Abstract While genetic mutations, natural selection and environmental pressures are well-known drivers of enzyme evolution, we show that their structural adaptations are significantly influenced by energy dissipation. Enzymes use chemical energy to do work, which results in a loss of free energy due to the irreversible nature of the process. By assuming that the catalytic process occurs along a potential barrier, we describe the kinetics of the conversion of enzyme-substrate complexes to enzyme-product complexes and calculate the energy dissipation. We show that the behaviour of the dissipated energy is a non-monotonic function of the energy of the intermediate state. This finding supports our main result that enzyme configurations evolve to minimise energy dissipation and simultaneously improve kinetic and thermodynamic efficiencies. Our study provides a novel insight into the complex process of enzyme evolution and highlights the crucial role of energy dissipation in shaping structural adaptations.
{"title":"Uncovering enzymatic structural adaptations from energy dissipation","authors":"A. Arango-Restrepo, D. Barragán, J. Rubí","doi":"10.1515/jnet-2023-0044","DOIUrl":"https://doi.org/10.1515/jnet-2023-0044","url":null,"abstract":"Abstract While genetic mutations, natural selection and environmental pressures are well-known drivers of enzyme evolution, we show that their structural adaptations are significantly influenced by energy dissipation. Enzymes use chemical energy to do work, which results in a loss of free energy due to the irreversible nature of the process. By assuming that the catalytic process occurs along a potential barrier, we describe the kinetics of the conversion of enzyme-substrate complexes to enzyme-product complexes and calculate the energy dissipation. We show that the behaviour of the dissipated energy is a non-monotonic function of the energy of the intermediate state. This finding supports our main result that enzyme configurations evolve to minimise energy dissipation and simultaneously improve kinetic and thermodynamic efficiencies. Our study provides a novel insight into the complex process of enzyme evolution and highlights the crucial role of energy dissipation in shaping structural adaptations.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":"0 1","pages":""},"PeriodicalIF":6.6,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42499241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Any real physical process that produces entropy, dissipates energy as heat, or generates mechanical work must do so on a finite timescale. Recently derived thermodynamic speed limits place bounds on these observables using intrinsic timescales of the process. Here, we derive relationships for the thermodynamic speeds for any composite stochastic observable in terms of the timescales of its individual components. From these speed limits, we find bounds on thermal efficiency of stochastic processes exchanging energy as heat and work and bound the rate of entropy change in a system with entropy production and flow. Using the time set by an external clock, we find bounds on the first time to reach any value for the entropy production. As an illustration, we compute these bounds for Brownian particles diffusing in space subject to a constant-temperature heat bath and a time-dependent external force.
{"title":"Relations between timescales of stochastic thermodynamic observables","authors":"Erez Aghion, Jason R. Green","doi":"10.1515/jnet-2022-0104","DOIUrl":"https://doi.org/10.1515/jnet-2022-0104","url":null,"abstract":"Abstract Any real physical process that produces entropy, dissipates energy as heat, or generates mechanical work must do so on a finite timescale. Recently derived thermodynamic speed limits place bounds on these observables using intrinsic timescales of the process. Here, we derive relationships for the thermodynamic speeds for any composite stochastic observable in terms of the timescales of its individual components. From these speed limits, we find bounds on thermal efficiency of stochastic processes exchanging energy as heat and work and bound the rate of entropy change in a system with entropy production and flow. Using the time set by an external clock, we find bounds on the first time to reach any value for the entropy production. As an illustration, we compute these bounds for Brownian particles diffusing in space subject to a constant-temperature heat bath and a time-dependent external force.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2023-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49521938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract 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 for which sub-systems are out of consideration. Taking sub-systems into account, as it is by definition necessary for decomposed systems, the interaction Hamiltonians –which are absent in undecomposed systems– can be a source of irreversibility in decomposed systems. Thus, the following two-stage task arises: How to modify von Neumann’s equation of undecomposed systems so that irreversibility appears, and how this modification affects decomposed systems? The first step was already done in Muschik (“Concepts of phenomenological irreversible quantum thermodynamics: closed undecomposed Schottky systems in semi-classical description,” J. Non-Equilibrium Thermodyn., vol. 44, pp. 1–13, 2019) and is repeated below, whereas the second step to formulate a quantum thermodynamics of decomposed systems is performed here by modifying the von Neumann equations of the sub-systems by a procedure wich is similar to that of Lindblad’s equation (G. Lindblad, “On the generators of quantum dynamical semigroups,” Commun. Math. Phys., vol. 48, p. 119130, 1976), but different because the sub-systems interact with one another through partitions.
