title: Prospects for advancing the understanding of complex biochemical systems.
abstract: The application of mathematical theories to understanding the behaviour of complex biochemical systems is reviewed. Key aspects of behaviour are identified as the flux through particular pathways in a steady state, the nature and stability of dynamical states, and the thermodynamic properties of systems. The first of these is dealt primarily in theories of metabolic control, and metabolic control analysis (MCA) is an important example. The valid application of this theory is limited to steady-state systems, and the cases where the essential features of control can be derived from calibration experiments which perturb the state of the system by a sufficiently small amount from its operating point. In practice, time-dependent systems exist, it is not always possible to know a priori whether applied perturbations are sufficiently small, and important features of control may lie farther from the operating point than the application of the theory permits. The nature and stability of dynamical and thermodynamical states is beyond the scope of MCA. To understand the significance of these limitations fully, and to address the dynamical and thermodynamical properties, more complete theories are required. Non-linear systems theory offers the possibility of studying important questions regarding control of steady and dynamical states. It can also link to thermodynamic properties of the system including the energetic efficiency of particular pathways. However, its application requires a more detailed characterisation of the system under study. This extra detail may be an essential feature of the study of non-equilibrium states in general, and non-ideal pathways in particular. Progress requires considerably more widespread integration of theoretical and experimental approaches than currently exists.
authors.affiliation: Centre for Nonlinear Systems in Biology, Scottish Crop Research Institute, Dundee, UK.
authors.forename: J
authors.initials: J
authors.lastname: Liu
authors.forename: J W
authors.initials: JW
authors.lastname: Crawford
authors.forename: R
authors.initials: R
authors.lastname: Viola
authors.forename: B
authors.initials: B
authors.lastname: Goodman
mesh_terms: D001671:Biochemistry / Q000639:trends; D004734:Energy Metabolism; D005544:Forecasting; D008660:Metabolism; D008962:Models, Theoretical