Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials
Abstract
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.
- Authors:
-
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1573021
- Report Number(s):
- PNNL-SA-114146
Journal ID: ISSN 1478-3975
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Physical Biology (Online)
- Additional Journal Information:
- Journal Name: Physical Biology (Online); Journal Volume: 14; Journal Issue: 5; Journal ID: ISSN 1478-3975
- Publisher:
- IOP Publishing
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 60 APPLIED LIFE SCIENCES; reaction dynamics; reaction kinetics; thermodynamics; chemical potentials; modeling; simulation; differential equations; fluctuation therory; stochastic dynamics; markov models
Citation Formats
Cannon, William R., and Baker, Scott E. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials. United States: N. p., 2017.
Web. doi:10.1088/1478-3975/aa7d80.
Cannon, William R., & Baker, Scott E. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials. United States. https://doi.org/10.1088/1478-3975/aa7d80
Cannon, William R., and Baker, Scott E. Tue .
"Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials". United States. https://doi.org/10.1088/1478-3975/aa7d80. https://www.osti.gov/servlets/purl/1573021.
@article{osti_1573021,
title = {Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials},
author = {Cannon, William R. and Baker, Scott E.},
abstractNote = {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.},
doi = {10.1088/1478-3975/aa7d80},
journal = {Physical Biology (Online)},
number = 5,
volume = 14,
place = {United States},
year = {Tue Jul 04 00:00:00 EDT 2017},
month = {Tue Jul 04 00:00:00 EDT 2017}
}
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Works referenced in this record:
Studies concerning affinity
journal, December 1986
- Waage, P.; Gulberg, C. M.
- Journal of Chemical Education, Vol. 63, Issue 12
Ueber die chemische Affinität. § 1. Einleitung
journal, March 1879
- Guldberg, C. M.; Waage, P.
- Journal für Praktische Chemie, Vol. 19, Issue 1
150 Years of the Mass Action Law
journal, January 2015
- Voit, Eberhard O.; Martens, Harald A.; Omholt, Stig W.
- PLoS Computational Biology, Vol. 11, Issue 1
Thermodynamics-Based Metabolic Flux Analysis
journal, March 2007
- Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily
- Biophysical Journal, Vol. 92, Issue 5
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
journal, February 2014
- Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.
- PLoS Computational Biology, Vol. 10, Issue 2
Conditions for duality between fluxes and concentrations in biochemical networks
journal, November 2016
- Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines
- Journal of Theoretical Biology, Vol. 409
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates
journal, January 1997
- Nielsen, Jens
- Biochemical Journal, Vol. 321, Issue 1
Linear relation between rate and thermodynamic force in enzyme-catalyzed reactions
journal, July 1980
- van der Meer, R.; Westerhoff, H. V.; Van Dam, K.
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 591, Issue 2
Consistency between kinetics and thermodynamics
journal, December 1976
- Boudart, M.
- The Journal of Physical Chemistry, Vol. 80, Issue 26
Consistency between Kinetics and Thermodynamics: General Scaling Conditions for Reaction Rates of Nonlinear Chemical Systems without Constraints Far from Equilibrium
journal, February 2011
- Vlad, Marcel O.; Popa, Vlad T.; Ross, John
- The Journal of Physical Chemistry A, Vol. 115, Issue 4
Biochemical Systems Theory: A Review
journal, January 2013
- Voit, Eberhard O.
- ISRN Biomathematics, Vol. 2013
Structural kinetic modeling of metabolic networks
journal, July 2006
- Steuer, R.; Gross, T.; Selbig, J.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 32
A Linear Steady-State Treatment of Enzymatic Chains. General Properties, Control and Effector Strength
journal, February 1974
- Heinrich, Reinhart; Rapoport, Tom A.
- European Journal of Biochemistry, Vol. 42, Issue 1
Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation
journal, January 2007
- Ciliberto, Andrea; Capuani, Fabrizio; Tyson, John J.
- PLoS Computational Biology, Vol. 3, Issue 3
Statistical Mechanics of Fluid Mixtures
journal, May 1935
- Kirkwood, John G.
