Mathematical Analysis of Chemical Reaction Systems

The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially distributed. Here we focus on mathematical models based on deterministic mass-action kinetics. These models are systems of coupled nonlinear differential equations on the positive orthant. We explain how mathematical properties of the solutions of mass-action systems are strongly related to key properties of the networks of chemical reactions that generate them, such as specific versions of reversibility and feedback interactions.

[1]  David Angeli,et al.  Persistence Results for Chemical Reaction Networks with Time-Dependent Kinetics and No Global Conservation Laws , 2011, SIAM J. Appl. Math..

[2]  Rudolf Wegscheider,et al.  Über simultane Gleichgewichte und die Beziehungen zwischen Thermodynamik und Reactionskinetik homogener Systeme , 1901 .

[3]  Murad Banaji,et al.  Some Results on Injectivity and Multistationarity in Chemical Reaction Networks , 2013, SIAM J. Appl. Dyn. Syst..

[4]  A. Tudorascu,et al.  Chemical reaction-diffusion networks: convergence of the method of lines , 2017, Journal of Mathematical Chemistry.

[5]  R. Jackson,et al.  General mass action kinetics , 1972 .

[6]  Bernd Sturmfels,et al.  Siphons in Chemical Reaction Networks , 2009, Bulletin of mathematical biology.

[7]  G N Lewis,et al.  A New Principle of Equilibrium. , 1925, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Thomas G. Kurtz,et al.  Finite Time Distributions of Stochastically Modeled Chemical Systems with Absolute Concentration Robustness , 2016, SIAM J. Appl. Dyn. Syst..

[9]  F. Horn Necessary and sufficient conditions for complex balancing in chemical kinetics , 1972 .

[10]  B. M. Fulk MATH , 1992 .

[11]  Martin Feinberg,et al.  Multiple Equilibria in Complex Chemical Reaction Networks: Ii. the Species-reactions Graph , 2022 .

[12]  K. Fellner,et al.  Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems , 2017, 1708.01427.

[13]  Matthew D. Johnston,et al.  Linear conjugacy of chemical reaction networks , 2011, 1101.1663.

[14]  M. Feinberg,et al.  Understanding bistability in complex enzyme-driven reaction networks. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Badal Joshi,et al.  A survey of methods for deciding whether a reaction network is multistationary , 2014, 1412.5257.

[16]  B. L. Clarke Stability of Complex Reaction Networks , 2007 .

[17]  Gheorghe Craciun,et al.  Robust Persistence and Permanence of Polynomial and Power Law Dynamical Systems , 2017, SIAM J. Appl. Math..

[18]  M. Feinberg The existence and uniqueness of steady states for a class of chemical reaction networks , 1995 .

[19]  Gilles Gnacadja,et al.  An Invitation to Pharmacostatics , 2019, Bulletin of mathematical biology.

[20]  J. Bauer,et al.  Chemical reaction network theory for in-silico biologists , 2003 .

[21]  Martin Feinberg,et al.  Multiple Equilibria in Complex Chemical Reaction Networks: Semiopen Mass Action Systems * , 2022 .

[22]  J. Higgins,et al.  Some remarks on Shear's Liapunov function for systems of chemical reactions. , 1968, Journal of theoretical biology.

[23]  U. Alon An introduction to systems biology : design principles of biological circuits , 2019 .

[24]  D Shear,et al.  An analog of the Boltzmann H-theorem (a Liapunov function) for systems of coupled chemical reactions. , 1967, Journal of theoretical biology.

[25]  Georg Regensburger,et al.  Generalized Mass Action Systems: Complex Balancing Equilibria and Sign Vectors of the Stoichiometric and Kinetic-Order Subspaces , 2012, SIAM J. Appl. Math..

[26]  Brian Ingalls,et al.  Mathematical Modeling in Systems Biology: An Introduction , 2013 .

[27]  Fedor Nazarov,et al.  Persistence and Permanence of Mass-Action and Power-Law Dynamical Systems , 2010, SIAM J. Appl. Math..

[28]  Polly Y. Yu,et al.  A generalization of Birchs theorem and vertex-balanced steady states for generalized mass-action systems. , 2018, Mathematical biosciences and engineering : MBE.

[29]  Bao Quoc Tang,et al.  Trend to Equilibrium for Reaction-Diffusion Systems Arising from Complex Balanced Chemical Reaction Networks , 2016, SIAM J. Math. Anal..

[30]  Eberhard O. Voit,et al.  150 Years of the Mass Action Law , 2015, PLoS Comput. Biol..

[31]  James Wei,et al.  The Structure and Analysis of Complex Reaction Systems , 1962 .

[32]  Badal Joshi,et al.  Simplifying the Jacobian Criterion for Precluding Multistationarity in Chemical Reaction Networks , 2011, SIAM J. Appl. Math..

