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Haugerud IS, Jaiswal P, Weber CA. Nonequilibrium Wet-Dry Cycling Acts as a Catalyst for Chemical Reactions. J Phys Chem B 2024; 128:1724-1736. [PMID: 38335971 PMCID: PMC10895654 DOI: 10.1021/acs.jpcb.3c05824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Recent experimental studies suggest that wet-dry cycles and coexisting phases can each strongly alter chemical processes. The mechanisms of why and to what degree chemical processes are altered when subjected to evaporation and condensation are unclear. To close this gap, we developed a theoretical framework for nondilute chemical reactions subject to nonequilibrium conditions of evaporation and condensation. We find that such conditions can change the half-time of the product's yield by more than an order of magnitude, depending on the substrate-solvent interaction. We show that the cycle frequency strongly affects the chemical turnover when the system is maintained out of equilibrium by wet-dry cycles. There exists a resonance behavior in the cycle frequency where the turnover is maximal. This resonance behavior enables wet-dry cycles to select specific chemical reactions, suggesting a potential mechanism for chemical evolution in prebiotic soups at early Earth.
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Affiliation(s)
- Ivar Svalheim Haugerud
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Pranay Jaiswal
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Christoph A Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
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2
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Sangchai T, Al Shehimy S, Penocchio E, Ragazzon G. Artificial Molecular Ratchets: Tools Enabling Endergonic Processes. Angew Chem Int Ed Engl 2023; 62:e202309501. [PMID: 37545196 DOI: 10.1002/anie.202309501] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.
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Affiliation(s)
- Thitiporn Sangchai
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Shaymaa Al Shehimy
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Emanuele Penocchio
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
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3
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Pattloch S, Dzubiella J. Mean-field models for the chemical fueling of transient soft matter states. SOFT MATTER 2023; 19:7804-7814. [PMID: 37795797 DOI: 10.1039/d3sm00742a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The chemical fueling of transient states (CFTS) is a powerful process to control the nonequilibrium structuring and the homeostatic function of adaptive soft matter systems. Here, we introduce a simple mean-field model of CFTS based on the activation of metastable equilibrium states in a tilted 'Landau' bistable energy landscape along a coarse-grained reaction coordinate (or 'order parameter') triggered by a nonmonotonic two-step chemical fueling reaction. Evaluation of the model in the quasi-static (QS) limit-valid for fast system relaxation-allows us to extract useful analytical laws for the critical activation concentration and duration of the transient states in dependence of physical parameters, such as rate constants, fuel concentrations, and the system's distance to its equilibrium transition point. We apply our model in the QS limit explicitly to recent experiments of CFTS of collapsing responsive microgels and find a very good performance with only a few global and physically interpretable fitting parameters, which can be employed for programmable material design. Moreover, our model framework also allows a thermodynamic analysis of the energy and performed work in the system. Finally, we go beyond the QS limit, where the system's response is slow and retarded versus the chemical reaction, using an overdamped Smoluchowski approach. The latter demonstrates how internal system time scales can be used to tune the time-dependent behavior and programmed delay of the transient states in full nonequilibrium.
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Affiliation(s)
- Sven Pattloch
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany.
- Cluster of Excellence livMatS@FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany.
- Cluster of Excellence livMatS@FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
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4
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Flatt S, Busiello DM, Zamuner S, De Los Rios P. ABC transporters are billion-year-old Maxwell Demons. COMMUNICATIONS PHYSICS 2023; 6:205. [PMID: 38665399 PMCID: PMC11041718 DOI: 10.1038/s42005-023-01320-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2023] [Indexed: 04/28/2024]
Abstract
ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady concentration gradient driven by ATP hydrolysis. Building upon the present biophysical and biochemical characterization of ABC transporters, we propose here a model whose solution reveals that these machines are an exact molecular realization of the autonomous Maxwell Demon, a century-old abstract device that uses an energy source to drive systems away from thermodynamic equilibrium. In particular, the Maxwell Demon does not perform any direct mechanical work on the system, but simply selects which spontaneous processes to allow and which ones to forbid based on information that it collects and processes. In its autonomous version, the measurement device is embedded in the system itself. In the molecular model introduced here, the different operations that characterize Maxwell Demons (measurement, feedback, resetting) are features that emerge from the biochemical and structural properties of ABC transporters, revealing the crucial role of allostery to process information. Our framework allows us to develop an explicit bridge between the molecular-level description and the higher-level language of information theory for ABC transporters.
