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An estimator of entropy production for partially accessible Markov networks based on the observation of blurred transitions

Published 13 Dec 2023 in cond-mat.stat-mech | (2312.08246v2)

Abstract: A central task in stochastic thermodynamics is the estimation of entropy production for partially accessible Markov networks. We establish an effective transition-based description for such networks with transitions that are not distinguishable and therefore blurred for an external observer. We demonstrate that, in contrast to a description based on fully resolved transitions, this effective description is typically non-Markovian at any point in time. Starting from an information-theoretic bound, we derive an operationally accessible entropy estimator for this observation scenario. We illustrate the operational relevance and the quality of this entropy estimator with a numerical analysis of various representative examples.

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  1. K. Sekimoto, Stochastic Energetics, Lecture Notes in Physics (Springer Berlin Heidelberg, Berlin, Heidelberg, 2010).
  2. C. Jarzynski, Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale, Annu. Rev. Condens. Matter Phys. 2, 329 (2011).
  3. U. Seifert, Stochastic thermodynamics, fluctuation theorems and molecular machines, Rep. Prog. Phys. 75, 126001 (2012).
  4. T. Schmiedl and U. Seifert, Stochastic thermodynamics of chemical reaction networks, J. Chem. Phys. 126, 044101 (2007).
  5. H. Ge, M. Qian, and H. Qian, Stochastic theory of nonequilibrium steady states. part ii: Applications in chemical biophysics, Phys. Rep. 510, 87 (2012).
  6. R. Rao and M. Esposito, Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics, Phys. Rev. X 6, 041064 (2016).
  7. M. Esposito, Stochastic thermodynamics under coarse graining, Phys. Rev. E 85, 041125 (2012).
  8. M. Uhl, P. Pietzonka, and U. Seifert, Fluctuations of apparent entropy production in networks with hidden slow degrees of freedom, J. Stat. Mech. 2018 (2), 023203.
  9. S. Bo and A. Celani, Multiple-scale stochastic processes: Decimation, averaging and beyond, Phys. Rep. 670, 1 (2017).
  10. S. Rahav and C. Jarzynski, Fluctuation relations and coarse-graining, J. Stat. Mech. 2007 (09), P09012.
  11. A. Gomez-Marin, J. M. R. Parrondo, and C. Van den Broeck, Lower bounds on dissipation upon coarse graining, Phys. Rev. E 78, 011107 (2008).
  12. S. Bo and A. Celani, Entropy production in stochastic systems with fast and slow time-scales, J. Stat. Phys. 154, 1325 (2014).
  13. D. Seiferth, P. Sollich, and S. Klumpp, Coarse graining of biochemical systems described by discrete stochastic dynamics, Phys. Rev. E 102, 062149 (2020).
  14. E. Roldán and J. M. R. Parrondo, Estimating dissipation from single stationary trajectories, Phys. Rev. Lett. 105, 150607 (2010).
  15. E. Roldán and J. M. R. Parrondo, Entropy production and Kullback-Leibler divergence between stationary trajectories of discrete systems, Phys. Rev. E 85, 031129 (2012).
  16. N. Shiraishi and T. Sagawa, Fluctuation theorem for partially masked nonequilibrium dynamics, Phys. Rev. E 91, 012130 (2015).
  17. M. Polettini and M. Esposito, Effective Thermodynamics for a Marginal Observer, Phys. Rev. Lett. 119, 240601 (2017).
  18. A. C. Barato and U. Seifert, Thermodynamic Uncertainty Relation for Biomolecular Processes, Phys. Rev. Lett. 114, 158101 (2015).
  19. P. Pietzonka, A. C. Barato, and U. Seifert, Universal bounds on current fluctuations, Phys. Rev. E 93, 052145 (2016).
  20. R. Marsland, W. Cui, and J. M. Horowitz, The thermodynamic uncertainty relation in biochemical oscillations, J. R. Soc. Interface 16, 20190098 (2019).
  21. J. M. Horowitz and T. R. Gingrich, Thermodynamic uncertainty relations constrain non-equilibrium fluctuations, Nat. Phys. 16, 15 (2020).
  22. P. Pietzonka and F. Coghi, Thermodynamic cost for precision of general counting observables, arXiv:2305.15392 [cond-mat.stat-mech]  (2023).
  23. G. Teza and A. L. Stella, Exact coarse graining preserves entropy production out of equilibrium, Phys. Rev. Lett. 125, 110601 (2020).
  24. J. Ehrich, Tightest bound on hidden entropy production from partially observed dynamics, J. Stat. Mech. 2021 (8), 083214.
  25. D. J. Skinner and J. Dunkel, Improved bounds on entropy production in living systems, Proc. Natl. Acad. Sci. 118 (2021a).
  26. R. Elber, Milestoning: An efficient approach for atomically detailed simulations of kinetics in biophysics, Annu. Rev. Biophys. 49, 69 (2020).
  27. D. Hartich and A. Godec, Violation of local detailed balance despite a clear time-scale separation, arXiv:2111.14734 [cond-mat.stat-mech]  (2021a).
  28. A. M. Berezhkovskii and D. E. Makarov, On the forward/backward symmetry of transition path time distributions in nonequilibrium systems, J. Chem. Phys. 151, 065102 (2019).
  29. D. Hartich and A. Godec, Emergent memory and kinetic hysteresis in strongly driven networks, Phys. Rev. X 11, 041047 (2021b).
  30. D. Hartich and A. Godec, Comment on ”inferring broken detailed balance in the absence of observable currents”, arXiv:2111.14734 [cond-mat.stat-mech]  (2021c).
  31. D. J. Skinner and J. Dunkel, Estimating Entropy Production from Waiting Time Distributions, Phys. Rev. Lett. 127, 198101 (2021b).
  32. 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).
  33. X. Li and A. B. Kolomeisky, Mechanisms and topology determination of complex chemical and biological network systems from first-passage theoretical approach, J. Chem. Phys 139, 10.1063/1.4824392 (2013).
  34. A. M. Berezhkovskii and D. E. Makarov, From Nonequilibrium Single-Molecule Trajectories to Underlying Dynamics, J. Phys. Chem. Lett. 11, 1682 (2020).
  35. B. Ertel, J. van der Meer, and U. Seifert, Waiting time distributions in hybrid models of motor–bead assays: A concept and tool for inference, Int. J. Mol. Sci. 24, 7610 (2023).
  36. 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).
  37. J. Degünther, J. van der Meer, and U. Seifert, Fluctuating entropy production on the coarse-grained level: Inference and localization of irreversibility, arXiv:2309.07665 [cond-mat.stat-mech]  (2023).
  38. H. Wang and H. Qian, On detailed balance and reversibility of semi-markov processes and single-molecule enzyme kinetics, J. Math. Phys. 48, 013303 (2007).
  39. C. Maes, K. Netočný, and B. Wynants, Dynamical fluctuations for semi-markov processes, J. Phys. A: Math. Theor. 42, 365002 (2009).
  40. B. Ertel, J. van der Meer, and U. Seifert, Operationally accessible uncertainty relations for thermodynamically consistent semi-markov processes, Phys. Rev. E 105, 044113 (2022).
  41. 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).
  42. T. L. Hill, Free Energy Transduction and Biochemical Cycle Kinetics (Springer New York, 1989).
  43. D.-Q. Jiang, M. Qian, and M.-P. Qian, Mathematical Theory of Nonequilibrium Steady States (Springer Berlin Heidelberg, 2004).
  44. T. M. Cover and J. A. Thomas, Elements of Information Theory (Wiley Series in Telecommunications and Signal Processing) (Wiley-Interscience, USA, 2006).
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