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Methods and conversations in (post)modern thermodynamics

2024-03-20
Francesco Avanzini , Massimo Bilancioni , Vasco Cavina +7 more
Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic … Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic and stochastic chemical reaction networks, metastability, martingales, quantum thermodynamics, and foundational issues.
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A [3]-catenane non-autonomous molecular motor model: Geometric phase, no-pumping theorem, and energy transduction

2023-06-13
Massimo Bilancioni , Massimiliano Esposito , Emanuele Penocchio
We study a model of a synthetic molecular motor-a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one-subjected to time-dependent driving using stochastic thermodynamics. The model presents … We study a model of a synthetic molecular motor-a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one-subjected to time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space, which corrects previous erroneous results. We also analyze the performance of the motor subjected to step-wise driving protocols in the absence and presence of an applied load. Optimization strategies for generating large currents and maximizing free energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.
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Methods and Conversations in (Post)Modern Thermodynamics

2023-01-01
Francesco Avanzini , Massimo Bilancioni , Vasco Cavina +7 more
Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic … Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic and stochastic chemical reaction networks, metastability, martingales, quantum thermodynamics, and foundational issues.
View PDF Chat

A [3]-catenane non-autonomous molecular motor model: geometric phase, no-pumping theorem, and energy transduction

2023-01-01
Massimo Bilancioni , M. Esposito , Emanuele Penocchio
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic … We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles, but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space which corrects previous erroneous results. We also analyze the performance of the motor subjected to a step-wise driving protocols in absence and in presence of an applied load. Optimization strategies for generating large currents and maximizing free-energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.

A chemical reaction network implementation of a Maxwell demon

2023-01-01
Massimo Bilancioni , Massimiliano Esposito , Nahuel Freitas
We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We … We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We characterize its scaling behavior in the macroscopic limit, its performances, and the impact of potential internal delays. We obtain analytical expressions for all quantities of interest, namely, the generated reverse chemical current, the output power, the transduction efficiency, and the correlations between the numbers of molecules. Due to a bound on the nonequilibrium response of its chemical reaction network, we find that, contrary to the electronic case, there is no way for the Maxwell demon to generate a finite output in the macroscopic limit. Finally, we analyze the information thermodynamics of the Maxwell demon from a bipartite perspective. In the limit of a fast demon, the information flow is obtained, its pattern in the state space is discussed, and the behavior of the partial efficiencies related to the measurement and the feedback processes is examined.
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Elementary Flux Modes as CRN Gears for Free Energy Transduction

2024-05-28
Massimo Bilancioni , Massimiliano Esposito
We demonstrate that, for a chemical reaction network (CRN) engaged in energy transduction, its optimal operation from a thermodynamic efficiency standpoint is contingent upon its working conditions. Analogously to the … We demonstrate that, for a chemical reaction network (CRN) engaged in energy transduction, its optimal operation from a thermodynamic efficiency standpoint is contingent upon its working conditions. Analogously to the bicycle gear system, CRNs have at their disposal several transducing mechanisms characterized by different yields. We highlight the critical role of the CRN's elementary flux modes in determining this "gearing" and their impact on maximizing energy transduction efficiency. Furthermore, we introduce an enzymatically regulated CRN, engineered to autonomously adjust its "gear", thereby optimizing its efficiency under different external conditions.
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Elementary Flux Modes as CRN Gears for Free Energy Transduction

2024-05-28
Massimo Bilancioni , Massimiliano Esposito
We demonstrate that, for a chemical reaction network (CRN) engaged in energy transduction, its optimal operation from a thermodynamic efficiency standpoint is contingent upon its working conditions. Analogously to the … We demonstrate that, for a chemical reaction network (CRN) engaged in energy transduction, its optimal operation from a thermodynamic efficiency standpoint is contingent upon its working conditions. Analogously to the bicycle gear system, CRNs have at their disposal several transducing mechanisms characterized by different yields. We highlight the critical role of the CRN's elementary flux modes in determining this "gearing" and their impact on maximizing energy transduction efficiency. Furthermore, we introduce an enzymatically regulated CRN, engineered to autonomously adjust its "gear", thereby optimizing its efficiency under different external conditions.
View PDF Chat

