Stochastic thermodynamics of chemical reaction networks
arXiv:cond-mat/0605080 · doi:10.1063/1.2428297
Abstract
For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations like a generalized Jarzynski relation and a generalized Clausius inequality are discussed. We illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.
14 pages, 2 figures, accepted for publication in J. Chem. Phys
References in corpus (2)
Cited by in corpus (53)
- Fluctuation theorems for stochastic dynamics
- Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws
- Stochastic approach to equilibrium and nonequilibrium thermodynamics
- Geometrical aspects of entropy production in stochastic thermodynamics based on Wasserstein distance
- Fluctuation relations and coarse-graining
- Entropy production in exactly solvable systems
- Is stochastic thermodynamics the key to understanding the energy costs of computation?
- Nonequilibrium Thermodynamics of Non-Ideal Chemical Reaction Networks
- Macroscopic Stochastic Thermodynamics
- Transient fluctuation relations for time-dependent particle transport
- Negative differential response in chemical reactions
- Non-equilibrium dynamics of gene expression and the Jarzynski equality
- Thermodynamics of Concentration vs Flux Control in Chemical Reaction Networks
- Nonequilibrium work statistics of an Aharonov-Bohm flux
- Methods and Conversations in (Post)Modern Thermodynamics
- Microscopic heat from the energetics of stochastic phenomena
- Quantum work distributions associated with the dynamical Casimir effect
- Trade-offs between number fluctuations and response in nonequilibrium chemical reaction networks
- Optimal time estimation and the clock uncertainty relation for stochastic processes
- Fluctuation relations and rare realizations of transport observables
- Linear response in large deviations theory: A method to compute non-equilibrium distributions
- Fluctuation Ratios in the Absence of Microscopic Time Reversibility
- Second Law of Thermodynamics without Einstein Relation
- An estimator of entropy production for partially accessible Markov networks based on the observation of blurred transitions
- Entropy estimation for partially accessible Markov networks based on imperfect observations: Role of finite resolution and finite statistics
- Relativistic multi-reference Fock-space coupled-cluster calculation of the forbidden $6s^2^1 S_0 \longrightarrow 6s5d^3 D_1$ magnetic-dipole transition in ytterbium
- A chemical reaction network implementation of a Maxwell demon
- Nonequilibrium fluctuations of chemical reaction networks at criticality: The Schlögl model as paradigmatic case
- Stochastic thermodynamics and fluctuation theorems for non-linear systems
- Thermodynamic inference in partially accessible Markov networks: A unifying perspective from transition-based waiting time distributions
- Characterizing the Conditions for Indefinite Growth in Open Chemical Reaction Networks
- Thermodynamic dissipation does not bound replicator growth and decay rates
- Universal dynamic scaling in chemical reactions at and away from equilibrium
- Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle
- Boltzmann stochastic thermodynamics
- Deficiency, Kinetic Invertibility, and Catalysis in Stochastic Chemical Reaction Networks
- Universal Slow Dynamics of Chemical Reaction Networks
- Thermodynamics of Growth in Open Chemical Reaction Networks
- A [3]-catenane non-autonomous molecular motor model: geometric phase, no-pumping theorem, and energy transduction
- Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming
- Thermodynamic Circuits: Modeling chemical reaction networks with nonequilibrium conductance matrices
- Illusory cracks in the second law of thermodynamics in quantum nanoelectronics
- Random walks on modular chains: Detecting structure through statistics
- Stochastic thermodynamics of a finite quantum system coupled to a heat bath
- Hidden energy flows in strongly coupled nonequilibrium systems
- Riemannian Geometry of Optimal Driving and Thermodynamic Length and its Application to Chemical Reaction Networks
- What is a chemostat? Insights from hybrid dynamics and stochastic thermodynamics
- Modified Jarzynski equality in a microcanonical ensemble
- Information geometric bound on general chemical reaction networks
- Coarse Graining Photo-Isomerization Reactions: Thermodynamic Consistency and Implications for Molecular Ratchets
- Unification of Stochastic and Quantum Thermodynamics in Scalar Field Theory via a Model with Brownian Thermostat
- Information geometry of nonmonotonic quantum natural gradient
- The Steady State Distribution of the Master Equation