Reuse & Permissions

It is not necessary to obtain permission to reuse this article or its components as it is available under the terms of the Creative Commons Attribution 4.0 International license. This license permits unrestricted use, distribution, and reproduction in any medium, provided attribution to the author(s) and the published article's title, journal citation, and DOI are maintained. Please note that some figures may have been included with permission from other third parties. It is your responsibility to obtain the proper permission from the rights holder directly for these figures.

Export citation

Export citation

Choose format for download:

Download Citation
  • Open Access

Thermodynamic bounds and error correction for faulty coarse graining

Jann van der Meer* and Keiji Saito†

  • Department of Physics No. 1, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan

  • *Contact author: vandermeer.jann.5t@kyoto-u.ac.jp
  • †Contact author: keiji.saitoh@scphys.kyoto-u.ac.jp

Phys. Rev. Research 7, 043260 – Published 5 December, 2025

DOI: https://doi.org/10.1103/p3zx-7txy

Abstract

At the nanoscale, random effects not only govern the dynamics of a physical system but may also affect its observation. This work introduces a paradigm for coarse graining that eschews the assignment of a unique coarse-grained trajectory to a microscopic one. Instead, observations are not only coarse-grained but also accompanied by a small chance of error. Formulating the problem in terms of path weights, we identify a condition on the structure of errors that ensures that the observed entropy production does not increase. As a result, the framework of stochastic thermodynamics for estimating entropy production can be extended to this broader class of systems. As an application, we consider Markov networks in which individual transitions can be observed but may be mistaken for each other. We motivate, derive, and illustrate thermodynamic bounds that relate the error sensitivity of the observed entropy production to the strength of the driving and are valid for arbitrary network topologies. If sufficiently many transitions in the network can be observed, redundancies in the coarse-grained trajectories can be used to detect and correct errors, which potentially improves naive estimates of entropy production. We conclude with an outlook on subsequent research on thermodynamic bounds for erroneous coarse graining.

View figure in article

Physics Subject Headings (PhySH)

Article Text

References (41)

