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Characterizing the detailed balance property by means of measurements in chemical networks

Published 20 Feb 2024 in math-ph, math.DS, and math.MP | (2402.12935v1)

Abstract: In this paper we study how to determine if a linear biochemical network satisfies the detailed balance condition, without knowing the details of all the reactions taking place in the network. To this end, we use the formalism of response functions $R_{ij} (t) $ that measure how the system reacts to the injection of the substance $j$ at time $t=0$, by measuring the concentration of the substance $i \neq j$ for $t >0$. In particular, we obtain a condition involving two reciprocal measurements (i.e.~$R_{ij}(t), \, R_{ji}(t)$) that is necessary, but not sufficient for the detailed balance condition to hold in the network. Moreover, we prove that this necessary condition is also sufficient if a topological condition is satisfied, as well as a stability property that guarantees that the chemical rates are not fine-tuned.

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References (28)
  1. Molecular biology of the cell. Garland Science, 4th edition, 2002.
  2. Broken detailed balance at mesoscopic scales in active biological systems. Science, 352(6285):604–607, 2016.
  3. H. Boeger. Kinetic proofreading. Annual Review of Biochemistry, 91(1):423–447, 2022.
  4. J. Bondy and U. Murty. Graph Theory with Applications. American Elsevier Publishing Company, 1976.
  5. R. Boyd. Detailed balance in chemical kinetics as a consequence of microscopic reversibility. The Journal of Chemical Physics, 60(4):1214–1222, 1974.
  6. Geometry of nonequilibrium reaction networks. Physical Review X, 13(2):021040, 2023.
  7. M. Feinberg. Complex balancing in general kinetic systems. Archive for Rational Mechanics and Analysis, 49(3):187–194, 1972.
  8. M. Feinberg. On chemical kinetics of a certain class. Archive for Rational Mechanics and Analysis, 46:1–41, 1972.
  9. M. Feinberg. Foundations of Chemical Reaction Network Theory. Springer International Publishing, 2019.
  10. W. Feller. An introduction to probability theory and its applications II. John Wiley & Sons, 1966.
  11. ABC transporters are billion-year-old Maxwell demons. Communications Physics, 6(1):205, 2023.
  12. Description of chemical systems by means of response functions. arXiv:2309.02021, 2023.
  13. J. Hefferon. Linear algebra. Orthogonal Publishing L3c, 2017.
  14. J. J. Hopfield. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proceedings of the National Academy of Sciences, 71(10):4135–4139, 1974.
  15. V. Isakov. Inverse problems for partial differential equations. Springer, 2006.
  16. Entropy production fluctuations of finite Markov chains. Journal of Mathematical Physics, 44(9):4176–4188, 2003.
  17. J. Keener and J. Sneyd. Mathematical physiology. Springer New York, 1998.
  18. S. Kurbel. Donnan effect on chloride ion distribution as a determinant of body fluid composition that allows action potentials to spread via fast sodium channels. Theoretical Biology and Medical Modelling, 8:1–9, 2011.
  19. Quantifying dissipation using fluctuating currents. Nature communications, 10(1):1666, 2019.
  20. M. O. Magnasco. Molecular combustion motors. Physical Review Letters, 72(16):2656, 1994.
  21. Inferring broken detailed balance in the absence of observable currents. Nature communications, 10(1):3542, 2019.
  22. Y. Mori. Mathematical properties of pump-leak models of cell volume control and electrolyte balance. Journal of Mathematical Biology, 65:875–918, 2012.
  23. J. Ninio. Kinetic amplification of enzyme discrimination. Biochimie, 57(5):587–595, 1975.
  24. Metabolite–enzyme coevolution: from single enzymes to metabolic pathways and networks. Annual Review of Biochemistry, 87:187–216, 2018.
  25. Modeling cell-to-cell communication networks using response-time distributions. Cell Systems, 6(3):355–367, 2018.
  26. Actin filaments and the growth, movement, and spread of the intracellular bacterial parasite, Listeria monocytogenes. The Journal of Cell Biology, 109(4):1597–1608, 1989.
  27. D. Tosteson and J. Hoffman. Regulation of cell volume by active cation transport in high and low potassium sheep red cells. The Journal of General Physiology, 44(1):169–194, 1960.
  28. R. K. Zia and B. Schmittmann. Probability currents as principal characteristics in the statistical mechanics of non-equilibrium steady states. Journal of Statistical Mechanics: Theory and Experiment, 2007(7):P07012, 2007.

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