Designing Attractive Models Via Automated Identification of Chaotic and Oscillatory Dynamical Regimes

Overview

Journal Nat Commun

Specialty Biology

Date 2011 Oct 6

PMID 21971504

Citations 10

Authors

Daniel Silk

Paul D W Kirk

Chris P Barnes

Tina Toni

Anna Rose

Simon Moon

Margaret J Dallman

Michael P H Stumpf

Affiliations

Soon will be listed here.

Abstract

Chaos and oscillations continue to capture the interest of both the scientific and public domains. Yet despite the importance of these qualitative features, most attempts at constructing mathematical models of such phenomena have taken an indirect, quantitative approach, for example, by fitting models to a finite number of data points. Here we develop a qualitative inference framework that allows us to both reverse-engineer and design systems exhibiting these and other dynamical behaviours by directly specifying the desired characteristics of the underlying dynamical attractor. This change in perspective from quantitative to qualitative dynamics, provides fundamental and new insights into the properties of dynamical systems.

Citing Articles

Chaos in synthetic microbial communities.

Karkaria B, Manhart A, Fedorec A, Barnes C PLoS Comput Biol. 2022; 18(10):e1010548.

PMID: 36215322 PMC: 9584520. DOI: 10.1371/journal.pcbi.1010548.

Parameter estimation in models of biological oscillators: an automated regularised estimation approach.

Pitt J, Banga J BMC Bioinformatics. 2019; 20(1):82.

PMID: 30770736 PMC: 6377730. DOI: 10.1186/s12859-019-2630-y.

Predicting the bounds of large chaotic systems using low-dimensional manifolds.

Haugaard A PLoS One. 2017; 12(6):e0179507.

PMID: 28644871 PMC: 5482462. DOI: 10.1371/journal.pone.0179507.

Efficient implementation of a real-time estimation system for thalamocortical hidden Parkinsonian properties.

Yang S, Deng B, Wang J, Li H, Liu C, Fietkiewicz C Sci Rep. 2017; 7:40152.

PMID: 28065938 PMC: 5220381. DOI: 10.1038/srep40152.

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.

Filippi S, Barnes C, Kirk P, Kudo T, Kunida K, McMahon S Cell Rep. 2016; 15(11):2524-35.

PMID: 27264188 PMC: 4914773. DOI: 10.1016/j.celrep.2016.05.024.

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