[33]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[34]  James B. Rawlings,et al.  The QSSA in Chemical Kinetics: As Taught and as Practiced , 2014 .

[35]  M. Feinberg,et al.  Dynamics of open chemical systems and the algebraic structure of the underlying reaction network , 1974 .

[36]  L. Onsager Reciprocal Relations in Irreversible Processes. II. , 1931 .

[37]  Julien Clinton Sprott,et al.  Coexistence and chaos in complex ecologies , 2005 .

[38]  Péter Érdi,et al.  Mathematical models of chemical reactions , 1989 .

[39]  Alicia Dickenstein,et al.  Toric dynamical systems , 2007, J. Symb. Comput..

[40]  Murad Banaji,et al.  P Matrix Properties, Injectivity, and Stability in Chemical Reaction Systems , 2007, SIAM J. Appl. Math..

[41]  Thomas G. Kurtz,et al.  Stochastic Analysis of Biochemical Systems , 2015 .

[42]  Alicia Dickenstein,et al.  Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry , 2013, Found. Comput. Math..

[43]  T. Kurtz The Relationship between Stochastic and Deterministic Models for Chemical Reactions , 1972 .

[44]  S. Schnell,et al.  Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws. , 2004, Progress in biophysics and molecular biology.

[45]  Elisenda Feliu,et al.  Preclusion of switch behavior in networks with mass-action kinetics , 2012, Appl. Math. Comput..

[46]  Martin Feinberg,et al.  Multiple Equilibria in Complex Chemical Reaction Networks: I. the Injectivity Property * , 2006 .

[47]  Murad Banaji,et al.  Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements , 2009, 0903.1190.

[48]  B. Boros,et al.  On the existence of the positive steady states of weakly reversible deficiency-one mass action systems. , 2013, Mathematical biosciences.

[49]  Gheorghe Craciun,et al.  Identifiability of chemical reaction networks , 2008 .

[50]  Casian Pantea,et al.  On the Persistence and Global Stability of Mass-Action Systems , 2011, SIAM J. Math. Anal..

[51]  David F. Anderson,et al.  A Proof of the Global Attractor Conjecture in the Single Linkage Class Case , 2011, SIAM J. Appl. Math..

[52]  Carsten Wiuf,et al.  Lyapunov Functions, Stationary Distributions, and Non-equilibrium Potential for Reaction Networks , 2015, Bulletin of mathematical biology.

[53]  G. Craciun,et al.  Graph-theoretic conditions for zero-eigenvalue Turing instability in general chemical reaction networks. , 2013, Mathematical biosciences and engineering : MBE.

[54]  Rud. Wegscheider Über simultane Gleichgewichte und die Beziehungen zwischen Thermodynamik und Reaktionskinetik homogener Systeme , 1902 .

[55]  M. Feinberg Chemical reaction network structure and the stability of complex isothermal reactors—I. The deficiency zero and deficiency one theorems , 1987 .

[56]  Michael A. Savageau,et al.  Introduction to S-systems and the underlying power-law formalism , 1988 .

[57]  D. Siegel,et al.  Global stability of complex balanced mechanisms , 2000 .

[58]  Shigeru Kondo,et al.  Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation , 2010, Science.

[59]  Ezra Miller,et al.  A Geometric Approach to the Global Attractor Conjecture , 2013, SIAM J. Appl. Dyn. Syst..

[60]  Martin Feinberg,et al.  Concordant chemical reaction networks and the Species-Reaction Graph. , 2012, Mathematical biosciences.

[61]  Gábor Szederkényi,et al.  A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks , 2011, Journal of Mathematical Chemistry.

[62]  Martin Feinberg,et al.  Concordant chemical reaction networks. , 2011, Mathematical biosciences.

[63]  David F. Anderson,et al.  Product-Form Stationary Distributions for Deficiency Zero Chemical Reaction Networks , 2008, Bulletin of mathematical biology.

[64]  Elisenda Feliu,et al.  Preclusion of switch behavior in reaction networks with mass-action kinetics , 2011, 1109.5149.

[65]  Eduardo D. Sontag Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction , 2001, IEEE Trans. Autom. Control..

[66]  Sauro Succi INVARIANT MANIFOLDS FOR PHYSICAL AND CHEMICAL KINETICS (Lecture Notes in Physics 660) By A. N. G ORBAN and I. V. K ARLIN : 495 pp., £77, ISBN 3-540-22684-2 (Springer, Heidelberg, 2005) , 2006 .

[67]  Raoul Kopelman,et al.  Fractal Reaction Kinetics , 1988, Science.

[68]  M. Feinberg Complex balancing in general kinetic systems , 1972 .

[69]  Gheorghe Craciun,et al.  Toric Differential Inclusions and a Proof of the Global Attractor Conjecture , 2015, 1501.02860.

[70]  R. Aris Prolegomena to the rational analysis of systems of chemical reactions , 1965 .