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Pietzonka P, Coghi F. Thermodynamic cost for precision of general counting observables. Phys Rev E 2024; 109:064128. [PMID: 39020906 DOI: 10.1103/physreve.109.064128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/13/2024] [Indexed: 07/20/2024]
Abstract
We analytically derive universal bounds that describe the tradeoff between thermodynamic cost and precision in a sequence of events related to some internal changes of an otherwise hidden physical system. The precision is quantified by the fluctuations in either the number of events counted over time or the waiting times between successive events. Our results are valid for the same broad class of nonequilibrium driven systems considered by the thermodynamic uncertainty relation, but they extend to both time-symmetric and asymmetric observables. We show how optimal precision saturating the bounds can be achieved. For waiting-time fluctuations of asymmetric observables, a phase transition in the optimal configuration arises, where higher precision can be achieved by combining several signals.
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Nie Y, Zheng Z, Li C, Zhan H, Kou L, Gu Y, Lü C. Resolving the dynamic properties of entangled linear polymers in non-equilibrium coarse grain simulation with a priori scaling factors. NANOSCALE 2024. [PMID: 38494916 DOI: 10.1039/d3nr06185j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The molecular weight of polymers can influence the material properties, but the molecular weight at the experiment level sometimes can be a huge burden for property prediction with full-atomic simulations. The traditional bottom-up coarse grain (CG) simulation can reduce the computation cost. However, the dynamic properties predicted by the CG simulation can deviate from the full-atomic simulation result. Usually, in CG simulations, the diffusion is faster and the viscosity and modulus are much lower. The fast dynamics in CG are usually solved by a posteriori scaling on time, temperature, or potential modifications, which usually have poor transferability to other non-fitted physical properties because of a lack of fundamental physics. In this work, a priori scaling factors were calculated by the loss of degrees of freedom and implemented in the iterative Boltzmann inversion. According to the simulation results on 3 different CG levels at different temperatures and loading rates, such a priori scaling factors can help in reproducing some dynamic properties of polycaprolactone in CG simulation more accurately, such as heat capacity, Young's modulus, and viscosity, while maintaining the accuracy in the structural distribution prediction. The transferability of entropy-enthalpy compensation and a dissipative particle dynamics thermostat is also presented for comparison. The proposed method reveals the huge potential for developing customized CG thermostats and offers a simple way to rebuild multiphysics CG models for polymers with good transferability.
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Affiliation(s)
- Yihan Nie
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Zhuoqun Zheng
- School of Astronautics, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Chengkai Li
- School of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, China
| | - Haifei Zhan
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Liangzhi Kou
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Yuantong Gu
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Chaofeng Lü
- Faculty of Mechanical Engineering & Mechanics, Ningbo University, Ningbo 315211, China
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
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Di Terlizzi I, Gironella M, Herraez-Aguilar D, Betz T, Monroy F, Baiesi M, Ritort F. Variance sum rule for entropy production. Science 2024; 383:971-976. [PMID: 38422150 DOI: 10.1126/science.adh1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024]
Abstract
Entropy production is the hallmark of nonequilibrium physics, quantifying irreversibility, dissipation, and the efficiency of energy transduction processes. Despite many efforts, its measurement at the nanoscale remains challenging. We introduce a variance sum rule (VSR) for displacement and force variances that permits us to measure the entropy production rate σ in nonequilibrium steady states. We first illustrate it for directly measurable forces, such as an active Brownian particle in an optical trap. We then apply the VSR to flickering experiments in human red blood cells. We find that σ is spatially heterogeneous with a finite correlation length, and its average value agrees with calorimetry measurements. The VSR paves the way to derive σ using force spectroscopy and time-resolved imaging in living and active matter.
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Affiliation(s)
- I Di Terlizzi
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
- Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - M Gironella
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, Spain
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - D Herraez-Aguilar
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda Km 1,800, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - T Betz
- Third Institute of Physics, Georg August Universität Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - F Monroy
- Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
- Translational Biophysics, Instituto de Investigación Sanitaria Hospital Doce de Octubre (IMAS12), Av. Andalucía, 28041 Madrid, Spain
| | - M Baiesi
- Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
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Ghosal A, Bisker G. Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining. Phys Chem Chem Phys 2022; 24:24021-24031. [PMID: 36065766 PMCID: PMC7613705 DOI: 10.1039/d2cp03064k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The entropy production rate (EPR) measures time-irreversibility in systems operating far from equilibrium. The challenge in estimating the EPR for a continuous variable system is the finite spatiotemporal resolution and the limited accessibility to all of the nonequilibrium degrees of freedom. Here, we estimate the irreversibility in partially observed systems following oscillatory dynamics governed by coupled overdamped Langevin equations. We coarse-grain an observed variable of a nonequilibrium driven system into a few discrete states and estimate a lower bound on the total EPR. As a model system, we use hair-cell bundle oscillations driven by molecular motors, such that the bundle tip position is observed, but the positions of the motors are hidden. In the observed variable space, the underlying driven process exhibits second-order semi-Markov statistics. The waiting time distributions (WTD), associated with transitions among the coarse-grained states, are non-exponential and convey the information on the broken time-reversal symmetry. By invoking the underlying time-irreversibility, we calculate a lower bound on the total EPR from the Kullback-Leibler divergence (KLD) between WTD. We show that the mean dwell-time asymmetry factor - the ratio between the mean dwell-times along the forward direction and the backward direction, can qualitatively measure the degree of broken time reversal symmetry and increases with finer spatial resolution. Finally, we apply our methodology to a continuous-time discrete Markov chain model, coarse-grained into a linear system exhibiting second-order semi-Markovian statistics, and demonstrate the estimation of a lower bound on the total EPR from irreversibility manifested only in the WTD.
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Affiliation(s)
- Aishani Ghosal
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Gili Bisker
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
- Center for Physics and Chemistry of Living Systems, Tel-Aviv University, Tel Aviv 6997801, Israel
- Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel Aviv 6997801, Israel
- Center for Light-Matter Interaction, Tel-Aviv University, Tel Aviv 6997801, Israel
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