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Affiliation(s)
- Solange Flatt
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, Lausanne, 1015 Switzerland
| | - Daniel Maria Busiello
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, Lausanne, 1015 Switzerland
- Max Planck Institute for the Physics of Complex Systems, Dresden, 01187 Germany
| | - Stefano Zamuner
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, Lausanne, 1015 Switzerland
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, Lausanne, 1015 Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne—EPFL, Lausanne, 1015 Switzerland
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5
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Contreras-Vergara O, Sánchez-Salas N, Valencia-Ortega G, Jiménez-Aquino JI. Carnot, Stirling, and Ericsson stochastic heat engines: Efficiency at maximum power. Phys Rev E 2023; 108:014123. [PMID: 37583186 DOI: 10.1103/physreve.108.014123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/26/2023] [Indexed: 08/17/2023]
Abstract
This work uses the low-dissipation strategy to obtain efficiency at maximum power from a stochastic heat engine performing Carnot-, Stirling- and Ericsson-like cycles at finite time. The heat engine consists of a colloidal particle trapped by optical tweezers, in contact with two thermal baths at different temperatures, namely hot (T_{h}) and cold (T_{c}). The particle dynamics is characterized by a Langevin equation with time-dependent control parameters bounded to a harmonic potential trap. In a low-dissipation approach, the equilibrium properties of the system are required, which in our case, can be calculated through a statelike equation for the mean value 〈x^{2}〉_{eq} coming from a macroscopic expression associated with the Langevin equation.
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Affiliation(s)
- O Contreras-Vergara
- Departamento de Física, Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edif. 9 UP Zacatenco, CP 07738, CDMX, México
| | - N Sánchez-Salas
- Departamento de Física, Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edif. 9 UP Zacatenco, CP 07738, CDMX, México
| | - G Valencia-Ortega
- División de Matemáticas e Ingeniería, Facultad de Estudios Superiores Acatlán, Universidad Nacional Autónoma de México, Av. Alcanfores y San Juan Totoltepec, Santa Cruz Acatlán, Naucalpan de Juárez, 53150, Estado de México, México
| | - J I Jiménez-Aquino
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, C.P. 09340, CDMX, México
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6
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van Duppen P, Daines E, Robinson WE, Huck WTS. Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network. J Am Chem Soc 2023; 145:7559-7568. [PMID: 36961990 PMCID: PMC10080678 DOI: 10.1021/jacs.3c00908] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Prebiotic environments are dynamic, containing a range of periodic and aperiodic variations in reaction conditions. However, the impact of the temporal dynamics of environmental conditions upon prebiotic chemical reaction networks has not been investigated. Here, we demonstrate how the magnitude and rate of temporal fluctuations of the catalysts Ca2+ and hydroxide control the product distributions of the formose reaction. Surprisingly, the product compositions of the formose reaction under dynamic conditions deviate significantly from those under steady state conditions. We attribute these compositional changes to the non-uniform propagation of fluctuations through the network, thereby shaping reaction outcomes. An examination of temporal concentration patterns showed that collections of compounds responded collectively to perturbations, indicating that key gating reactions branching from the Breslow cycle may be important responsive features of the formose reaction. Our findings show how the compositions of prebiotic reaction networks were shaped by sequential environmental events, illustrating the necessity for considering the temporal traits of prebiotic environments that supported the origin of life.
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Affiliation(s)
- Peer van Duppen
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elena Daines
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - William E Robinson
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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7
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Padmanabha P, Busiello DM, Maritan A, Gupta D. Fluctuations of entropy production of a run-and-tumble particle. Phys Rev E 2023; 107:014129. [PMID: 36797901 DOI: 10.1103/physreve.107.014129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Out-of-equilibrium systems continuously generate entropy, with its rate of production being a fingerprint of nonequilibrium conditions. In small-scale dissipative systems subject to thermal noise, fluctuations of entropy production are significant. Hitherto, mean and variance have been abundantly studied, even if higher moments might be important to fully characterize the system of interest. Here, we introduce a graphical method to compute any moment of entropy production for a generic discrete-state system. Then, we focus on a paradigmatic model of active particles, i.e., run-and-tumble dynamics, which resembles the motion observed in several micro-organisms. Employing our framework, we compute the first three cumulants of the entropy production for a discrete version of this model. We also compare our analytical results with numerical simulations. We find that as the number of states increases, the distribution of entropy production deviates from a Gaussian. Finally, we extend our framework to a continuous state-space run-and-tumble model, using an appropriate scaling of the transition rates. The approach presented here might help uncover the features of nonequilibrium fluctuations of any current in biological systems operating out-of-equilibrium.
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Affiliation(s)
- Prajwal Padmanabha
- Department of Physics and Astronomy "G. Galilei," University of Padova, Padova 35131, Italy
| | | | - Amos Maritan
- Department of Physics and Astronomy "G. Galilei," University of Padova, Padova 35131, Italy
| | - Deepak Gupta
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
- Institute for Theoretical Physics, Technical University of Berlin, Hardenbergstrasse 36, D-10623 Berlin, Germany
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8
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Mamede IN, Stable ALL, Fiore CE. Obtaining efficient collisional engines via velocity-dependent drivings. Phys Rev E 2022; 106:064125. [PMID: 36671179 DOI: 10.1103/physreve.106.064125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Brownian particles interacting sequentially with distinct temperatures and driving forces at each stroke have been tackled as a reliable alternative for the construction of engine setups. However, they can behave very inefficiently depending on the driving used for the work source and/or when temperatures of each stage are very different from each other. Inspired by some models for molecular motors and recent experimental studies, a coupling between driving and velocities is introduced and detail investigated from stochastic thermodynamics. Exact expressions for thermodynamic quantities and distinct maximization routes have been obtained. The search of an optimal coupling provides a substantial increase of engine performance (mainly efficiency), even for large ΔT. A simple and general argument for the optimal coupling can be estimated, irrespective of the driving and other model details.
