title: Systems biology towards life in silico: mathematics of the control of living cells.
abstract: Systems Biology is the science that aims to understand how biological function absent from macromolecules in isolation, arises when they are components of their system. Dedicated to the memory of Reinhart Heinrich, this paper discusses the origin and evolution of the new part of systems biology that relates to metabolic and signal-transduction pathways and extends mathematical biology so as to address postgenomic experimental reality. Various approaches to modeling the dynamics generated by metabolic and signal-transduction pathways are compared. The silicon cell approach aims to describe the intracellular network of interest precisely, by numerically integrating the precise rate equations that characterize the ways macromolecules' interact with each other. The non-equilibrium thermodynamic or 'lin-log' approach approximates the enzyme rate equations in terms of linear functions of the logarithms of the concentrations. Biochemical Systems Analysis approximates in terms of power laws. Importantly all these approaches link system behavior to molecular interaction properties. The latter two do this less precisely but enable analytical solutions. By limiting the questions asked, to optimal flux patterns, or to control of fluxes and concentrations around the (patho)physiological state, Flux Balance Analysis and Metabolic/Hierarchical Control Analysis again enable analytical solutions. Both the silicon cell approach and Metabolic/Hierarchical Control Analysis are able to highlight where and how system function derives from molecular interactions. The latter approach has also discovered a set of fundamental principles underlying the control of biological systems. The new law that relates concentration control to control by time is illustrated for an important signal transduction pathway, i.e. nuclear hormone receptor signaling such as relevant to bone formation. It is envisaged that there is much more Mathematical Biology to be discovered in the area between molecules and Life.
authors.affiliation: Molecular Cell Physiology, Institute of Molecular Cell Biology, Netherlands Institute for Systems Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands. hans.westerhoff@manchester.ac.uk
authors.forename: Hans V
authors.initials: HV
authors.lastname: Westerhoff
authors.forename: Alexey
authors.initials: A
authors.lastname: Kolodkin
authors.forename: Riaan
authors.initials: R
authors.lastname: Conradie
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Wilkinson
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Bruggeman
authors.forename: Klaas
authors.initials: K
authors.lastname: Krab
authors.forename: Jan H
authors.initials: JH
authors.lastname: van Schuppen
authors.forename: Hanna
authors.initials: H
authors.lastname: Hardin
authors.forename: Barbara M
authors.initials: BM
authors.lastname: Bakker
authors.forename: Martijn J
authors.initials: MJ
authors.lastname: Moné
authors.forename: Katja N
authors.initials: KN
authors.lastname: Rybakova
authors.forename: Marco
authors.initials: M
authors.lastname: Eijken
authors.forename: Hans J P
authors.initials: HJ
authors.lastname: van Leeuwen
authors.forename: Jacky L
authors.initials: JL
authors.lastname: Snoep
mesh_terms: D007700:Kinetics; D055432:Metabolomics; D008954:Models, Biological; D015398:Signal Transduction; D049490:Systems Biology; D013816:Thermodynamics