Sensitivity and network topology in chemical reaction systems.

@article{Okada2017SensitivityAN,
  title={Sensitivity and network topology in chemical reaction systems.},
  author={Takashi Okada and Atsushi Mochizuki},
  journal={Physical review. E},
  year={2017},
  volume={96 2-1},
  pages={
          022322
        }
}
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… 
[PDF] Semantic Reader
6 Citations
Background Citations
1

6 Citations

A structural approach to understanding enzymatic regulation of chemical reaction networks
TLDR
A novel mathematical theory is introduced, structural sensitivity analysis, by which the responses of reaction systems upon the changes in enzyme activities/amounts are determined from network structure alone, implying that the network topology is one of the origins of biological robustness.
Structural bifurcation analysis in chemical reaction networks.
TLDR
A mathematical method is proposed to analyze bifurcation behaviors of network systems using their structures alone, and a whole network is decomposed into subnetworks, and for each of them the bIfurcation condition can be studied independently.
Sign-sensitivities for reaction networks: an algebraic approach.
  • E. Feliu
  • Mathematics
    Mathematical biosciences and engineering : MBE
  • 2019
TLDR
An algebraic framework to study sign-sensitivities for reaction networks modeled by means of systems of ordinary differential equations is presented and a sign-based criterion is found to determine, without computing the sensitivities, whether the sign depends on the steady state and parameters of the system.
Sensitivity analysis for reproducible candidate values of model parameters in signaling hub model
Mathematical models for signaling pathways are helpful for understanding molecular mechanism in the pathways and predicting dynamic behavior of the signal activity. To analyze the robustness of such…
Structural reduction of chemical reaction networks based on topology
TLDR
This work develops a model-independent reduction method of open chemical reaction systems based on the stoichiometry, which can reduce a reaction network while preserving its original steady-state properties, which allows the method to study large complex reaction systems efficiently.
Sensitivity of metabolic networks: perturbing metabolite concentrations
TLDR
This work studies the network response to perturbations of the concentrations of metabolites at an equilibrium, and investigates the responses in the network, both of the metabolite concentrations and of the reaction fluxes.

References

SHOWING 1-10 OF 21 REFERENCES
Law of Localization in Chemical Reaction Networks.
TLDR
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.
Paradoxical results in perturbation-based signaling network reconstruction.
Multiple equilibria in complex chemical reaction networks: extensions to entrapped species models.
TLDR
This research is intended to indicate a general way in which results about uniqueness of equilibria in the classical CFSTR context extend to entrapped species models.
The existence and uniqueness of steady states for a class of chemical reaction networks
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…
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
TLDR
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.
Collective dynamics of ‘small-world’ networks
TLDR
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
TLDR
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.
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates
TLDR
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.
...
...