# Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint

arXiv: https://arxiv.org/abs/2108.05396 · HTML: https://mlsanity.com/paper/2108.05396/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 11 Aug 2021.

## Built on by (most cited first, 1 of 1)

- [HJ-sampler: A Bayesian sampler for inverse problems of a stochastic process by leveraging Hamilton-Jacobi PDEs and score-based generative models](https://mlsanity.com/paper/2409.09614/) (2024)

## Abstract (arXiv)

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.