Fractional Cooperativity of a Few-State System in the Environment

Authors

  • V. I. Teslenko Bogolyubov Institute for Theoretical Physics, Nat. Acad. of Sci. of Ukraine
  • O. L. Kapitanchuk Bogolyubov Institute for Theoretical Physics, Nat. Acad. of Sci. of Ukraine

DOI:

https://doi.org/10.15407/ujpe60.11.1163

Keywords:

irreversible kinetic processes, energy fluctuations, dissipating environment, cooperativity, Hill’s coefficient, ligand-receptor assembly

Abstract

Cooperativity represents a type of the not well-defined quantities implemented in different fields ranging from physics to chemistry, biology, informatics, etc. In the present work, we define the cooperativity from the physical point of view by relating it to the stability of a few-state system with respect to the irreversibility. First, we reduce this system evolving in time to the pair of fluctuating energy levels of different dimensionalities with the initial population of one level, different probabilities of microscopically reversible transitions between the levels, and some probability of irreversible decay of another level. Then we make an average of the reduced system over the energy level fluctuations to provide between-level transition rates with the explicit impacts of external controls on levels’ positions and dimensionalities. Finally, we demonstrate the emergence of the cooperativity of a fractional degree ranging between 2/e and unity when normalized in this system and observe that, at the lower bound of such degree, the system becomes unstable, so that, to restore the stability, one needs either to decrease the irreversible decay rate or to make the reversible backward transitions faster.

References

J. Gates, The Ownership Solution (Penguin, London, 1998).

J. Rothschild and J. Allen-Whitt, The Cooperative Workplace (Cambridge Univ. Press, Cambridge, 1986).

H. Hotelling, Economic J. 39, 41 (1929). https://doi.org/10.2307/2224214

C. Bohr, Zentralblatt Physiol. 23, 688 (1904).

A.J. Clark, The Mode of Action of Drugs on Cells (Edward Arnold, London, 1933)

J.B.S. Haldane, Enzymes (MIT Press, Cambridge, MA, 1965).

F.C. Frank, Proc. Roy. Soc. A 215, 43 (1952). https://doi.org/10.1098/rspa.1952.0194

A.W. Adamson, J. Am. Chem. Soc. 76, 1578 (1954). https://doi.org/10.1021/ja01635a030

F.H. Stillinger and T.A. Weber, Phys. Rev. A 28, 2408 (1983). https://doi.org/10.1103/PhysRevA.28.2408

K.A. Connors, Binding Constants: The Measurements of Molecular Complex Stability (Wiley, New York, 1987).

P. Hobza and R. Zahradnik, Intermolecular Complexes (Elsevier, Amsterdam, 1988).

J.-M. Lehn, Supramolecular Chemistry: Concepts and Perspectives (Wiley-VCH, Weinheim, 1995). https://doi.org/10.1002/3527607439

J.C. Dyre, Rev. Mod. Phys. 78, 953 (2006). https://doi.org/10.1103/RevModPhys.78.953

A.V. Hill, J. Physiol. 40, 389 (1910). https://doi.org/10.1113/jphysiol.1910.sp001377

R. Heinrich and T.A. Rapoport, Acta Biol. Med. Ger. 31, 479 (1973).

J. H. Hofmeyr and A. Cornish-Bowden, Eur. J. Biochem. 200, 223 (1991). https://doi.org/10.1111/j.1432-1033.1991.tb21071.x

R. Heinrich and S. Schuster, The Regulation of Cellular Systems (Chapman and Hall, New York, 1996).

G.S. Adair, J. Biol. Chem. 63, 529 (1925).

L. Pauling, Proc. Nat. Acad. Sci. USA 21, 186 (1935). https://doi.org/10.1073/pnas.21.4.186

J. Monod, J. Wyman and J.-P. Changeux, J. Mol. Biol. 12, 88 (1965). https://doi.org/10.1016/S0022-2836(65)80285-6

D.E. Koshland, Jr., G. Nemethy, and D. Filmer, Biochemistry 5, 365 (1966). https://doi.org/10.1021/bi00865a047

W.G. Bardsley and R.E. Childs, Biochem. J. 149, 313 (1975). https://doi.org/10.1042/bj1490313

J. Ricard and A. Cornish-Bowden, Eur. J. Biochem. 166, 255 (1987). https://doi.org/10.1111/j.1432-1033.1987.tb13510.x

A.L. Horovitz and A.R. Fersht, J. Mol. Biol. 214, 613 (1990). https://doi.org/10.1016/0022-2836(90)90275-Q

T. Shem-Ad and O. Yifrach, J. Gen. Physiol. 141, 507 (2013). https://doi.org/10.1085/jgp.201310976

A. Cornish-Bowden, FEBS J. 281, 621 (2014). https://doi.org/10.1111/febs.12469

Q. Cui and M. Karplus, Protein Sci. 17, 1295 (2008). https://doi.org/10.1110/ps.03259908

G.R. Fleming and M. Ratner, Phys. Today July, 28 (2008). https://doi.org/10.1063/1.2963009

H.E. Stanley, Rev. Mod. Phys. 71, S358 (1999). https://doi.org/10.1103/RevModPhys.71.S358

K. Lindenberg and B.J. West, The Nonequilibrium Statistical Mechanics of Open and Closed Systems (Wiley-VCH, New York, 1990).

