title: The role of non-equilibrium fluxes in the relaxation processes of the linear chemical master equation.
abstract: We propose a non-equilibrium thermodynamical description in terms of the Chemical Master Equation (CME) to characterize the dynamics of a chemical cycle chain reaction among m different species. These systems can be closed or open for energy and molecules exchange with the environment, which determines how they relax to the stationary state. Closed systems reach an equilibrium state (characterized by the detailed balance condition (D.B.)), while open systems will reach a non-equilibrium steady state (NESS). The principal difference between D.B. and NESS is due to the presence of chemical fluxes. In the D.B. condition the fluxes are absent while for the NESS case, the chemical fluxes are necessary for the state maintaining. All the biological systems are characterized by their "far from equilibrium behavior," hence the NESS is a good candidate for a realistic description of the dynamical and thermodynamical properties of living organisms. In this work we consider a CME written in terms of a discrete Kolmogorov forward equation, which lead us to write explicitly the non-equilibrium chemical fluxes. For systems in NESS, we show that there is a non-conservative "external vector field" whose is linearly proportional to the chemical fluxes. We also demonstrate that the modulation of these external fields does not change their stationary distributions, which ensure us to study the same system and outline the differences in the system's behavior when it switches from the D.B. regime to NESS. We were interested to see how the non-equilibrium fluxes influence the relaxation process during the reaching of the stationary distribution. By performing analytical and numerical analysis, our central result is that the presence of the non-equilibrium chemical fluxes reduces the characteristic relaxation time with respect to the D.B. condition. Within a biochemical and biological perspective, this result can be related to the "plasticity property" of biological systems and to their capabilities to switch from one state to another as is observed during synaptic plasticity, cell fate determination, and differentiation.
authors.affiliation: Physics and Astronomy Department, Bologna University and INFN Sezione di Bologna, Italy.
authors.forename: Luciana Renata
authors.initials: LR
authors.lastname: de Oliveira
authors.affiliation: Physics and Astronomy Department, Bologna University and INFN Sezione di Bologna, Italy.
authors.forename: Armando
authors.initials: A
authors.lastname: Bazzani
authors.affiliation: Physics and Astronomy Department, Bologna University and INFN Sezione di Bologna, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Giampieri
authors.affiliation: Physics and Astronomy Department, Bologna University and INFN Sezione di Bologna, Italy.
authors.forename: Gastone C
authors.initials: GC
authors.lastname: Castellani
mesh_terms: D019277:Entropy; D008956:Models, Chemical; D010766:Phosphorylation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D011506:Proteins