Skip to main content
SpringerLink
Log in

Introduction

  • Chapter
  • First Online:
Stochastic Dynamics and Energetics of Biomolecular Systems

Part of the book series: Springer Theses ((Springer Theses))

  • 590 Accesses

Abstract

The chapter presents introduction and outline of the book.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. D. Chowdhury, L. Santen, A. Schadschneider, Statistical physics of vehicular traffic and some related systems. Phys. Rep. 329, 199 (2000). doi:10.1016/S0370-1573(99)00117-9

    Article  MathSciNet  ADS  Google Scholar 

  2. R.J. Boucherie, N.M. van Dijk (eds.), Queueing Networks (Springer, New York, 2011). ISBN 978-1-4419-6471-7. doi:10.1007/978-1-4419-6472-4

    Google Scholar 

  3. D. Helbing, P. Molnár, I.J. Farkas, K. Bolay, Self-organizing pedestrian movement. Env. Plan. B 28, 361 (2001). doi:10.1068/b2697

    Article  Google Scholar 

  4. A. John, A. Schadschneider, D. Chowdhury, K. Nishinari, Trafficlike collective movement of ants on trails: absence of a jammed phase. Phys. Rev. Lett. 102, 108001 (2009). doi:10.1103/PhysRevLett.102.108001

    Article  ADS  Google Scholar 

  5. J. Männik, R. Driessen, P. Galajda, J.E. Keymer, C. Dekker, Bacterial growth and motility in sub-micron constrictions. PNAS 106, 14861 (2009). doi:10.1073/pnas.0907542106

    Article  ADS  Google Scholar 

  6. P.C. Bressloff, J.M. Newby, Stochastic models of intracellular transport. Rev. Mod. Phys. 85, 135 (2013). doi:10.1103/RevModPhys.85.135

    Article  ADS  Google Scholar 

  7. B. Alberts, D. Bray, K. Hopkin, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter, Essential Cell Biology, 3rd edn. (Taylor and Francis Group, Garland Science, New York, 2010)

    Google Scholar 

  8. A.L. Hodgkin, R.D. Keynes, The potassium permeability of a giant nerve fibre. J. Physiol. 128, 61 (1955). http://jp.physoc.org/content/128/1/61

    Google Scholar 

  9. A. Granéli, C.C. Yeykal, R.B. Robertson, E.C. Greene, Long-distance lateral diffusion of human Rad51 on double-stranded DNA. PNAS 103, 1221 (2006). doi:10.1073/pnas.0508366103

    Article  ADS  Google Scholar 

  10. G.-W. Li, O.G. Berg, J. Elf, Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat. Phys. 5, 294 (2009). doi:10.1038/nphys1222

    Article  Google Scholar 

  11. P.M. Richards, Theory of one-dimensional hopping conductivity and diffusion. Phys. Rev. B 16, 1393 (1977). doi:10.1103/PhysRevB.16.1393

    Article  MathSciNet  ADS  Google Scholar 

  12. P.A. Fedders, Two-point correlation functions for a distinguishable particle hopping on a uniform one-dimensional chain. Phys. Rev. B 17, 40 (1978). doi:10.1103/PhysRevB.17.40

    Article  ADS  Google Scholar 

  13. T.T. Perkins, D.E. Smith, S. Chu, Direct observation of tube-like motion of a single polymer chain. Science 264, 819 (1994). doi:10.1126/science.8171335

    Article  ADS  Google Scholar 

  14. K. Hahn, J. Kärger, V. Kukla, Single-file diffusion observation. Phys. Rev. Lett. 76, 2762 (1995). doi:10.1103/PhysRevLett.76.2762

    Article  ADS  Google Scholar 

  15. V. Gupta, S.S. Nivarthi, A.V. McCormick, H.T. Davis, Evidence for single file diffusion of ethane in the molecular sieve AlPO\(_{4}\)-5. Chem. Phys. Lett. 247, 596 (1995). doi:10.1016/S0009-2614(95)01246-X

    Article  ADS  Google Scholar 

  16. V. Kukla, J. Kornatowski, D. Demuth, I. Girnus, H. Pfeifer, L.V.C. Rees, S. Schunk, K.K. Unger, J. Kärger, NMR studies of single-file diffusion in unidimensional channel zeolites. Science 272, 702 (1996). doi:10.1126/science.272.5262.702

    Article  ADS  Google Scholar 

  17. D. Keffer, The temperature dependence of single-file separation mechanisms in one-dimensional nanoporous materials. Chem. Eng. J. 74, 33 (1999). doi:10.1016/S1385-8947(99)00061-3

    Article  Google Scholar 

  18. J. Kärger, D.M. Ruthven, D.N. Theodorou, Diffusion in Nanoporous Materials, vol. 1 (Wiley, Weinheim, 2012)

    Book  Google Scholar 

  19. C.-Y. Cheng, C.R. Bowers, Observation of Single-File diffusion in dipeptide nanotubes by continuous-flow hyperpolarized xenon-129 NMR spectroscopy. ChemPhysChem 8, 2077 (2007). doi:10.1002/cphc.200700336

