Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

Cannon, William R.; Baker, Scott E.

doi:10.1088/1478-3975/aa7d80

Title: Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

Journal Article · Tue Jul 04 00:00:00 EDT 2017 · Physical Biology (Online)

DOI:https://doi.org/10.1088/1478-3975/aa7d80· OSTI ID:1573021

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Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

A new formulation of the law of mass action is presented that uses chemical potentials instead of rate constants, potentially leading to large scale, physics-based simulations for metabolism and cellular simulations.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1573021

Report Number(s):: PNNL-SA-114146

Journal Information:: Physical Biology (Online), Vol. 14, Issue 5; ISSN 1478-3975

Publisher:: IOP PublishingCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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References (35)

Studies concerning affinity Waage, P.; Gulberg, C. M. Journal of Chemical Education, Vol. 63, Issue 12 https://doi.org/10.1021/ed063p1044	journal	December 1986
Ueber die chemische Affinität. § 1. Einleitung Guldberg, C. M.; Waage, P. Journal für Praktische Chemie, Vol. 19, Issue 1 https://doi.org/10.1002/prac.18790190111	journal	March 1879
150 Years of the Mass Action Law Voit, Eberhard O.; Martens, Harald A.; Omholt, Stig W. PLoS Computational Biology, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pcbi.1004012	journal	January 2015
Thermodynamics-Based Metabolic Flux Analysis Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily Biophysical Journal, Vol. 92, Issue 5 https://doi.org/10.1529/biophysj.106.093138	journal	March 2007
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D. PLoS Computational Biology, Vol. 10, Issue 2 https://doi.org/10.1371/journal.pcbi.1003487	journal	February 2014
Conditions for duality between fluxes and concentrations in biochemical networks Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines Journal of Theoretical Biology, Vol. 409 https://doi.org/10.1016/j.jtbi.2016.06.033	journal	November 2016
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates Nielsen, Jens Biochemical Journal, Vol. 321, Issue 1 https://doi.org/10.1042/bj3210133	journal	January 1997
Linear relation between rate and thermodynamic force in enzyme-catalyzed reactions van der Meer, R.; Westerhoff, H. V.; Van Dam, K. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 591, Issue 2 https://doi.org/10.1016/0005-2728(80)90179-6	journal	July 1980
Consistency between kinetics and thermodynamics Boudart, M. The Journal of Physical Chemistry, Vol. 80, Issue 26 https://doi.org/10.1021/j100567a012	journal	December 1976
Consistency between Kinetics and Thermodynamics: General Scaling Conditions for Reaction Rates of Nonlinear Chemical Systems without Constraints Far from Equilibrium Vlad, Marcel O.; Popa, Vlad T.; Ross, John The Journal of Physical Chemistry A, Vol. 115, Issue 4 https://doi.org/10.1021/jp107020k	journal	February 2011
Biochemical Systems Theory: A Review Voit, Eberhard O. ISRN Biomathematics, Vol. 2013 https://doi.org/10.1155/2013/897658	journal	January 2013
Structural kinetic modeling of metabolic networks Steuer, R.; Gross, T.; Selbig, J. Proceedings of the National Academy of Sciences, Vol. 103, Issue 32 https://doi.org/10.1073/pnas.0600013103	journal	July 2006
A Linear Steady-State Treatment of Enzymatic Chains. General Properties, Control and Effector Strength Heinrich, Reinhart; Rapoport, Tom A. European Journal of Biochemistry, Vol. 42, Issue 1 https://doi.org/10.1111/j.1432-1033.1974.tb03318.x	journal	February 1974
Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation Ciliberto, Andrea; Capuani, Fabrizio; Tyson, John J. PLoS Computational Biology, Vol. 3, Issue 3 https://doi.org/10.1371/journal.pcbi.0030045	journal	January 2007
Statistical Mechanics of Fluid Mixtures Kirkwood, John G. The Journal of Chemical Physics, Vol. 3, Issue 5 https://doi.org/10.1063/1.1749657	journal	May 1935
