Biochemical oscillations in delayed negative cyclic feedback

Existence and profiles

Yutaka Hori, Masaaki Takada, Shinji Hara

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

In this paper, we propose a theoretical framework to systematically analyze the existence and the profiles of chemical oscillations in gene regulatory networks with negative cyclic feedback. In particular, we analytically derive the existence conditions and the profiles of oscillations in terms of reaction kinetic parameters and reveal dimensionless quantities that essentially characterize the oscillatory dynamics. These discoveries then allow us to provide general biological insights that are useful for the design of synthetic gene circuits and wet-lab experiments. We point out that time delays due to splicing and transport play an important role for both of the existence and the profiles of oscillations. To this end, we first show that local instability leads to oscillations in cyclic gene regulatory networks, and we derive the existence conditions based on local instability analysis. Then, we analyze the period, phase and amplitude of oscillations using multivariable harmonic balance analysis. These results are demonstrated with two existing biochemical networks, the Pentilator and a self-repression network of a Hes protein.

Original languageEnglish
Pages (from-to)2581-2590
Number of pages10
JournalAutomatica
Volume49
Issue number9
DOIs
Publication statusPublished - 2013 Sep
Externally publishedYes

Fingerprint

Genes
Feedback
Kinetic parameters
Reaction kinetics
Time delay
Proteins
Networks (circuits)
Experiments

Keywords

  • Application of nonlinear analysis and design
  • Cellular, metabolic, cardiovascular, neurosystems
  • Gene regulatory networks
  • Large scale complex systems
  • Systems with time-delays

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Electrical and Electronic Engineering

Cite this

Biochemical oscillations in delayed negative cyclic feedback : Existence and profiles. / Hori, Yutaka; Takada, Masaaki; Hara, Shinji.

In: Automatica, Vol. 49, No. 9, 09.2013, p. 2581-2590.

Research output: Contribution to journalArticle

Hori, Yutaka ; Takada, Masaaki ; Hara, Shinji. / Biochemical oscillations in delayed negative cyclic feedback : Existence and profiles. In: Automatica. 2013 ; Vol. 49, No. 9. pp. 2581-2590.
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