{"title":"Concepts of phenomenological irreversible quantum thermodynamics II: time dependent statistical ensembles of bipartite systems","authors":"W. Muschik","doi":"10.1515/jnet-2023-0023","DOIUrl":"https://doi.org/10.1515/jnet-2023-0023","url":null,"abstract":"Abstract 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 for which sub-systems are out of consideration. Taking sub-systems into account, as it is by definition necessary for decomposed systems, the interaction Hamiltonians –which are absent in undecomposed systems– can be a source of irreversibility in decomposed systems. Thus, the following two-stage task arises: How to modify von Neumann’s equation of undecomposed systems so that irreversibility appears, and how this modification affects decomposed systems? The first step was already done in Muschik (“Concepts of phenomenological irreversible quantum thermodynamics: closed undecomposed Schottky systems in semi-classical description,” J. Non-Equilibrium Thermodyn., vol. 44, pp. 1–13, 2019) and is repeated below, whereas the second step to formulate a quantum thermodynamics of decomposed systems is performed here by modifying the von Neumann equations of the sub-systems by a procedure wich is similar to that of Lindblad’s equation (G. Lindblad, “On the generators of quantum dynamical semigroups,” Commun. Math. Phys., vol. 48, p. 119130, 1976), but different because the sub-systems interact with one another through partitions.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42969255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Kosheleva, T. Karapantsios, M. Kostoglou, A. Mitropoulos
Abstract This study examines the effect of a short term rotation on a system of constant volume. Adsorption of CO2 is performed on Activated Carbon (AC) at 281, 293 and 298 K with a special designed device that allows rotation. The adsorption isotherms were conducted up to 10 bar for both No Rotational (NoROT) and Rotational (ROT) cases. The ROT case refers to 60 s of rotation at 5000 rpm. The experimental results were fitted to Langmuir as well as to Dubinin–Astakhov (D–A) models with the latter presenting the best fit. A detailed thermodynamic analysis is performed in order to quantify the overall contribution of the rotation on gas adsorption compared to static case. For the ROT case, the maximum amount adsorbed (q max) is by 12 % higher than the NoROT counterpart, while a decrease in chemical potential as surface loading is increased, indicates that the process after rotation is entropy driven. The outcome of this work suggests that rotation enables gas molecules to access previously inaccessible sites, thus gaining more vacancies due to better rearrangement of the adsorbed CO2 molecules.
{"title":"Thermodynamic analysis of the effect of rotation on gas adsorption","authors":"R. Kosheleva, T. Karapantsios, M. Kostoglou, A. Mitropoulos","doi":"10.1515/jnet-2022-0086","DOIUrl":"https://doi.org/10.1515/jnet-2022-0086","url":null,"abstract":"Abstract This study examines the effect of a short term rotation on a system of constant volume. Adsorption of CO2 is performed on Activated Carbon (AC) at 281, 293 and 298 K with a special designed device that allows rotation. The adsorption isotherms were conducted up to 10 bar for both No Rotational (NoROT) and Rotational (ROT) cases. The ROT case refers to 60 s of rotation at 5000 rpm. The experimental results were fitted to Langmuir as well as to Dubinin–Astakhov (D–A) models with the latter presenting the best fit. A detailed thermodynamic analysis is performed in order to quantify the overall contribution of the rotation on gas adsorption compared to static case. For the ROT case, the maximum amount adsorbed (q max) is by 12 % higher than the NoROT counterpart, while a decrease in chemical potential as surface loading is increased, indicates that the process after rotation is entropy driven. The outcome of this work suggests that rotation enables gas molecules to access previously inaccessible sites, thus gaining more vacancies due to better rearrangement of the adsorbed CO2 molecules.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2023-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42933247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Avramenko, A. I. Tyrinov, I. V. Shevchuk, Nataliya P. Dmitrenko
Abstract The main attention is paid to the analytical analysis of an oblique shock wave in a turbulent adiabatic gas flow. For this purpose, a modified Rankine–Hugoniot model was obtained. On its basis, a solution was derived for the Rankine–Hugoniot conditions for a gas flow with various degrees of turbulence, as well as the equation of the modified Hugoniot adiabat. The behavior of the velocity of an adiabatic turbulent gas flow during its passage through an oblique shock wave at different levels of turbulence is demonstrated. A modification of Prandtl’s law for the velocity coefficients was obtained. The shock polar was also analyzed. The relationship between the angular gas flow and the angle of the shock wave was derived. Finally, the condition for the appearance of an outgoing bow shock wave was obtained.
