Journal ArticleDOI
Chemical Cycle Kinetics: Removing the Limitation of Linearity of a Non-equilibrium Thermodynamic Description
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In this paper, the connection between kinetic and thermodynamic approaches is deeper than thought and holds in the nonlinear domain far from equilibrium, for higher values of the affinity, for cyclic reactions.Abstract:
Chemical cycle kinetics is customarily analyzed by means of the law of mass action which describes how the concentrations of the substances vary with time. The connection of this approach with non-equilibrium thermodynamics (NET) has traditionally been restricted to the linear domain close to equilibrium in which the reaction rates are linear functions of the affinities. We show, by a pertinent formulation of the concept of local equilibrium in the mesoscopic description along the reaction coordinates, that the connection between kinetic and thermodynamic approaches is deeper than thought and holds in the nonlinear domain far from equilibrium, for higher values of the affinity. This new perspective indicates how to overcome the inherent limitation of classical NET in treating cyclic reactions, providing a description of closed and open cycles operating far from equilibrium, in accordance with thermodynamic principles. We propose that the new set of equations are tested and used for data reduction in chemical reaction kinetics.read more
Citations
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Self-assembling outside equilibrium: emergence of structures mediated by dissipation
TL;DR: It is hoped that the knowledge of the intimate mechanisms leading to the formation of structures will make the implementation of re-configurable and bio-inspired materials possible and give a simpler perspective on the understanding of the emergence of life.
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The Role of Energy and Matter Dissipation in Determining the Architecture of Self-Assembled Structures.
TL;DR: It is found that only a small amount of extra energy is needed to yield smooth changes in the form of the assembled structures and may constitute a selection criterion which shows why a set of disordered units may gives rise to a determined self-assembled structure.
Thermodynamics "beyond" local equilibrium
Jose M. G. Vilar,Miguel Rubi +1 more
TL;DR: In this paper, it was shown that diffusion processes that occur far away from equilibrium can be viewed as local equilibrium in a space that includes all the relevant variables in addition to the spatial coordinate.
Journal ArticleDOI
Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
TL;DR: By deriving equations describing the multiple repression mechanisms, it is found that their combination can synergistically generate a sharply ultrasensitive transcription response and thus strong oscillations, which rationalizes why themultiple repression mechanisms are used together in various biological oscillators.
Journal ArticleDOI
Far-from-equilibrium kinetic processes
TL;DR: In this article, the authors analyzed the kinetics of activated processes that take place under far-from-equilibrium conditions, when the system is subjected to external driving forces or gradients or at high values of affinities.
References
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TL;DR: In this paper, the authors present a crash-course on Equilibrium Thermodynamics and a list of applications of beyond-equilibrium thermodynamics, as well as a solution to Exercises.
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Free Energy Transduction and Biochemical Cycle Kinetics
TL;DR: In this paper, the authors present a survey of the elements of free energy transduction, including states, diagrams, cycles, and free energy dissipation, as well as their application to muscle contraction.