary condition and forms an adaptive and robust network. This observation suggests that the whole Physarum can be represented as a local protoplasmic flow system. Here, we show that a system composed of particles, which move and are modified based upon the particle transformation that contains the relationship between the parts and the whole, can emulate the network formed by Physarum. This system balances the exploration-exploitation trade-off and shows a scale-free sub-domain. By decreasing the number of particles, our model, VP-S, can emulate the Physarum adaptive network as it is attracted to a food stimulus. By increasing the number of particles, our model, VP-D, can emulate the pattern of a growing Physarum. The patterns produced by our model were compared with those of the Physarum pattern quantitatively, which showed that both patterns balance exploration with exploitation. This model should have a wide applicability to study biological collective phenomena in general.

KW - Asynchronous automata

KW - Exploration-exploitation dilemma

KW - Flock

KW - Physarum

KW - Unconventional computing

UR - http://www.scopus.com/inward/record.url?scp=78650775262&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650775262&partnerID=8YFLogxK

U2 - 10.1016/j.jtbi.2010.12.013

DO - 10.1016/j.jtbi.2010.12.013

M3 - Article

VL - 272

SP - 187

EP - 200

JO - Journal of Theoretical Biology

JF - Journal of Theoretical Biology

SN - 0022-5193

IS - 1

ER -