Sensitivity and network topology in chemical reaction systems.

  title={Sensitivity and network topology in chemical reaction systems.},
  author={Takashi Okada and Atsushi Mochizuki},
  journal={Physical review. E},
  volume={96 2-1},
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved… 
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Law of Localization in Chemical Reaction Networks.
A theory to predict the sensitivity, i.e., the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone is developed, implying that network topology is an origin of biological robustness.
Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.
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My purpose here is to draw some general relationships between the structure of a chemical reaction network and the nature of the set of equilibrium states for the corresponding system of nonlinear
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E. coli seems to use complementary strategies that result in a metabolic network robust against perturbations, and actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate.
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Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Advances in flux balance analysis.
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
  • J. EdwardsB. Palsson
  • Biology, Engineering
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.
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A flux balance approach was used to determine optimal metabolic performance of Escherichia coli under variable oxygen limitations and increased oxygen limitations were found to result in the secretion of acetate, formate, and ethanol in that order.