title: Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory.
abstract: Gibbs' macroscopic chemical thermodynamics is one of the most important theories in chemistry. Generalizing it to mesoscaled nonequilibrium systems is essential to biophysics. The nonequilibrium stochastic thermodynamics of chemical reaction kinetics suggested a free energy balance equation dF^{(meso)}/dt=E_{in}-e_{p} in which the free energy input rate E_{in} and dissipation rate e_{p} are both non-negative, and E_{in}≤e_{p}. We prove that in the macroscopic limit by merely allowing the molecular numbers to be infinite, the generalized mesoscopic free energy F^{(meso)} converges to φ^{ss}, the large deviation rate function for the stationary distributions. This generalized macroscopic free energy φ^{ss} now satisfies a balance equation dφ^{ss}(x)/dt=cmf(x)-σ(x), in which x represents chemical concentration. The chemical motive force cmf(x) and entropy production rate σ(x) are both non-negative, and cmf(x)≤σ(x). The balance equation is valid generally in isothermal driven systems and is different from mechanical energy conservation and the first law; it is actually an unknown form of the second law. Consequences of the emergent thermodynamic quantities and equalities are further discussed. The emergent "law" is independent of underlying kinetic details. Our theory provides an example showing how a macroscopic law emerges from a level below.
authors.affiliation: Beijing International Center for Mathematical Research (BICMR), Peking University, Beijing 100871, People's Republic of China.|Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, People's Republic of China.
authors.forename: Hao
authors.initials: H
authors.lastname: Ge
authors.affiliation: Department of Applied Mathematics, University of Washington, Seattle, Washington 98195-3925, USA.
authors.forename: Hong
authors.initials: H
authors.lastname: Qian