Nonlinear Stochastic Dynamics of Complex Systems, III: Noneqilibrium   Thermodynamics of Self-Replication Kinetics
  We briefly review the recently developed, Markov process based isothermal chemical thermodynamics for nonlinear, driven mesoscopic kinetic systems. Both the instantaneous Shannon entropy {\boldmath $S[p_{\alpha}(t)]$} and relative entropy {\boldmath $F[p_{\alpha}(t)]$}, defined based on probability distribution {\boldmath $\{p_{\alpha}(t)\}$}, play prominent roles. The theory is general; and as a special case when a chemical reaction system is situated in an equilibrium environment, it agrees perfectly with Gibbsian chemical thermodynamics: {\boldmath $k_BS$} and {\boldmath $k_BTF$} become thermodynamic entropy and free energy, respectively. We apply this theory to a fully reversible autocatalytic reaction kinetics, represented by a Delbr\"{u}ck-Gillespie process, in a chemostatic nonequilibrium environment. The open, driven chemical system serves as an archetype for biochemical self-replication. The significance of {\em thermodynamically consistent} kinetic coarse-graining is emphasized. In a kinetic system where death of a biological organism is treated as the reversal of its birth, the meaning of mathematically emergent "dissipation", which is not related to the heat measured in terms of {\boldmath $k_BT$}, remains to be further investigated. 
David B. Saakian and Hong Qian
cond-mat.stat-mech physics.chem-ph