Intrinsic and extrinsic thermodynamics for stochastic population processes with multi-level large-deviation structure

Abstract: A set of core features is set forth as the essence of a thermodynamic description, which derive from large-deviation properties in systems with hierarchies of timescales, but which are \emph{not} dependent upon conservation laws or microscopic reversibility in the substrate hosting the process. The most fundamental elements are the concept of a macrostate in relation to the large-deviation entropy, and the decomposition of contributions to irreversibility among interacting subsystems, which is the origin of the dependence on a concept of heat in both classical and stochastic thermodynamics. A natural decomposition is shown to exist, into a relative entropy and a housekeeping entropy rate, which define respectively the \textit{intensive} thermodynamics of a system and an \textit{extensive} thermodynamic vector embedding the system in its context. Both intensive and extensive components are functions of Hartley information of the momentary system stationary state, which is information \emph{about} the joint effect of system processes on its contribution to irreversibility. Results are derived for stochastic Chemical Reaction Networks, including a Legendre duality for the housekeeping entropy rate to thermodynamically characterize fully-irreversible processes on an equal footing with those at the opposite limit of detailed-balance. The work is meant to encourage development of inherent thermodynamic descriptions for rule-based systems and the living state, which are not conceived as reductive explanations to heat flows.