Related papers: Thermodynamic validity criterion for the irreversi…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high temperature processes, particularly for ionic…
In a previous paper [Physical Review B \textbf{103}, 035417 (2021)], we showed that the equilibrium molecular dynamics (EMD) method can be used to compute the apparent thermal conductivity of finite systems. It has been shown that the…
Reversibility is a key concept in Markov models and Master-equation models of molecular kinetics. The analysis and interpretation of the transition matrix encoding the kinetic properties of the model relies heavily on the reversibility…
The wide-spread opinion is that original quantum mechanics is a reversible theory, but this statement is only true for undecomposed systems, that are those systems which sub-systems are out of consideration. Taking sub-systems into account,…
Genetically identical cells under the same environmental conditions can show strong variations in protein copy numbers due to inherently stochastic events in individual cells. We here develop a theoretical framework to address how…
The principle of microscopic reversibility says that, in equilibrium, two-time cross-correlations are symmetric under the exchange of observables. Thus, the asymmetry of cross-correlations is a fundamental, measurable, and often-used…
The quantum master equation obtained from two different thermodynamic arguments is seriously nonlinear. We argue that, for quantum systems, nonlinearity occurs naturally in the step from reversible to irreversible equations and we analyze…
Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…
We use molecular dynamics computer simulations to investigate a critical temperature T_c for a dynamical glass transition as proposed by the mode-coupling theory (MCT) of dense liquids in a glass forming Ni_{0.8}Zr_{0.2}-system. The…
A unified (classical-quantum-statistical) formalism for a system with continuous spectrum is introduced. For this kind of systems ergodicity behavior and the existence of microcanonical and canonical (KMS) equilibrium is proved. It is…
Instabilities in thermodynamic systems are often undesirable, as they can lead to loss of control or even catastrophic behavior. Yet, the same mechanisms can also generate rich nonequilibrium behavior and may play a constructive role in…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
Recently a number of approaches has been developed to connect the microscopic dynamics of particle systems to the macroscopic properties of systems in nonequilibrium stationary states, via the theory of dynamical systems. This way a direct…
The claims by Baras, Garcia, and Malek Mansour [Phys. Rev. E 107, 014106 (2023)] on 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…
Living cells exhibit non-equilibrium dynamics emergent from the intricate interplay between molecular motor activity and its viscoelastic cytoskeletal matrix. The deviation from thermal equilibrium can be quantified through…
The resource theory of thermal operations, an established model for small-scale thermodynamics, provides an extension of equilibrium thermodynamics to nonequilibrium situations. On a lattice of any dimension with any translation-invariant…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
The resource-theoretic approach to quantum thermodynamics assumes complete knowledge of the thermal equilibrium against which thermodynamic resources are defined. In practice, however, this state is determined by the system Hamiltonian and…
In biochemical systems the Michaelis-Menten (MM) scheme is one of the best-known models of the enzyme- catalyzed kinetics. In the academic literature the MM approximation has been thoroughly studied in the context of differential equation…