Rhythms Emerge in a Collection of 'Blind' Chemicals by the Use of 'Genetic Switches'

Hiroshi Inayoshi[1] (inayoshi@etl.go.jp)
Hitoshi Iba[2] (iba@etl.go.jp)

[1] Computer Science Division
Electrotechnical Laboratory (ETL) 1-1-4 Umezono, Tsukuba 305, Japan
[2] Machine Understanding Division
Electrotechnical Laboratory (ETL) 1-1-4 Umezono, Tsukuba 305, Japan


Abstract

This paper presents a new computational method in the modeling and simulation of gene expression by introducing the artificial chemical system. The artificial chemical system is specified by its four items: (1) components (five kinds of particles and DNA with Genetic Switches); (2) space (2-dimensional polar grids); (3) simple reaction rules (construction and destruction of molecules, etc.); (4) simple behavioral rules (stochastic movements and stochastic collisions, etc.). The simulation demonstrates the capability of the system to exhibit emergent behavior: that is, global order of the system (regular rhythms, i.e. regular oscillations in the amounts of some gene products, in this case) emerges out of the randomness (through stochastic movements and collisions) of the components.

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Japanese Society for Bioinformatics