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Affiliation(s)
- Iago N Mamede
- Universidade de São Paulo, Instituto de Física, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - Angel L L Stable
- Universidade de São Paulo, Instituto de Física, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - C E Fiore
- Universidade de São Paulo, Instituto de Física, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
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9
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Nicoletti G, Busiello DM. Mutual information in changing environments: Nonlinear interactions, out-of-equilibrium systems, and continuously varying diffusivities. Phys Rev E 2022; 106:014153. [PMID: 35974654 DOI: 10.1103/physreve.106.014153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Biochemistry, ecology, and neuroscience are examples of prominent fields aiming at describing interacting systems that exhibit nontrivial couplings to complex, ever-changing environments. We have recently shown that linear interactions and a switching environment are encoded separately in the mutual information of the overall system. Here we first generalize these findings to a broad class of nonlinear interacting models. We find that a new term in the mutual information appears, quantifying the interplay between nonlinear interactions and environmental changes, and leading to either constructive or destructive information interference. Furthermore, we show that a higher mutual information emerges in out-of-equilibrium environments with respect to an equilibrium scenario. Finally, we generalize our framework to the case of continuously varying environments. We find that environmental changes can be mapped exactly into an effective spatially varying diffusion coefficient, shedding light on modeling of biophysical systems in inhomogeneous media.
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Affiliation(s)
- Giorgio Nicoletti
- Laboratory of Interdisciplinary Physics, Department of Physics and Astronomy "G. Galilei," University of Padova, Padova 35121, Italy
| | - Daniel Maria Busiello
- Institute of Physics, École Polytechnique Fédérale de Lausanne-EPFL, 1015 Lausanne, Switzerland
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10
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Liang S, De Los Rios P, Busiello DM. Dissipation-Driven Selection under Finite Diffusion: Hints from Equilibrium and Separation of Time Scales. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1068. [PMID: 34441208 PMCID: PMC8394842 DOI: 10.3390/e23081068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022]
Abstract
When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available energy, might be dominant in dictating the stationary populations of all chemical states out of equilibrium. This phenomenology has been theoretically explored mainly in the infinite diffusion limit. Here, we show that the regime in which the diffusion rate is finite, and also slower than some chemical reactions, might bring about interesting features, such as the maximisation of selection or the switch of the selected state at stationarity. We introduce a framework, rooted in a time-scale separation analysis, which is able to capture leading non-equilibrium features using only equilibrium arguments under well-defined conditions. In particular, it is possible to identify fast-dissipation sub-networks of reactions whose Boltzmann equilibrium dominates the steady-state of the entire system as a whole. Finally, we also show that the dissipated heat (and so the entropy production) can be estimated, under some approximations, through the heat capacity of fast-dissipation sub-networks. This work provides a tool to develop an intuitive equilibrium-based grasp on complex non-isothermal reaction networks, which are important paradigms to understand the emergence of complex structures from basic building blocks.
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Affiliation(s)
- Shiling Liang
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, 1015 Lausanne, Switzerland; (S.L.); (P.D.L.R.)
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, 1015 Lausanne, Switzerland; (S.L.); (P.D.L.R.)
- Institute of Bioengineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, 1015 Lausanne, Switzerland
| | - Daniel Maria Busiello
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne—EPFL, 1015 Lausanne, Switzerland; (S.L.); (P.D.L.R.)
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11
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Dass AV, Georgelin T, Westall F, Foucher F, De Los Rios P, Busiello DM, Liang S, Piazza F. Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network. Nat Commun 2021; 12:2749. [PMID: 33980850 PMCID: PMC8115175 DOI: 10.1038/s41467-021-22818-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/19/2021] [Indexed: 11/08/2022] Open
Abstract
The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.
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Affiliation(s)
- Avinash Vicholous Dass
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Department of Physics, Ludwig Maximilians University, München, Germany
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
- Laboratoire de Réactivité de Surface, UMR 7197, Sorbonne Université, Paris, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Frédéric Foucher
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Daniel Maria Busiello
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Shiling Liang
- Institute of Physics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne-EPFL, Lausanne, Switzerland
| | - Francesco Piazza
- Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, Orléans, France.
- Université d'Orléans, UFR CoST Sciences et Techniques, Orléans, France.
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