Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint
From MaRDI portal
Publication:2675353
conservative-dissipative decompositionlarge deviation principlepositive entropy production ratethermodynamic limittime reversaltransition path with energy barrier
Hamilton-Jacobi equations (35F21) Special integral transforms (Legendre, Hilbert, etc.) (44A15) Hamilton-Jacobi equations in optimal control and differential games (49L12) Large deviations (60F10) Point processes (e.g., Poisson, Cox, Hawkes processes) (60G55) Chemical kinetics in thermodynamics and heat transfer (80A30) Chemically reacting flows (80A32) Semiclassical techniques, including WKB and Maslov methods applied to problems in quantum theory (81Q20) Biochemistry, molecular biology (92C40)
Abstract: Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be modeled by a random time-changed Poisson processes. To characterize macroscopic behaviors in the large volume limit, the law of large numbers in the path space determines a mean-field limit nonlinear reaction rate equation describing the dynamics of the concentration of species, while the WKB expansion for the chemical master equation yields a Hamilton-Jacobi equation (HJE) and the Lagrangian gives the good rate function in the large deviation principle. We decompose a general macroscopic reaction rate equation into a conservative part and a dissipative part in terms of the stationary solution to HJE. This stationary solution is used to determine the energy landscape and thermodynamics for general chemical reactions, which particularly maintains a positive entropy production rate at a non-equilibrium steady state. The associated energy dissipation law is proved together with the passage from the mesoscopic to macroscopic one. Furthermore, we use a reversible Hamiltonian to study a class of non-equilibrium enzyme reactions, which identifies a new concept of balance within the same reaction vector due to flux grouping degeneracy. This macroscopic reversibility, brought by the reversibility of the chemical reaction jumping process, gives an Onsager-type strong gradient flow. The reversible Hamiltonian also yields a time reversal symmetry for the corresponding Lagrangian. Thus a modified time reversed least action path serves as the transition paths with associated path affinities and energy barriers.
Recommendations
- Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics
- Hamiltonian classical thermodynamics and chemical kinetics
- Variational and extremum properties of homogeneous chemical kinetics. I. Lagrangian- and Hamiltonian-like formulations
- Mathematical formalism of nonequilibrium thermodynamics for nonlinear chemical reaction systems with general rate law
- Anisothermal chemical reactions: Onsager-Machlup and macroscopic fluctuation theory
Cites work
- A detailed balanced reaction network is sufficient but not necessary for its Markov chain to be detailed balanced
- A Gallavotti-Cohen-type symmetry in the large deviation functional for stochastic dynamics
- A simple framework to justify linear response theory
- Asymptotic probabilities and differential equations
- Controlled Markov processes and viscosity solutions
- Extending the definition of entropy to nonequilibrium steady states
- Extinction Times for Birth-Death Processes: Exact Results, Continuum Asymptotics, and the Failure of the Fokker--Planck Approximation
- Fluctuation symmetry leads to GENERIC equations with non-quadratic dissipation
- Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory
- Foundations of chemical reaction network theory
- Gamma-convergence of gradient flows with applications to Ginzburg-Landau
- Global Asymptotic Stability for a Class of Nonlinear Chemical Equations
- Hamilton–Jacobi Equations
- scientific article; zbMATH DE number 4194836 (Why is no real title available?)
- scientific article; zbMATH DE number 4088693 (Why is no real title available?)
- scientific article; zbMATH DE number 847278 (Why is no real title available?)
- scientific article; zbMATH DE number 3187569 (Why is no real title available?)
- Large deviations for finite state Markov jump processes with mean-field interaction via the comparison principle for an associated Hamilton-Jacobi equation
- Large deviations for stochastic processes.
- Large deviations in stochastic heat-conduction processes provide a gradient-flow structure for heat conduction
- Large deviations of jump process fluxes
- Large deviations theory for Markov jump models of chemical reaction networks
- Limit theorems for sequences of jump Markov processes approximating ordinary differential processes
- Macroscopic fluctuation theory for stationary nonequilibrium states
- Mathematical formalism of nonequilibrium thermodynamics for nonlinear chemical reaction systems with general rate law
- Modeling of chemical reaction systems with detailed balance using gradient structures
- Modern Thermodynamics
- On backward stochastic differential equations
- On microscopic origins of generalized gradient structures
- On the relation between gradient flows and the large-deviation principle, with applications to Markov chains and diffusion
- On time reversal
- Physical chemistry. A molecular approach.
- Product-form stationary distributions for deficiency zero chemical reaction networks
- Random Perturbations of Dynamical Systems
- Regularity and approximability of the solutions to the chemical master equation
- Representations of Markov processes as multiparameter time changes
- Semicontinuous Viscosity Solutions For Hamilton–Jacobi Equations With Convex Hamiltonians
- Statistical Mechanics of Fluid Mixtures
- Stochastic analysis of biochemical systems
- Stochastic chemical reaction systems in biology
- Stochastic processes in physics and chemistry.
- Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction
- The exponential resolvent of a Markov process and large deviations for Markov processes via Hamilton-Jacobi equations
- The vanishing discount problem for Hamilton-Jacobi equations in the Euclidean space
- Towards a theory of transition paths
- Transition Path Theory for Markov Jump Processes
- WKB theory of large deviations in stochastic populations
Cited in
(11)- Data-driven efficient solvers for Langevin dynamics on manifold in high dimensions
- Effect of mesoscopic conservative phenomena in the dynamics of chemical reactions at the macroscopic scale
- Controlling conservation laws. I: entropy-entropy flux
- Random Walk Approximation for Irreversible Drift-Diffusion Process on Manifold: Ergodicity, Unconditional Stability and Convergence
- Large Deviation Principle and Thermodynamic Limit of Chemical Master Equation via Nonlinear Semigroup
- A Selection Principle for Weak KAM Solutions via Freidlin–Wentzell Large Deviation Principle of Invariant Measures
- Hamilton Dynamics in Chemical Reactions: the Maupertuis Principle, Transition Paths and Energy Landscape
- Transition Path Theory for Langevin Dynamics on Manifolds: Optimal Control and Data-Driven Solver
- Structure preserving schemes for Fokker-Planck equations of irreversible processes
- Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective
- Fast-slow chemical reactions: convergence of Hamilton-Jacobi equation and variational representation
This page was built for publication: Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2675353)