Methods and conversations in (post)modern thermodynamics

2024-03-20
Francesco Avanzini , Massimo Bilancioni , Vasco Cavina +7 more
Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic … Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic and stochastic chemical reaction networks, metastability, martingales, quantum thermodynamics, and foundational issues.
View PDF Chat

A [3]-catenane non-autonomous molecular motor model: Geometric phase, no-pumping theorem, and energy transduction

2023-06-13
Massimo Bilancioni , Massimiliano Esposito , Emanuele Penocchio
We study a model of a synthetic molecular motor-a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one-subjected to time-dependent driving using stochastic thermodynamics. The model presents … We study a model of a synthetic molecular motor-a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one-subjected to time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space, which corrects previous erroneous results. We also analyze the performance of the motor subjected to step-wise driving protocols in the absence and presence of an applied load. Optimization strategies for generating large currents and maximizing free energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.
View PDF Chat

A [3]-catenane non-autonomous molecular motor model: geometric phase, no-pumping theorem, and energy transduction

2023-01-01
Massimo Bilancioni , M. Esposito , Emanuele Penocchio
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic … We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents nontrivial features due to the two interacting small macrocycles, but is simple enough to be treated analytically in limiting regimes. Among the results obtained, we find a mapping into an equivalent [2]-catenane that reveals the implications of the no-pumping theorem stating that to generate net motion of the small macrocycles, both energies and barriers need to change. In the adiabatic limit (slow driving), we fully characterize the motor's dynamics and show that the net motion of the small macrocycles is expressed as a surface integral in parameter space which corrects previous erroneous results. We also analyze the performance of the motor subjected to a step-wise driving protocols in absence and in presence of an applied load. Optimization strategies for generating large currents and maximizing free-energy transduction are proposed. This simple model provides interesting clues into the working principles of non-autonomous molecular motors and their optimization.

A chemical reaction network implementation of a Maxwell demon

2023-01-01
Massimo Bilancioni , Massimiliano Esposito , Nahuel Freitas
We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We … We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We characterize its scaling behavior in the macroscopic limit, its performances, and the impact of potential internal delays. We obtain analytical expressions for all quantities of interest, namely, the generated reverse chemical current, the output power, the transduction efficiency, and the correlations between the numbers of molecules. Due to a bound on the nonequilibrium response of its chemical reaction network, we find that, contrary to the electronic case, there is no way for the Maxwell demon to generate a finite output in the macroscopic limit. Finally, we analyze the information thermodynamics of the Maxwell demon from a bipartite perspective. In the limit of a fast demon, the information flow is obtained, its pattern in the state space is discussed, and the behavior of the partial efficiencies related to the measurement and the feedback processes is examined.
View PDF Chat

Methods and Conversations in (Post)Modern Thermodynamics

2023-01-01
Francesco Avanzini , Massimo Bilancioni , Vasco Cavina +7 more
Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic … Lecture notes after the doctoral school (Post)Modern Thermodynamics held at the University of Luxembourg, December 2022, 5-7, covering and advancing continuous-time Markov chains, network theory, stochastic thermodynamics, large deviations, deterministic and stochastic chemical reaction networks, metastability, martingales, quantum thermodynamics, and foundational issues.
View PDF Chat
Coauthor Papers Together
Massimiliano Esposito 4
Emanuele Penocchio 4
Gianmaria Falasco 2
Pedro E. Harunari 2
Alberto Garilli 2
Danilo Forastiere 2
Adarsh Raghu 2
Sara Dal Cengio 2
William D. Piñeros 2
Matteo Polettini 2
M. Esposito 2
Izaak Neri 2
Charles Moslonka 2
Paul Raux 2
Vivien Lecomte 2
Francesco Avanzini 2
Ariane Soret 2
Alexandre Lazarescu 2
Ken Sekimoto 2
Shesha Gopal Marehalli Srinivas 2
Vasco Cavina 2
Nahuel Freitas 2
José Nahuel Freitas 1