Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
- PMID: 15829355
- DOI: 10.1016/j.bpc.2004.12.001
Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
Abstract
The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.
Similar articles
-
Thermodynamic constraints for biochemical networks.J Theor Biol. 2004 Jun 7;228(3):327-33. doi: 10.1016/j.jtbi.2004.01.008. J Theor Biol. 2004. PMID: 15135031
-
Stoichiometric network theory for nonequilibrium biochemical systems.Eur J Biochem. 2003 Feb;270(3):415-21. doi: 10.1046/j.1432-1033.2003.03357.x. Eur J Biochem. 2003. PMID: 12542691 Review.
-
Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations.J Phys Chem B. 2006 Aug 10;110(31):15063-74. doi: 10.1021/jp061858z. J Phys Chem B. 2006. PMID: 16884217
-
Stochastic thermodynamics of chemical reaction networks.J Chem Phys. 2007 Jan 28;126(4):044101. doi: 10.1063/1.2428297. J Chem Phys. 2007. PMID: 17286456
-
Thermodynamics and evolution.J Theor Biol. 2000 Sep 7;206(1):1-16. doi: 10.1006/jtbi.2000.2106. J Theor Biol. 2000. PMID: 10968933 Review.
Cited by
-
Free energy, value, and attractors.Comput Math Methods Med. 2012;2012:937860. doi: 10.1155/2012/937860. Epub 2011 Dec 21. Comput Math Methods Med. 2012. PMID: 22229042 Free PMC article.
-
Robustness in Escherichia coli glutamate and glutamine synthesis studied by a kinetic model.J Biol Phys. 2008 Apr;34(1-2):91-106. doi: 10.1007/s10867-008-9109-9. Epub 2008 Aug 30. J Biol Phys. 2008. PMID: 19669495 Free PMC article.
-
Stochastic thermodynamics of single enzymes and molecular motors.Eur Phys J E Soft Matter. 2011 Mar;34(3):26. doi: 10.1140/epje/i2011-11026-7. Epub 2011 Mar 15. Eur Phys J E Soft Matter. 2011. PMID: 21400047
-
Relationship between thermodynamic driving force and one-way fluxes in reversible processes.PLoS One. 2007 Jan 3;2(1):e144. doi: 10.1371/journal.pone.0000144. PLoS One. 2007. PMID: 17206279 Free PMC article.
-
Energetic scaling in microbial growth.Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2107668118. doi: 10.1073/pnas.2107668118. Proc Natl Acad Sci U S A. 2021. PMID: 34799445 Free PMC article.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
