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Computational Systems Biology pp 269–309Cite as

Network Dynamics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 541))

Abstract

Probably one of the most characteristic features of a living system is its continual propensity to change as it juggles the demands of survival with the need to replicate. Internally these adjustments are manifest as changes in metabolite, protein, and gene activities. Such changes have become increasingly obvious to experimentalists, with the advent of high-throughput technologies. In this chapter we highlight some of the quantitative approaches used to rationalize the study of cellular dynamics. The chapter focuses attention on the analysis of quantitative models based on differential equations using biochemical control theory. Basic pathway motifs are discussed, including straight chain, branched, and cyclic systems. In addition, some of the properties conferred by positive and negative feedback loops are discussed, particularly in relation to bistability and oscillatory dynamics.

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Acknowledgments

I wish to acknowledge Ravishankar R. Vallabhajosyula for assistance in preparing the simulation data and figures for the gene cascade circuits. This work was support by a generous grant from the NSF (award number CCF- 0432190).

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  1. Department of Bioengineering, University of Washington, Seattle, WA, USA

    Herbert M. Sauro

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Correspondence to Herbert M. Sauro .

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    Sauro, H.M. (2009). Network Dynamics. In: Ireton, R., Montgomery, K., Bumgarner, R., Samudrala, R., McDermott, J. (eds) Computational Systems Biology. Methods in Molecular Biology, vol 541. Humana Press. https://doi.org/10.1007/978-1-59745-243-4_13

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