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

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.