A. Rivas and S.F. Huelga, Open Quantum Systems: An Introduction (Springer, Heidelberg, 2012). https://doi.org/10.1007/978-3-642-23354-8

C.H. Fleming and B.L. Hu, Ann. Phys. 327, 1238 (2012). https://doi.org/10.1016/j.aop.2011.12.006

M.A. Miller, J.P.K. Doe, and D.J. Wales, Phys. Rev. E 60, 3701 (1999). https://doi.org/10.1103/PhysRevE.60.3701

Y. Levy, J. Jortner, and R.S. Berry, Phys. Chem. Chem. Phys. 4, 5052 (2002). https://doi.org/10.1039/b203534k

J. Cao and R.J. Silbey, J. Phys. Chem. A 113, 13825 (2009). https://doi.org/10.1021/jp9032589

Y.R. Chemla, J.R. Moffitt, and C. Bustamante, J. Phys. Chem. B 112, 6025 (2008). https://doi.org/10.1021/jp076153r

A.I. Burshtein, Adv. Phys. Chem. 2009, 214219 (2009). https://doi.org/10.1155/2009/214219

G. Lindblad, Nonequilibrium Entropy and Irreversibility (Reidel, Dordrecht, 1983). https://doi.org/10.1007/978-94-009-7206-3

E.C.G. Sudarshan, Phys. Rev. A 46, 37 (1992). https://doi.org/10.1103/PhysRevA.46.37

N.N. Bogoliubov, Lectures on Quantum Statistics (Gordon and Breach, New York, 1967), Vol. 1.

N.N. Bogoliubov, Lectures on Quantum Statistics (Gordon and Breach, New York, 1970), Vol. 2.

S. Nakajima, Progr. Theor. Phys. 20, 948 (1958). https://doi.org/10.1143/PTP.20.948

R. Zwanzig, J. Chem. Phys. 33, 1338 (1960). https://doi.org/10.1063/1.1731409

E.G. Petrov, Eur. Phys. J. Special Topics 216, 205 (2013). https://doi.org/10.1140/epjst/e2013-01744-0

I. Goychuk and P. Hanggi, Adv. Phys. 54, 525 (2005). https://doi.org/10.1080/00018730500429701

E.G. Petrov and V.I. Teslenko, Theor. Math. Phys. 84, 986 (1991). https://doi.org/10.1007/BF01017358

E.G. Petrov, V.I. Teslenko, and I.A. Goychuk, Phys. Rev. E 49, 3894 (1994). https://doi.org/10.1103/PhysRevE.49.3894

E.G. Petrov, I.A. Goychuk, and V. May, Physica A 233, 560 (1996). https://doi.org/10.1016/S0378-4371(96)00252-X

V.I. Teslenko, E.G. Petrov, A. Verkhatsky, and O.A. Krishtal, Phys. Rev. Lett. 104, 178105 (2010). https://doi.org/10.1103/PhysRevLett.104.178105

E.G. Petrov and V.I. Teslenko, Chem. Phys. 375, 243 (2010). https://doi.org/10.1016/j.chemphys.2010.05.029

V.I. Teslenko and O.L. Kapitanchuk, Int. J. Mod. Phys. B 27, 1350169 (2013). https://doi.org/10.1142/S0217979213501695

E. Langmann and G. Lindblad, J. Stat. Phys. 134, 749 (2009). https://doi.org/10.1007/s10955-009-9700-x

A. Nitzan, Chemical Dynamics in Condensed Phases (Oxford Univ. Press, Oxford, 2006).

R.D. Coalson, D.G. Evans, and A. Nitzan, J. Chem. Phys. 101, 436 (1994). https://doi.org/10.1063/1.468153

J. Jortner, J. Chem. Phys. 64, 4860 (1976). https://doi.org/10.1063/1.432142

J. Gunawardena, Mol. Biol. Cell 23, 517 (2012). https://doi.org/10.1091/mbc.E11-07-0643

B. Efron and R. Tibshirani, Science 253, 390 (1991). https://doi.org/10.1126/science.253.5018.390

K. Banerjee, B. Das, and G. Gangopadhyay, J. Chem. Phys. 136, 154502 (2012). https://doi.org/10.1063/1.3703505

S.S. Plotkin, J. Wang, and P.G. Wolynes, J. Phys. I 7, 395 (1997). https://doi.org/10.1051/jp1:1997168

V.N. Smelyanskiy, M.I. Dykman, H. Rabitz, and B.E. Vugmeister, Phys. Rev. Lett. 79, 3113 (1997). https://doi.org/10.1103/PhysRevLett.79.3113

A. Fiasconaro, B. Spagnolo, and S. Boccaletti, Phys. Rev E 72, 061110 (2005). https://doi.org/10.1103/PhysRevE.72.061110

G.G. Hammes, Proc. Natl. Acad. Sci. USA 79, 6881 (1982). https://doi.org/10.1073/pnas.79.22.6881

D. Alvarado, D.E. Klein, and M.A. Lemmon, Cell 142, 568 (2010). https://doi.org/10.1016/j.cell.2010.07.015

C. Czaplewski, A. Liwo, D.R. Ripoll, and H.A. Scheraga, J. Phys. Chem. B 109, 8108 (2005). https://doi.org/10.1021/jp040691b

L. Wang, R.A. Freisner, and B.J. Berne, Faraday Discuss. 146, 247 (2010). https://doi.org/10.1039/b925521b

A. Cornish-Bowden, Fundamentals of Enzyme Kinetics (Wiley-VCH, Weinheim, 2012).

H. Hooyberghs, B. Van Schaeybroeck, and J.O. Indekeu, Physica A 389, 2920 (2010). https://doi.org/10.1016/j.physa.2009.12.068

D. Wren and A.G. Bedeian, The Evolution of the Management Thought (Wiley, New York, 2009).

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Published

2019-01-10

Issue

Section

General problems of theoretical physics

How to Cite

Fractional Cooperativity of a Few-State System in the Environment. (2019). Ukrainian Journal of Physics, 60(11), 1163. https://doi.org/10.15407/ujpe60.11.1163

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