    Article  Google Scholar 

  20. Q.-H. Wei, C. Bechinger, P. Leiderer, Single-file diffusion of colloids in one-dimensional channels. Science 287, 625 (2000). doi:10.1126/science.287.5453.625

    Article  ADS  Google Scholar 

  21. C. Lutz, M. Kollmann, P. Leiderer, C. Bechinger, Diffusion of colloids in one-dimensional light channels. J. Phys. Condens. Matter 16, S4075 (2004). doi:10.1088/0953-8984/16/38/022

    Article  ADS  Google Scholar 

  22. C. Lutz, M. Kollmann, C. Bechinger, Single-file diffusion of colloids in one-dimensional channels. Phys. Rev. Lett. 93, 026001 (2004). doi:10.1103/PhysRevLett.93.026001

    Article  ADS  Google Scholar 

  23. B. Cui, H. Diamant, B. Lin, Screened hydrodynamic interaction in a narrow channel. Phys. Rev. Lett. 89, 188302 (2002). doi:10.1103/PhysRevLett.89.188302

    Article  ADS  Google Scholar 

  24. B. Lin, M. Meron, B. Cui, S.A. Rice, H. Diamant, From random walk to single-file diffusion. Phys. Rev. Lett. 94, 216001 (2005). doi:10.1103/PhysRevLett.94.216001

    Article  ADS  Google Scholar 

  25. P. Tierno, F. Sagués, T.H. Johansen, I.M. Sokolov, Evidence of Rouse-like dynamics in magnetically ratchetting colloidal chains. Soft Matter 7, 7944 (2011). doi:10.1039/c1sm05601h

    Article  ADS  Google Scholar 

  26. U. Siems, C. Kreuter, A. Erbe, N. Schwierz, S. Sengupta, P. Leiderer, P. Nielaba, Non-monotonic crossover from single-file to regular diffusion in micro-channels. Sci. Rep. 2, 1015 (2012). doi:10.1038/srep01015

    Article  ADS  Google Scholar 

  27. T.E. Harris, Diffusion with “collisions” between particles. J. Appl. Probab. 2, 323 (1965). doi:10.2307/3212197

    Article  Google Scholar 

  28. T. Chou, K. Mallick, R.K.P. Zia, Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport. Rep. Prog. Phys. 74, 116601 (2011). doi:10.1088/0034-4885/74/11/116601

    Article  MathSciNet  ADS  Google Scholar 

  29. R.A. Blythe, M.R. Evans, Nonequilibrium steady states of matrix-product form: a solver’s guide. J. Phys. A Math. Theor. 40, R333 (2007). doi:10.1088/1751-8113/40/46/R01

    Article  MathSciNet  ADS  MATH  Google Scholar 

  30. M.R. Evans, T. Hanney, Nonequilibrium statistical mechanics of the zero-range process and related models. J. Phys. A Math. Gen. 38, R195 (2005). doi:10.1088/0305-4470/38/19/R01

    Article  MathSciNet  ADS  MATH  Google Scholar 

  31. G.M. Schütz, Critical phenomena and universal dynamics in one-dimensional driven diffusive systems with two species of particles. J. Phys. A Math. Gen. 36, R339 (2003). doi:10.1088/0305-4470/36/36/201

    Article  MATH  Google Scholar 

  32. P.L. Krapivsky, S. Redner, E. Ben-Naim, A Kinetic View of Statistical Physics (Cambridge University Press, Cambridge, 2010). ISBN -13 978-0-521-85103-9

    Book  MATH  Google Scholar 

  33. H. Risken, The Fokker-Planck Equation: Methods of Solutions and Applications, 2nd edn. (Springer, Berlin, 1989)

    Book  MATH  Google Scholar 

  34. K. Sekimoto, Stochastic Energetics. in Lecture Notes in Physics, vol. 799. (Springer, Berlin, 2010). ISBN 978-3-642-05410-5. doi:10.1007/978-3-642-05411-2

    Google Scholar 

  35. U. Seifert, Stochastic thermodynamics, fluctuation theorems and molecular machines. Rep. Prog. Phys. 75, 126001 (2012). doi:10.1088/0034-4885/75/12/126001

    Article  ADS  Google Scholar 

  36. K. Sekimoto, Kinetic characterization of heat bath and the energetics of thermal ratchet models. J. Phys. Soc. Jpn. 66, 1234 (1997). doi:10.1143/JPSJ.66.1234

    Article  ADS  Google Scholar 

  37. K. Sekimoto, Langevin equation and thermodynamics. Prog. Theor. Phys. Suppl. 130, 17 (1998). doi:10.1143/PTPS.130.17

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Macromolecular Physics, Charles University in Prague, Prague, Czech Republic

    Artem Ryabov

Authors
  1. Artem Ryabov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Artem Ryabov .

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Ryabov, A. (2016). Introduction. In: Stochastic Dynamics and Energetics of Biomolecular Systems. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-27188-0_1

Download citation

Publish with us

Policies and ethics

Search

Navigation