Translated Chemical Reaction Networks

被引:38
|
作者
Johnston, Matthew D. [1 ]
机构
[1] Univ Wisconsin, Dept Math, Madison, WI 53706 USA
关键词
Chemical kinetics; Steady state; Mass action system; Complex balancing; Weakly reversible; COMPLEX ISOTHERMAL REACTORS; SPARSE POLYNOMIAL SYSTEMS; MULTIPLE STEADY-STATES; MASS-ACTION SYSTEMS; MULTISITE PHOSPHORYLATION; SUFFICIENT CONDITIONS; EQUILIBRIA; MULTISTATIONARITY; STABILITY;
D O I
10.1007/s11538-014-9947-5
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analyzed via a variety of techniques, including stoichiometric network analysis, deficiency theory, and algebraic techniques (e.g., Grobner bases). In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a network's capacity to permit a particular class of steady states, called toric steady states, to topological properties of a generalized network called a translated chemical reaction network. These networks share their reaction vectors with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.
引用
收藏
页码:1081 / 1116
页数:36
相关论文
共 50 条
  • [21] Atoms of multistationarity in chemical reaction networks
    Joshi, Badal
    Shiu, Anne
    [J]. JOURNAL OF MATHEMATICAL CHEMISTRY, 2013, 51 (01) : 153 - 178
  • [22] Independent Decompositions of Chemical Reaction Networks
    Bryan S. Hernandez
    Ralph John L. De la Cruz
    [J]. Bulletin of Mathematical Biology, 2021, 83
  • [23] Automated learning of chemical reaction networks
    Wilson, Zachary T.
    Sahinidis, Nikolaos, V
    [J]. COMPUTERS & CHEMICAL ENGINEERING, 2019, 127 : 88 - 98
  • [24] On finding hypercycles in chemical reaction networks
    Oezturan, Can
    [J]. APPLIED MATHEMATICS LETTERS, 2008, 21 (09) : 881 - 884
  • [25] On the Complexity of Reconstructing Chemical Reaction Networks
    Fagerberg R.
    Flamm C.
    Merkle D.
    Peters P.
    Stadler P.F.
    [J]. Mathematics in Computer Science, 2013, 7 (3) : 275 - 292
  • [26] Analysis of Degenerate Chemical Reaction Networks
    Uhr, Markus
    Kaltenbach, Hans-Michael
    Conradi, Carsten
    Stelling, Jorg
    [J]. POSITIVE SYSTEMS, PROCEEDINGS, 2009, 389 : 163 - +
  • [27] Computing with chemical reaction networks: a tutorial
    Robert Brijder
    [J]. Natural Computing, 2019, 18 : 119 - 137
  • [28] Bistability and oscillations in chemical reaction networks
    Mirela Domijan
    Markus Kirkilionis
    [J]. Journal of Mathematical Biology, 2009, 59 : 467 - 501
  • [29] Linear conjugacy of chemical reaction networks
    Johnston, Matthew D.
    Siegel, David
    [J]. JOURNAL OF MATHEMATICAL CHEMISTRY, 2011, 49 (07) : 1263 - 1282
  • [30] Circuit Theory for Chemical Reaction Networks
    Avanzini, Francesco
    Freitas, Nahuel
    Esposito, Massimiliano
    [J]. PHYSICAL REVIEW X, 2023, 13 (02)