- The Journal of Chemical Physics, Vol. 3, Issue 5
Multiconfiguration thermodynamic integration
journal, July 1991
- Straatsma, T. P.; McCammon, J. A.
- The Journal of Chemical Physics, Vol. 95, Issue 2
Stochastic thermodynamics of reactive systems: An extended local equilibrium approach
journal, April 2016
- De Decker, Yannick; Derivaux, Jean-François; Nicolis, Grégoire
- Physical Review E, Vol. 93, Issue 4
Simulating Metabolism with Statistical Thermodynamics
journal, August 2014
- Cannon, William R.
- PLoS ONE, Vol. 9, Issue 8
Exact stochastic simulation of coupled chemical reactions
journal, December 1977
- Gillespie, Daniel T.
- The Journal of Physical Chemistry, Vol. 81, Issue 25
Analysis and implementation of TR-BDF2
journal, February 1996
- Hosea, M. E.; Shampine, L. F.
- Applied Numerical Mathematics, Vol. 20, Issue 1-2
Stoichiometric network theory for nonequilibrium biochemical systems
journal, February 2003
- Qian, Hong; Beard, Daniel A.; Liang, Shou-dan
- European Journal of Biochemistry, Vol. 270, Issue 3
Network theory of microscopic and macroscopic behavior of master equation systems
journal, October 1976
- Schnakenberg, J.
- Reviews of Modern Physics, Vol. 48, Issue 4
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes
journal, January 2007
- Beard, Daniel A.; Qian, Hong
- PLoS ONE, Vol. 2, Issue 1
Thermodynamics and foundations of mass-action kinetics
journal, June 2005
- Pekař, Miloslav
- Progress in Reaction Kinetics and Mechanism, Vol. 30, Issue 1-2
Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
journal, June 1987
- Fierke, Carol A.; Johnson, Kenneth A.; Benkovic, Stephen J.
- Biochemistry, Vol. 26, Issue 13
13C Metabolic Flux Analysis
journal, July 2001
- Wiechert, Wolfgang
- Metabolic Engineering, Vol. 3, Issue 3
Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states
journal, January 2003
- Dewar, Roderick
- Journal of Physics A: Mathematical and General, Vol. 36, Issue 3
Natural Selection as a Physical Principle
journal, June 1922
- Lotka, A. J.
- Proceedings of the National Academy of Sciences, Vol. 8, Issue 6
Contribution to the Energetics of Evolution
journal, June 1922
- Lotka, A. J.
- Proceedings of the National Academy of Sciences, Vol. 8, Issue 6
The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies
journal, July 2006
- Wlaschin, Aaron P.; Trinh, Cong T.; Carlson, Ross
- Metabolic Engineering, Vol. 8, Issue 4
Proposed Principles of Maximum Local Entropy Production
journal, June 2012
- Ross, John; Corlan, Alexandru D.; Müller, Stefan C.
- The Journal of Physical Chemistry B, Vol. 116, Issue 27
Metabolic networks evolve towards states of maximum entropy production
journal, November 2011
- Unrean, Pornkamol; Srienc, Friedrich
- Metabolic Engineering, Vol. 13, Issue 6
Stochastic thermodynamics of chemical reaction networks
journal, January 2007
- Schmiedl, Tim; Seifert, Udo
- The Journal of Chemical Physics, Vol. 126, Issue 4
Environmental Statistics and Optimal Regulation
journal, September 2014
- Sivak, David A.; Thomson, Matt
- PLoS Computational Biology, Vol. 10, Issue 9
Error Propagation Analysis for Quantitative Intracellular Metabolomics
journal, November 2012
- Tillack, Jana; Paczia, Nicole; Nöh, Katharina
- Metabolites, Vol. 2, Issue 4
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journal, July 2019
- Vergara, Rodrigo C.; Jaramillo-Riveri, Sebastián; Luarte, Alejandro
- Frontiers in Computational Neuroscience, Vol. 13
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journal, May 2018
- Cannon, William; Zucker, Jeremy; Baxter, Douglas
- Processes, Vol. 6, Issue 6
The Energy Homeostasis Principle: Neuronal Energy Regulation Drives Local Network Dynamics Generating Behavior
journal, July 2019
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