  1. K. Sekimoto, Stochastic Energetics (Springer, Berlin, 2010).
  2. L. Peliti and S. Pigolotti, Stochastic Thermodynamics: An Introduction (Princeton University Press, Princeton, NJ, USA, 2021).
  3. N. Shiraishi, An Introduction to Stochastic Thermodynamics: From Basic to Advanced (Springer Nature Singapore Pte Ltd., Singapore, 2023).
  4. U. Seifert, Stochastic Thermodynamics (Cambridge University Press, Cambridge, UK, 2025).
  5. U. Seifert, From stochastic thermodynamics to thermodynamic inference, Annu. Rev. Condens. Matter Phys. 10, 171 (2019).
  6. A. C. Barato and U. Seifert, Thermodynamic uncertainty relation for biomolecular processes, Phys. Rev. Lett. 114, 158101 (2015).
  7. T. R. Gingrich, J. M. Horowitz, N. Perunov, and J. L. England, Dissipation bounds all steady-state current fluctuations, Phys. Rev. Lett. 116, 120601 (2016).
  8. J. M. Horowitz and T. R. Gingrich, Thermodynamic uncertainty relations constrain non-equilibrium fluctuations, Nat. Phys. 16, 15 (2020).
  9. E. Aurell, C. Mejía-Monasterio, and P. Muratore-Ginanneschi, Optimal protocols and optimal transport in stochastic thermodynamics, Phys. Rev. Lett. 106, 250601 (2011).
  10. N. Shiraishi, K. Funo, and K. Saito, Speed limit for classical stochastic processes, Phys. Rev. Lett. 121, 070601 (2018).
  11. S. Ito and A. Dechant, Stochastic time evolution, information geometry, and the Cramér-Rao bound, Phys. Rev. X 10, 021056 (2020).
  12. T. Van Vu and K. Saito, Thermodynamic unification of optimal transport: Thermodynamic uncertainty relation, minimum dissipation, and thermodynamic speed limits, Phys. Rev. X 13, 011013 (2023).
  13. A. Dechant and S. I. Sasa, Improving thermodynamic bounds using correlations, Phys. Rev. X 11, 041061 (2021).
  14. A. Dechant, J. Garnier-Brun, and S.-i. Sasa, Thermodynamic bounds on correlation times, Phys. Rev. Lett. 131, 167101 (2023).
  15. N. Ohga, S. Ito, and A. Kolchinsky, Thermodynamic bound on the asymmetry of cross-correlations, Phys. Rev. Lett. 131, 077101 (2023).
  16. D. J. Skinner and J. Dunkel, Estimating entropy production from waiting time distributions, Phys. Rev. Lett. 127, 198101 (2021).
  17. J. van der Meer, B. Ertel, and U. Seifert, Thermodynamic inference in partially accessible Markov networks: A unifying perspective from transition-based waiting time distributions, Phys. Rev. X 12, 031025 (2022).
  18. P. E. Harunari, A. Dutta, M. Polettini, and E. Roldan, What to learn from a few visible transitions’ statistics? Phys. Rev. X 12, 041026 (2022).
  19. J. van der Meer, J. Degünther, and U. Seifert, Time-Resolved statistics of snippets as general framework for model-free entropy estimators, Phys. Rev. Lett. 130, 257101 (2023).
  20. K. Blom, K. Song, E. Vouga, A. Godec, and D. E. Makarov, Milestoning estimators of dissipation in systems observed at a coarse resolution, Proc. Natl. Acad. Sci. USA 121, e2318333121 (2024).
  21. A. Murugan, D. A. Huse, and S. Leibler, Speed, dissipation, and error in kinetic proofreading, Proc. Natl. Acad. Sci. USA 109, 12034 (2012).
  22. P. Sartori and S. Pigolotti, Thermodynamics of error correction, Phys. Rev. X 5, 041039 (2015).
  23. J. D. Mallory, O. A. Igoshin, and A. B. Kolomeisky, Do we understand the mechanisms used by biological systems to correct their errors? J. Phys. Chem. B 124, 9289 (2020).
  24. H. Boeger, Kinetic proofreading, Annu. Rev. Biochem. 91, 423 (2022).
  25. J. Degünther, J. van der Meer, and U. Seifert, General theory for localizing the where and when of entropy production meets single-molecule experiments, Proc. Natl. Acad. Sci. USA 121, e2405371121 (2024).
  26. L. Vollmar, R. Bebon, J. Schimpf, B. Flietel, S. Celiksoy, C. Sönnichsen, A. Godec, and T. Hugel, Model-free inference of memory in conformational dynamics of a multi-domain protein, J. Phys. A: Math. Theor. 57, 365001 (2024).
  27. O. A. Igoshin, A. B. Kolomeisky, and D. E. Makarov, Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states, J. Chem. Phys. 162, 034111 (2025).
  28. D. Hartich and A. Godec, Emergent memory and kinetic hysteresis in strongly driven networks, Phys. Rev. X 11, 041047 (2021).
  29. A. Godec and D. E. Makarov, Challenges in inferring the directionality of active molecular processes from single-molecule fluorescence resonance energy transfer trajectories, J. Phys. Chem. Lett. 14, 49 (2023).
  30. J. Mehl, B. Lander, C. Bechinger, V. Blickle, and U. Seifert, Role of hidden slow degrees of freedom in the fluctuation theorem, Phys. Rev. Lett. 108, 220601 (2012).
  31. T. Ariga, M. Tomishige, and D. Mizuno, Nonequilibrium energetics of molecular motor kinesin, Phys. Rev. Lett. 121, 218101 (2018).
  32. Y. Nakayama and S. Toyabe, Optimal rectification without forward-current suppression by biological molecular motor, Phys. Rev. Lett. 126, 208101 (2021).
  33. K. Song, D. E. Makarov, and E. Vouga, Information-theoretical limit on the estimates of dissipation by molecular machines using single-molecule fluorescence resonance energy transfer experiments, J. Chem. Phys. 161, 044111 (2024).
  34. R. Kawai, J. M. R. Parrondo, and C. van den Broeck, Dissipation: The phase-space perspective, Phys. Rev. Lett. 98, 080602 (2007).
  35. A. Gomez-Marin, J. Parrondo, and C. van den Broeck, The “footprints” of irreversibility, Europhys. Lett. 82, 50002 (2008).
  36. E. Roldan and J. M. R. Parrondo, Estimating dissipation from single stationary trajectories, Phys. Rev. Lett. 105, 150607 (2010).
  37. M. Nielsen and I. Chuang, Quantum Computation and Quantum Information: 10th Anniversary Edition (Cambridge University Press, Cambridge, UK, 2010).
  38. D. Hartich and A. Godec, Comment on “Inferring broken detailed balance in the absence of observable currents”, Nat. Commun. 15, 8678 (2024).
  39. G. Bisker, I. A. Martínez, J. M. Horowitz, and J. M. R. Parrondo, Reply to: Comment on “Inferring broken detailed balance in the absence of observable currents”, Nat. Commun. 15, 8679 (2024).
  40. R. Bao, N. Ohga, and S. Ito, Measuring irreversibility by counting: A random coarse-graining framework, arXiv:2508.11586.
  41. K. Sekimoto, Derivation of the first passage time distribution for Markovian process on discrete network, arXiv:2110.02216.

Outline

Information

Sign In to Your Journals Account

Filter

Filter

Article Lookup

Enter a citation