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Self-organization of enzyme-catalyzed reactions studied by the maximum entropy production principle
Andrej Dobovišek, Marko Vitas, Tina Blaževič, Rene Markovič, Marko Marhl, Aleš Fajmut, 2023, original scientific article

Abstract: The self-organization of open reaction systems is closely related to specific mechanisms that allow the export of internally generated entropy from systems to their environment. According to the second law of thermodynamics, systems with effective entropy export to the environment are better internally organized. Therefore, they are in thermodynamic states with low entropy. In this context, we study how self-organization in enzymatic reactions depends on their kinetic reaction mechanisms. Enzymatic reactions in an open system are considered to operate in a non-equilibrium steady state, which is achieved by satisfying the principle of maximum entropy production (MEPP). The latter is a general theoretical framework for our theoretical analysis. Detailed theoretical studies and comparisons of the linear irreversible kinetic schemes of an enzyme reaction in two and three states are performed. In both cases, in the optimal and statistically most probable thermodynamic steady state, a diffusion-limited flux is predicted by MEPP. Several thermodynamic quantities and enzymatic kinetic parameters, such as the entropy production rate, the Shannon information entropy, reaction stability, sensitivity, and specificity constants, are predicted. Our results show that the optimal enzyme performance may strongly depend on the number of reaction steps when linear reaction mechanisms are considered. Simple reaction mechanisms with a smaller number of intermediate reaction steps could be better organized internally and could allow fast and stable catalysis. These could be features of the evolutionary mechanisms of highly specialized enzymes.
Keywords: enzymes, kinetic data analysis, steady state, self-organization, maximum entropy production
Published in DKUM: 08.05.2024; Views: 86; Downloads: 8
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The maximum entropy production principle and linear irreversible processes
Paško Županović, Domagoj Kuić, Željana Bonačić Lošić, Dražen Petrov, Davor Juretić, Milan Brumen, 2010, original scientific article

Abstract: It is shown that Onsager’s principle of the least dissipation of energy is equivalent to the maximum entropy production principle. It is known that solutions of the linearized Boltzmann equation make extrema of entropy production. It is argued, in the case of stationary processes, that this extremum is a maximum rather than a minimum.
Keywords: entropy production, linear nonequilibrium thermodynamics, linearized Boltzmann equation
Published in DKUM: 21.06.2017; Views: 1138; Downloads: 388
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On the problem of formulating principles in nonequilibrium thermodynamics
Paško Županović, Domagoj Kuić, Davor Juretić, Andrej Dobovišek, 2010, original scientific article

Abstract: In this work, we consider the choice of a system suitable for the formulation of principles in nonequilibrium thermodynamics. It is argued that an isolated system is a much better candidate than a system in contact with a bath. In other words, relaxation processes rather than stationary processes are more appropriate for the formulation of principles in nonequilibrium thermodynamics. Arguing that slow varying relaxation can be described with quasi-stationary process, it is shown for two special cases, linear nonequilibrium thermodynamics and linearized Boltzmann equation, that solutions of these problems are in accordance with the maximum entropy production principle.
Keywords: thermodynamics, entropy, relaxation, stationary process, entropy production
Published in DKUM: 07.06.2012; Views: 1538; Downloads: 391
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