Multiconfiguration thermodynamic integration Straatsma, T. P.; McCammon, J. A. The Journal of Chemical Physics, Vol. 95, Issue 2 https://doi.org/10.1063/1.461148	journal	July 1991
Stochastic thermodynamics of reactive systems: An extended local equilibrium approach De Decker, Yannick; Derivaux, Jean-François; Nicolis, Grégoire Physical Review E, Vol. 93, Issue 4 https://doi.org/10.1103/PhysRevE.93.042127	journal	April 2016
Simulating Metabolism with Statistical Thermodynamics Cannon, William R. PLoS ONE, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pone.0103582	journal	August 2014
Exact stochastic simulation of coupled chemical reactions Gillespie, Daniel T. The Journal of Physical Chemistry, Vol. 81, Issue 25 https://doi.org/10.1021/j100540a008	journal	December 1977
Analysis and implementation of TR-BDF2 Hosea, M. E.; Shampine, L. F. Applied Numerical Mathematics, Vol. 20, Issue 1-2 https://doi.org/10.1016/0168-9274(95)00115-8	journal	February 1996
Stoichiometric network theory for nonequilibrium biochemical systems Qian, Hong; Beard, Daniel A.; Liang, Shou-dan European Journal of Biochemistry, Vol. 270, Issue 3 https://doi.org/10.1046/j.1432-1033.2003.03357.x	journal	February 2003
Network theory of microscopic and macroscopic behavior of master equation systems Schnakenberg, J. Reviews of Modern Physics, Vol. 48, Issue 4 https://doi.org/10.1103/RevModPhys.48.571	journal	October 1976
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes Beard, Daniel A.; Qian, Hong PLoS ONE, Vol. 2, Issue 1 https://doi.org/10.1371/journal.pone.0000144	journal	January 2007
Thermodynamics and foundations of mass-action kinetics Pekař, Miloslav Progress in Reaction Kinetics and Mechanism, Vol. 30, Issue 1-2 https://doi.org/10.3184/007967405777874868	journal	June 2005
Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli Fierke, Carol A.; Johnson, Kenneth A.; Benkovic, Stephen J. Biochemistry, Vol. 26, Issue 13 https://doi.org/10.1021/bi00387a052	journal	June 1987
13C Metabolic Flux Analysis Wiechert, Wolfgang Metabolic Engineering, Vol. 3, Issue 3 https://doi.org/10.1006/mben.2001.0187	journal	July 2001
Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states Dewar, Roderick Journal of Physics A: Mathematical and General, Vol. 36, Issue 3 https://doi.org/10.1088/0305-4470/36/3/303	journal	January 2003
Natural Selection as a Physical Principle Lotka, A. J. Proceedings of the National Academy of Sciences, Vol. 8, Issue 6 https://doi.org/10.1073/pnas.8.6.151	journal	June 1922
Contribution to the Energetics of Evolution Lotka, A. J. Proceedings of the National Academy of Sciences, Vol. 8, Issue 6 https://doi.org/10.1073/pnas.8.6.147	journal	June 1922
The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies Wlaschin, Aaron P.; Trinh, Cong T.; Carlson, Ross Metabolic Engineering, Vol. 8, Issue 4 https://doi.org/10.1016/j.ymben.2006.01.007	journal	July 2006
Proposed Principles of Maximum Local Entropy Production Ross, John; Corlan, Alexandru D.; Müller, Stefan C. The Journal of Physical Chemistry B, Vol. 116, Issue 27 https://doi.org/10.1021/jp302088y	journal	June 2012
Metabolic networks evolve towards states of maximum entropy production Unrean, Pornkamol; Srienc, Friedrich Metabolic Engineering, Vol. 13, Issue 6 https://doi.org/10.1016/j.ymben.2011.08.003	journal	November 2011
Stochastic thermodynamics of chemical reaction networks Schmiedl, Tim; Seifert, Udo The Journal of Chemical Physics, Vol. 126, Issue 4 https://doi.org/10.1063/1.2428297	journal	January 2007
Environmental Statistics and Optimal Regulation Sivak, David A.; Thomson, Matt PLoS Computational Biology, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pcbi.1003826	journal	September 2014
Error Propagation Analysis for Quantitative Intracellular Metabolomics Tillack, Jana; Paczia, Nicole; Nöh, Katharina Metabolites, Vol. 2, Issue 4 https://doi.org/10.3390/metabo2041012	journal	November 2012

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Title: Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

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