Bibliography of: Systems Theory

  1. Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E.D.. "Metabolic network structure determines key aspects of functionality and regulation." Nature. 420 (6912). 2002. pp. 190-3.
    [ .pdf ] [ PubMed ]

    The relationship between structure, function and regulation in complex cellular networks is a still largely open question. Systems biology aims to explain this relationship by combining experimental and theoretical approaches. Current theories have various strengths and shortcomings in providing an integrated, predictive description of cellular networks. Specifically, dynamic mathematical modelling of large-scale networks meets difficulties because the necessary mechanistic detail and kinetic parameters are rarely available. In contrast, structure-oriented analyses only require network topology, which is well known in many cases. Previous approaches of this type focus on network robustness or metabolic phenotype, but do not give predictions on cellular regulation. Here, we devise a theoretical method for simultaneously predicting key aspects of network functionality, robustness and gene regulation from network structure alone. This is achieved by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes). We use the example of Escherichia coli central metabolism to illustrate the method.

    Keywords: Biomass ; Cell Physiology ; Computational Biology ; Computer Simulation ; *Energy Metabolism ; Escherichia coli_genetics ; Escherichia coli_growth and development ; Escherichia coli_*metabolism ; Gene Expression Regulation Bacterial ; *Models Biological ; Phenotype ; Systems Theory


  2. Sharov, A.A.. "Self-reproducing systems: structure, niche relations and evolution." Biosystems. 25 (4). 1991. pp. 237-49.
    [ PubMed ]

    A formal definition of a self-reproducing system is proposed using Petri nets. A potential self-reproducing system is a set of places in the Petri net such that the number of tokens in each place increases due to some sequence of internal transitions (a transition is called internal to the marked subset of places if at least one of its starting places and one of its terminating places belongs to that subset). An actual self-reproducing system is a system that compensates the outflow of its components by reproduction. In a suitable environment every potential self-reproducing system becomes an actual one. Each Petri net can be considered as an ecosystem with the web of ecological niches bound together with trophic and other relations. The stationary dynamics of the ecosystem is characterized by the set of filled niches. The process of evolution is described in terms of niche composition change. Perspectives of the theory of self-reproducing systems in biology are discussed.

    Keywords: *Evolution ; Models Biological ; Reproduction ; Selection (Genetics) ; Systems Theory