July 14, 2006
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May 25, 2018
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially distributed. Here we focus on mathematical models based on deterministic mass-action kinetics. These models are systems of coupled nonlinear differential equations on the positive orthant. We explain how mathematical properties of the solutions of ...
January 29, 1999
There are only a very few known relations in statistical dynamics that are valid for systems driven arbitrarily far-from-equilibrium. One of these is the fluctuation theorem, which places conditions on the entropy production probability distribution of nonequilibrium systems. Another recently discovered far-from-equilibrium expression relates nonequilibrium measurements of the work done on a system to equilibrium free energy differences. In this paper, we derive a generalized...
April 20, 2011
We illustrate some of the static and dynamic relations discovered by Cohen, Crooks, Evans, Jarzynski, Kirkwood, Morriss, Searles, and Zwanzig. These relations link nonequilibrium processes to equilibrium isothermal free energy changes and to dynamical path probabilities. We include ideas suggested by Dellago, Geissler, Oberhofer, and Schoell-Paschinger. Our treatment is intended to be pedagogical, for use in an updated version of our book: Time Reversibility, Computer Simulat...
August 24, 2020
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical potentials, and makes use of the topological properties of the network (conservation laws and cycles). Our approach is proven to be exact if the network results from a bigger network of elementary reactions where the fast-evolving species have...
June 29, 2016
In this article a definition of reversible processes in terms of differences in intensive Thermodynamics properties (Affinities) is proposed. This definition makes it possible to both define reversible processes before introducing the concept of entropy and avoid the circularity problem that follows from the Clausius definition of entropy changes. The convenience of this new definition compared to those commonly found in textbooks is demonstrated with examples.
August 17, 2009
This study examines a new formulation of non-equilibrium thermodynamics, which gives a conditional derivation of the ``maximum entropy production'' (MEP) principle for flow and/or chemical reaction systems at steady state. The analysis uses a dimensionless potential function $\phi_{st}$ for non-equilibrium systems, analogous to the free energy concept of equilibrium thermodynamics. Spontaneous reductions in $\phi_{st}$ arise from increases in the ``flux entropy'' of the syste...
November 20, 2012
In nature stationary nonequilibrium systems cannot exist on their own, rather they need to be driven from outside in order to keep them away from equilibrium. While the internal mean entropy of such stationary systems is constant, the external drive will on average increase the entropy in the environment. This external entropy production is usually quantified by a simple formula, stating that each microscopic transition of the system between two configurations $c \to c'$ with...
December 17, 2004
We show that active transport processes in biological systems can be understood through a local equilibrium description formulated at the mesoscale, the scale to describe stochastic processes. This new approach uses the method established by nonequilibrium thermodynamics to account for the irreversible processes occurring at this scale and provides nonlinear kinetic equations for the rates in terms of the driving forces. The results show that the application domain of nonequi...
May 17, 2019
Diverse physical systems are characterized by their response to small perturbations. Near thermodynamic equilibrium, the fluctuation-dissipation theorem provides a powerful theoretical and experimental tool to determine the nature of response by observing spontaneous equilibrium fluctuations. In this spirit, we derive here a collection of equalities and inequalities valid arbitrarily far from equilibrium that constrain the response of nonequilibrium steady states in terms of ...
February 19, 2019
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it shall be supported by a correct implementation of thermodynamic constraints. In this article we review the latter aspect highlighting its computational challenges and physical insights. The ...