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We introduce axiomatically a complete thermodynamic formalism for a singlemacromolecule, either with or without detailed balance, in an isothermalambient fluid based on its stochastic dynamics. With detailed balance, thenovel theory yields mesoscopic, nonequilibrium generalizations for entropy andfree energy of the macromolecule. Mesoscopic energy and entropy fluctuate.Expectation of entropy production equals zero if and only if the macromoleculeis at thermal equilibrium, in which we show entropy still fluctuates but freeenergy is a constant. The entropy fluctuation a la L.D. Landau, preciselymatches the fluctuation in the internal energy, which in turn equals thefluctuation in heat dissipation. As a generalization of Clausius' classicresult, the dynamic fluctuations in the entropy and energy of the macromoleculeare exactly compensated at thermal equilibrium. For systems with detailedbalance, Helmholtz free energy is shown to be the potential of Onsager'sthermodynamic force.Comment: 6 page

Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation