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  • Open Access

Thermodynamic uncertainty relation for first-passage times on Markov chains

Arnab Pal1,*, Shlomi Reuveni1,†, and Saar Rahav2,‡

  • 1School of Chemistry, Center for the Physics & Chemistry of Living Systems, Ratner Institute for Single Molecule Chemistry, and the Sackler Center for Computational Molecular & Materials Science, Tel Aviv University, 6997801 Tel Aviv, Israel
  • 2Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 3200008, Israel

  • *Corresponding author: arnabpal@mail.tau.ac.il
  • †shlomire@tauex.tau.ac.il
  • ‡rahavs@technion.ac.il

Phys. Rev. Research 3, L032034 – Published 6 August, 2021

DOI: https://doi.org/10.1103/PhysRevResearch.3.L032034

Abstract

We derive a thermodynamic uncertainty relation (TUR) for first-passage times (FPTs) on continuous time Markov chains. The TUR utilizes the entropy production coming from bidirectional transitions, and the net flux coming from unidirectional transitions, to provide a lower bound on FPT fluctuations. As every bidirectional transition can also be seen as a pair of separate unidirectional ones, our approach typically yields an ensemble of TURs. The tightest bound on FPT fluctuations can then be obtained from this ensemble by a simple and physically motivated optimization procedure. The results presented herein are valid for arbitrary initial conditions, out-of-equilibrium dynamics, and are therefore well suited to describe the inherently irreversible first-passage event. They can thus be readily applied to a myriad of first-passage problems that arise across a wide range of disciplines.

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References (75)

  1. S. Redner, A Guide to First-Passage Processes (Cambridge University Press, Cambridge, England 2001).
  2. A. Szabo, K. Schulten, and Z. Schulten, First passage time approach to diffusion controlled reactions, J. Chem. Phys. 72, 4350 (1980).
  3. A. Szabo, G. Lamm, and G. H. Weiss, Localized partial traps in diffusion processes and random walks, J. Stat. Phys. 34, 225 (1984).
  4. A. Nitzan, Chemical Dynamics in Condensed Phases: Relaxation, Transfer and Reactions in Condensed Molecular Systems (Oxford University Press, Oxford, 2006).
  5. O. Bénichou, C. Chevalier, J. Klafter, B. Meyer, and R. Voituriez, Geometry-controlled kinetics, Nat. Chem. 2, 472 (2010).
  6. Y. Scher and S. Reuveni, A Unified Approach to Gated Reactions on Networks, Phys. Rev. Lett. 127, 018301 (2021).
  7. J. J. Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc. Natl. Acad. Sci. USA 71, 4135 (1974).
  8. J. Ninio, Alternative to the steady-state method: Derivation of reaction rates from first-passage times and pathway probabilities, Proc. Natl. Acad. Sci. USA 84, 663 (1987).
  9. J. Cao, Michaelis-Menten equation and detailed balance in enzymatic networks, J. Phys. Chem. B 115, 5493 (2011).
  10. A. Murugan, D. A. Huse, and S. Leibler, Speed, dissipation, and error in kinetic proofreading, Proc. Natl. Acad. Sci. USA 109, 12034 (2012).
  11. S. Reuveni, M. Urbakh, and J. Klafter, Role of substrate unbinding in Michaelis-Menten enzymatic reactions, Proc. Natl. Acad. Sci. USA 111, 4391 (2014).
  12. D. Singh and S. Chaudhury, Statistical properties of fluctuating enzymes with dynamic cooperativity using a first passage time distribution formalism, J. Chem. Phys. 146, 145103 (2017).
  13. T. Robin, S. Reuveni, and M. Urbakh, Single-molecule theory of enzymatic inhibition, Nat. Commun. 9, 779 (2018).
  14. S. Condamin, O. Bénichou, V. Tejedor, R. Voituriez, and J. Klafter, First-passage times in complex scale-invariant media, Nature (London) 450, 77 (2007).
  15. I. Eliazar, T. Koren, and J. Klafter, Searching circular DNA strands, J. Phys.: Condens. Matter 19, 065140 (2007).
  16. O. Bénichou, C. Loverdo, M. Moreau, and R. Voituriez, Intermittent search strategies, Rev. Mod. Phys. 83, 81 (2011).
  17. T. Chou and M. R. D'Orsogna, First passage problems in biology, in First-Passage Phenomena and Their Applications (World Scientific, Singapore, 2014), pp. 306–345.
  18. S. Iyer-Biswas and A. Zilman, First-passage processes in cellular biology, in Advances in Chemical Physics, edited by S. A. Rice and A. R. Dinner (Wiley Online Library, New York, 2016), Vol. 160.
  19. A. J. Bray, S. N. Majumdar, and G. Schehr, Persistence and first-passage properties in nonequilibrium systems, Adv. Phys. 62, 225 (2013).
  20. R. Metzler, S. Redner, and G. Oshanin, Eds., First-Passage Phenomena and Their Applications (World Scientific, Singapore, 2014), Vol. 35.
  21. J. Klafter and I. M. Sokolov, First Steps in Random Walks: From Tools to Applications (Oxford University Press, New York, 2011).
  22. B. P. English, W. Min, A. M. Van Oijen, K. T. Lee, G. Luo, H. Sun, B. J. Cherayil, S. C. Kou, and X. S. Xie, Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited, Nat. Chem. Biol. 2, 87 (2006).
  23. S. C. Kou, B. J. Cherayil, W. Min, B. P. English, and X. S. Xie, Single-molecule Michaelis-Menten equations, J. Phys. Chem. B 109, 19068 (2005).
  24. J. R. Moffitt, Y. R. Chemla, and C. Bustamante, Methods in statistical kinetics, Methods Enzymol. 475, 221 (2010).
  25. J. R. Moffitt, Y. R. Chemla, and C. Bustamante, Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations, Proc. Natl. Acad. Sci. USA 107, 15739 (2010).
  26. J. R. Moffitt and C. Bustamante, Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations, FEBS J. 281, 498 (2014).
  27. A. L. Thorneywork, J. Gladrow, Y. Qing, M. Rico-Pasto, F. Ritort, H. Bayley, A. B. Kolomeisky, and U. F. Keyser, Direct detection of molecular intermediates from first-passage times, Sci. Adv. 6, eaaz4642 (2020).
  28. M. J. Schnitzer and S. M. Block, Statistical kinetics of processive enzymes, in Cold Spring Harbor Symposia on Quantitative Biology (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1995), Vol. 60, pp. 793–802.
  29. J. W. Shaevitz, S. M. Block, and M. J. Schnitzer, Statistical kinetics of macromolecular dynamics, Biophys. J. 89, 2277 (2005).
  30. A. B. Kolomeisky and M. E. Fisher, Molecular motors: A theorist's perspective, Annu. Rev. Phys. Chem. 58, 675 (2007).
  31. W. Xu, J. S. Kong, and P. Chen, Single-molecule kinetic theory of heterogeneous and enzyme catalysis, J. Phys. Chem. C 113, 2393 (2009).
  32. S. Yang, J. Cao, R. J. Silbey, and J. Sung, Quantitative interpretation of the randomness in single enzyme turnover times, Biophys. J. 101, 519 (2011).
  33. S. Chaudhury, Poisson indicator and Fano factor for probing dynamic disorder in single-molecule enzyme inhibition kinetics, J. Phys. Chem. B 118, 10405 (2014).
  34. S. Reuveni, Optimal Stochastic Restart Renders Fluctuations in First Passage Times Universal, Phys. Rev. Lett. 116, 170601 (2016).
  35. A. Pal and S. Reuveni, First Passage under Restart, Phys. Rev. Lett. 118, 030603 (2017).
  36. D. Singh and S. Chaudhury, Single-molecule kinetics of an enzyme in the presence of multiple substrates, ChemBioChem 19, 842 (2018).
  37. A. Pal, I. Eliazar, and S. Reuveni, First Passage under Restart with Branching, Phys. Rev. Lett. 122, 020602 (2019).
  38. A. Pal, Ł. Kuśmierz, and S. Reuveni, Search with home returns provides advantage under high uncertainty, Phys. Rev. Res. 2, 043174 (2020).
  39. K. Sekimoto, Stochastic Energetics (Springer, Berlin, 2010), Vol. 799.
  40. U. Seifert, Stochastic thermodynamics, fluctuation theorems and molecular machines, Rep. Prog. Phys. 75, 126001 (2012).
  41. C. Jarzynski, Equalities and inequalities: Irreversibility and the second law of thermodynamics at the nanoscale, Annu. Rev. Condens. Matter Phys. 2, 329 (2011).
  42. R. Klages, W. Just, and C. Jarzynski, Eds., Nonequilibrium Statistical Physics of Small Systems (Wiley-VCH, Berlin, 2013).
  43. C. Van den Broeck and M. Esposito, Ensemble and trajectory thermodynamics: A brief introduction, Physica A 418, 6 (2015).
  44. S. Ciliberto, Experiments in Stochastic Thermodynamics: Short History and Perspectives, Phys. Rev. X 7, 021051 (2017).
  45. C. Pezzato, C. Cheng, J. F. Stoddart, and R. D. Astumian, Mastering the non-equilibrium assembly and operation of molecular machines, Chem. Soc. Rev. 46, 5491 (2017).
  46. A. C. Barato and U. Seifert, Thermodynamic Uncertainty Relation for Biomolecular Processes, Phys. Rev. Lett. 114, 158101 (2015).
  47. 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).
  48. J. M. Horowitz and T. R. Gingrich, Thermodynamic uncertainty relations constrain non-equilibrium fluctuations, Nat. Phys. 16, 15 (2020).
  49. U. Seifert, From stochastic thermodynamics to thermodynamic inference, Annu. Rev. Condens. Matter Phys. 10, 171 (2019).
  50. J. M. Horowitz and T. R. Gingrich, Proof of the finite-time thermodynamic uncertainty relation for steady-state currents, Phys. Rev. E 96, 020103 (2017).
  51. P. Pietzonka, F. Ritort, and U. Seifert, Finite-time generalization of the thermodynamic uncertainty relation, Phys. Rev. E 96, 012101 (2017).
  52. K. Proesmans and C. Van den Broeck, Discrete-time thermodynamic uncertainty relation, Europhys. Lett. 119, 20001 (2017).
  53. A. C. Barato, R. Chetrite, A. Faggionato, and D. Gabrielli, Bounds on current fluctuations in periodically driven systems, New J. Phys. 20, 103023 (2018).
  54. A. Dechant and S. I. Sasa, Current fluctuations and transport efficiency for general Langevin systems, J. Stat. Mech. (2018) 063209.
  55. Y. Hasegawa and T. Van Vu, Uncertainty relations in stochastic processes: An information inequality approach, Phys. Rev. E 99, 062126 (2019).
  56. S. Ito and A. Dechant, Stochastic Time Evolution, Information Geometry, and the Cramér-Rao Bound, Phys. Rev. X 10, 021056 (2020).
  57. Y. Hasegawa and T. Van Vu, Fluctuation Theorem Uncertainty Relation, Phys. Rev. Lett. 123, 110602 (2019).
  58. G. Falasco, M. Esposito, and J. C. Delvenne, Unifying thermodynamic uncertainty relations, New J. Phys. 22, 053046 (2020).
  59. A. Pal, S. Reuveni, and S. Rahav, Thermodynamic uncertainty relation for systems with unidirectional transitions, Phys. Rev. Res. 3, 013273 (2021).
  60. K. Liu, Z. Gong, and M. Ueda, Thermodynamic Uncertainty Relation for Arbitrary Initial States, Phys. Rev. Lett. 125, 140602 (2020).
  61. T. Koyuk and U. Seifert, Thermodynamic Uncertainty Relation for Time-Dependent Driving, Phys. Rev. Lett. 125, 260604 (2020).
  62. J. P. Garrahan, Simple bounds on fluctuations and uncertainty relations for first-passage times of counting observables, Phys. Rev. E 95, 032134 (2017).
  63. T. R. Gingrich and J. M. Horowitz, Fundamental Bounds on First Passage Time Fluctuations for Currents, Phys. Rev. Lett. 119, 170601 (2017).
  64. G. Falasco and M. Esposito, Dissipation-Time Uncertainty Relation, Phys. Rev. Lett. 125, 120604 (2020).
  65. D. T. Gillespie, Markov Processes: An Introduction for Physical Scientists (Elsevier, Amsterdam, 1991).
  66. K. Hiura and S. I. Sasa, Kinetic uncertainty relation on first-passage time for accumulated current, Phys. Rev. E 103, L050103 (2021).
  67. V. Holubec, K. Kroy, and S. Steffenoni, Physically consistent numerical solver for time-dependent Fokker-Planck equations, Phys. Rev. E 99, 032117 (2019).
  68. J. S. Chang and G. Cooper, A practical difference scheme for Fokker-Planck equations, J. Comput. Phys. 6, 1 (1970).
  69. I. Di Terlizzi and M. Baiesi, Kinetic uncertainty relation, J. Phys. A: Math. Theor. 52, 02LT03 (2018).
  70. A. Dechant and S. I. Sasa, Fluctuation-response inequality out of equilibrium, Proc. Natl. Acad. Sci. USA 117, 6430 (2020).
  71. A. David and S. Larry, The least variable phase type distribution is Erlang, Stochastic Models 3, 467 (1987).
  72. A. C. Barato and U. Seifert, Skewness and Kurtosis in Statistical Kinetics, Phys. Rev. Lett. 115, 188103 (2015).
  73. S. Rahav and U. Harbola, An integral fluctuation theorem for systems with unidirectional transitions, J. Stat. Mech. (2014) P10044.
  74. A. Pal and S. Rahav, Integral fluctuation theorems for stochastic resetting systems, Phys. Rev. E 96, 062135 (2017).
  75. D. Gupta, C. A. Plata, and A. Pal, Work Fluctuations and Jarzynski Equality in Stochastic Resetting, Phys. Rev. Lett. 124, 110608 (2020).

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