{"title":"Oblique shock wave in turbulent flow","authors":"A. Avramenko, A. I. Tyrinov, I. V. Shevchuk, Nataliya P. Dmitrenko","doi":"10.1515/jnet-2022-0093","DOIUrl":"https://doi.org/10.1515/jnet-2022-0093","url":null,"abstract":"Abstract The main attention is paid to the analytical analysis of an oblique shock wave in a turbulent adiabatic gas flow. For this purpose, a modified Rankine–Hugoniot model was obtained. On its basis, a solution was derived for the Rankine–Hugoniot conditions for a gas flow with various degrees of turbulence, as well as the equation of the modified Hugoniot adiabat. The behavior of the velocity of an adiabatic turbulent gas flow during its passage through an oblique shock wave at different levels of turbulence is demonstrated. A modification of Prandtl’s law for the velocity coefficients was obtained. The shock polar was also analyzed. The relationship between the angular gas flow and the angle of the shock wave was derived. Finally, the condition for the appearance of an outgoing bow shock wave was obtained.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2023-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46747360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Dispersive diffusion and wave propagation seem to be unconnected and fundamentally different evolution equations. In the context of anomalous diffusion however modeling approaches based on fractional diffusion equations have been presented, which allow to build a continuous bridge between the two regimes. The transition from irreversible dispersive diffusion to reversible wave propagation shows an unexpected increase in entropy production. This seemingly paradoxical behavior of fractional diffusion is reviewed and compared to the behavior of a tree-based diffusion model.
{"title":"The entropy production paradox for fractional diffusion","authors":"K. Hoffmann, C. Essex, J. Prehl, K. Kulmus","doi":"10.1515/jnet-2023-0020","DOIUrl":"https://doi.org/10.1515/jnet-2023-0020","url":null,"abstract":"Abstract Dispersive diffusion and wave propagation seem to be unconnected and fundamentally different evolution equations. In the context of anomalous diffusion however modeling approaches based on fractional diffusion equations have been presented, which allow to build a continuous bridge between the two regimes. The transition from irreversible dispersive diffusion to reversible wave propagation shows an unexpected increase in entropy production. This seemingly paradoxical behavior of fractional diffusion is reviewed and compared to the behavior of a tree-based diffusion model.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":"48 1","pages":"137 - 148"},"PeriodicalIF":6.6,"publicationDate":"2023-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42081460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Onsager fluxes proposed by D.G.B. Edelen assume that the same symmetry, nonlinear Onsager reciprocal relations, holds near and far from equilibrium. This assumption leads to exact differential 1-form J ⋅ dX everywhere, where J and X are thermodynamic fluxes and forces, respectively. However, thermodynamic fluxes far from equilibrium are characterized by symmetry breaking, which lead to the inexact differential 1-form. It is shown in this paper that the inexact differential 1-form J ⋅ dX should be represented by multiple independent scalar-valued functions. Generalized Onsager fluxes are obtained based on such representation. Generalized Onsager fluxes do not satisfy the nonlinear Onsager reciprocal relations and contain multiple independent scalar-valued functions, so they are suitable to thermodynamic fluxes far from equilibrium. Generalized Onsager fluxes embody Onsager fluxes as a special case. Therefore, generalized Onsager fluxes provide a unified framework for thermodynamic fluxes near and far from equilibrium.
{"title":"Generalized Onsager fluxes based on inexact differential 1-form","authors":"Qiang Yang, K. Leng, Man Zhang, Yaoru Liu","doi":"10.1515/jnet-2022-0094","DOIUrl":"https://doi.org/10.1515/jnet-2022-0094","url":null,"abstract":"Abstract Onsager fluxes proposed by D.G.B. Edelen assume that the same symmetry, nonlinear Onsager reciprocal relations, holds near and far from equilibrium. This assumption leads to exact differential 1-form J ⋅ dX everywhere, where J and X are thermodynamic fluxes and forces, respectively. However, thermodynamic fluxes far from equilibrium are characterized by symmetry breaking, which lead to the inexact differential 1-form. It is shown in this paper that the inexact differential 1-form J ⋅ dX should be represented by multiple independent scalar-valued functions. Generalized Onsager fluxes are obtained based on such representation. Generalized Onsager fluxes do not satisfy the nonlinear Onsager reciprocal relations and contain multiple independent scalar-valued functions, so they are suitable to thermodynamic fluxes far from equilibrium. Generalized Onsager fluxes embody Onsager fluxes as a special case. Therefore, generalized Onsager fluxes provide a unified framework for thermodynamic fluxes near and far from equilibrium.","PeriodicalId":16428,"journal":{"name":"Journal of Non-Equilibrium Thermodynamics","volume":"48 1","pages":"345 - 352"},"PeriodicalIF":6.6,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45060158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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