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Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

Abstract

To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.
Authors:
Zhou, Peipei; [1]  Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)]; Cai, Shuiming; [2]  Liu, Zengrong; [1]  Chen, Luonan; [3]  Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan)]; Wang, Ruiqi [1] 
  1. Institute of Systems Biology, Shanghai University, Shanghai 200444 (China)
  2. Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)
  3. Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Center for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China)
Publication Date:
May 15, 2013
Product Type:
Journal Article
Resource Relation:
Journal Name: Chaos, Solitons and Fractals; Journal Volume: 50; Other Information: Copyright (c) 2012 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; FUNCTIONS; GAIN; INTERACTIONS; OSCILLATORS; SHAPE; SIGNALS; SWITCHES
OSTI ID:
22231634
Country of Origin:
United Kingdom
Language:
English
Other Identifying Numbers:
Journal ID: ISSN 0960-0779; Other: PII: S0960-0779(12)00221-4; TRN: GB14R2338052721
Availability:
Available from http://dx.doi.org/10.1016/j.chaos.2012.11.011
Submitting Site:
INIS
Size:
page(s) 115-126
Announcement Date:
May 30, 2014

Citation Formats

Zhou, Peipei, Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)], Cai, Shuiming, Liu, Zengrong, Chen, Luonan, Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan)], and Wang, Ruiqi. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems. United Kingdom: N. p., 2013. Web. doi:10.1016/J.CHAOS.2012.11.011.
Zhou, Peipei, Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)], Cai, Shuiming, Liu, Zengrong, Chen, Luonan, Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan)], & Wang, Ruiqi. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems. United Kingdom. https://doi.org/10.1016/J.CHAOS.2012.11.011
Zhou, Peipei, Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)], Cai, Shuiming, Liu, Zengrong, Chen, Luonan, Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan)], and Wang, Ruiqi. 2013. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems." United Kingdom. https://doi.org/10.1016/J.CHAOS.2012.11.011.
@misc{etde_22231634,
title = {Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems}
author = {Zhou, Peipei, Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China)], Cai, Shuiming, Liu, Zengrong, Chen, Luonan, Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan)], and Wang, Ruiqi}
abstractNote = {To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.}
doi = {10.1016/J.CHAOS.2012.11.011}
journal = []
volume = {50}
journal type = {AC}
place = {United Kingdom}
year = {2013}
month = {May}
}