Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws
arXiv:1404.1181 · doi:10.1063/1.4886396
Abstract
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated to nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation between the number of fundamental affinities , that of broken conservation laws and the number of chemostats . We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction and of thermodynamic constraints for network reconstruction.
18 pages
References in corpus (2)
Cited by in corpus (44)
- Stochastic Thermodynamics of Non-Linear Electronic Circuits: A Realistic Framework for Computing around kT
- Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs
- Housekeeping and excess entropy production for general nonlinear dynamics
- Nonequilibrium Thermodynamics of Non-Ideal Chemical Reaction Networks
- Circuit Theory for Chemical Reaction Networks
- Nonequilibrium thermodynamics of light-induced reactions
- Transient fluctuation theorems for the currents and initial equilibrium ensembles
- A Nernst heat theorem for nonequilibrium jump processes
- Energetic and entropic cost due to overlapping of Turing-Hopf instabilities in presence of Cross Diffusion
- Thermodynamics of Concentration vs Flux Control in Chemical Reaction Networks
- Structural reduction of chemical reaction networks based on topology
- Thermodynamics of Non-Elementary Chemical Reaction Networks
- Methods and Conversations in (Post)Modern Thermodynamics
- Cycle/cocycle oblique projections on oriented graphs
- Nonequilibrium Thermodynamics of Non-Ideal Reaction-Diffusion Systems: Implications for Active Self-Organization
- Trade-offs between number fluctuations and response in nonequilibrium chemical reaction networks
- Network Thermodynamical Modelling of Bioelectrical Systems: A Bond Graph Approach
- Intrinsic and extrinsic thermodynamics for stochastic population processes with multi-level large-deviation structure
- Energy-based Modelling of the Feedback Control of Biomolecular Systems with Cyclic Flow Modulation
- Linear response in large deviations theory: A method to compute non-equilibrium distributions
- Stochastic approach to entropy production in chemical chaos
- Nonequilibrium thermodynamics of glycolytic traveling wave: Benjamin-Feir instability
- Mutual Multilinearity of Nonequilibrium Network Currents
- Universal dynamic scaling in chemical reactions at and away from equilibrium
- Characterizing the Conditions for Indefinite Growth in Open Chemical Reaction Networks
- Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle
- Thermodynamic Circuits I: Association of devices in stationary nonequilibrium
- Universal Slow Dynamics of Chemical Reaction Networks
- Force-current structure in Markovian open quantum systems and its applications: geometric housekeeping-excess decomposition and thermodynamic trade-off relations
- Thermodynamics of Growth in Open Chemical Reaction Networks
- Thermodynamics of Darwinian selection in molecular replicators
- Dynamical equivalence classes for Markov jump processes
- Information-geometric structure for chemical thermodynamics: An explicit construction of dual affine coordinates
- Thermodynamic Circuits: Modeling chemical reaction networks with nonequilibrium conductance matrices
- Eikonal solutions for moment hierarchies of Chemical Reaction Networks in the limits of large particle number
- The information geometry of 2-field functional integrals
- Reaction extent or advancement of the reaction: A new general definition
- Generalized free energy and excess/housekeeping decomposition in nonequilibrium systems: from large deviations to thermodynamic speed limits
- Riemannian Geometry of Optimal Driving and Thermodynamic Length and its Application to Chemical Reaction Networks
- Interplay of energy, dissipation, and error in kinetic proofreading: Control via concentration and binding energy
- Energy Transduction in Complex Networks with Multiple Resources: The Chemistry Paradigm
- Free-Energy Transduction in Chemical Reaction Networks: from Enzymes to Metabolism
- The limit of mesoscopic one-way fluxes in a nonequilibrium chemical reaction with complex mechanism
- Bond Graphs Unify Stoichiometric Analysis and Thermodynamics