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The assertions made in a recent paper [Phys. Rev. E 107, 014106 (2023)10.1103/PhysRevE.107.014106] regarding the validity of path thermodynamics are ill founded and contradict well-known results. Following up on a previous Comment, I show that, for both models of chemical reaction networks considered in the aforementioned paper, path thermodynamics yields values of the entropy production rates fully consistent with those expected from standard chemical thermodynamics in the large-system limit.

The macroscopic hydrodynamic equations are derived for many-body systems in the local-equilibrium approach, using the Schrödinger picture of quantum mechanics. In this approach, statistical operators are defined in terms of microscopic densities associated with the fundamentally conserved quantities and other slow modes possibly emerging from continuous symmetry breaking, as well as macrofields conjugated to these densities. Functional identities can be deduced, allowing us to identify the reversible and dissipative parts of the mean current densities, to obtain general equations for the time evolution of the conjugate macrofields, and to establish the relationship to projection-operator methods. The entropy production is shown to be nonnegative by applying the Peierls-Bogoliubov inequality to a quantum integral fluctuation theorem. Using the expansion in the gradients of the conjugate macrofields, the transport coefficients are given by Green-Kubo formulas and the entropy production rate can be expressed in terms of quantum Einstein-Helfand formulas, implying its nonnegativity in agreement with the second law of thermodynamics. The results apply to multicomponent fluids and can be extended to condensed matter phases with broken continuous symmetries.

The paper by Malek Mansour and Garcia [Phys. Rev. E 101, 052135 (2020)2470-004510.1103/PhysRevE.101.052135] is shown to be based on misconceptions in the stochastic formulation of chemical thermodynamics in reactive systems. Their erroneous claims, asserting that entropy production cannot be correctly evaluated using path probabilities whenever the reactive system involves more than one elementary reaction leading to the same composition changes, are refuted.

We present a stochastic approach for charge transport in transistors. In this approach, the electron and hole densities are governed by diffusion-reaction stochastic differential equations satisfying local detailed balance and the electric field is determined with the Poisson equation. The approach is consistent with the laws of electricity, thermodynamics, and microreversibility. In this way, the signal amplifying effect of transistors is verified under their working conditions. We also perform the full counting statistics of the two electric currents coupled together in transistors and we show that the fluctuation theorem holds for their joint probability distribution. Similar results are obtained including the displacement currents. In addition, the Onsager reciprocal relations and their generalizations to nonlinear transport properties deduced from the fluctuation theorem are numerically shown to be satisfied.

A stochastic approach for charge transport in diodes is developed in consistency with the laws of electricity, thermodynamics, and microreversibility. In this approach, the electron and hole densities are ruled by diffusion-reaction stochastic partial differential equations and the electric field generated by the charges is determined with the Poisson equation. These equations are discretized in space for the numerical simulations of the mean density profiles, the mean electric potential, and the current-voltage characteristics. Moreover, the full counting statistics of the carrier current and the measured total current including the contribution of the displacement current are investigated. On the basis of local detailed balance, the fluctuation theorem is shown to hold for both currents.

The kinetic equations of DNA replication are shown to be exactly solved in terms of iterated function systems, running along the template sequence and giving the statistical properties of the copy sequences, as well as the kinetic and thermodynamic properties of the replication process. With this method, different effects due to sequence heterogeneity can be studied, in particular, a transition between linear and sublinear growths in time of the copies, and a transition between continuous and fractal distributions of the local velocities of the DNA polymerase along the template. The method is applied to the human mitochondrial DNA polymerase γ without and with exonuclease proofreading.

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorporated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a 100-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependencies on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production are calculated analytically in terms of the rate constants and the concentrations. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.