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The European Physical Journal E

, Volume 28, Issue 4, pp 385–393 | Cite as

Polymer translocation in a double-force arrangement

  • S. T. T. Ollila
  • K. F. Luo
  • T. Ala-Nissila
  • S. -C. Ying
Regular Article

Abstract

Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F E < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared to the case under a single monomer pulling force of magnitude F - F E , but scaling of the translocation time as a function of the chain length \( \tau\)N 2 does not change. The waiting time \( \tau\)(m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m \( \approx\) N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing errors in double-force experiments.

PACS

36.20.-r Macromolecules and polymer molecules 82.37.-j Single molecule kinetics 

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References

  1. 1.
    J.J. Kasianowiczs, E. Brandin, D. Branton, D.W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996).Google Scholar
  2. 2.
    A. Meller, J. Phys.: Condens. Matter 15, R581 (2003).Google Scholar
  3. 3.
    M. Akeson, D. Branton, J.J. Kasianowicz, E. Brandin, D.W. Deamer, Biophys. J. 77, 3227 (1999).Google Scholar
  4. 4.
    A. Meller, L. Nivon, E. Brandin, J.A. Golovchenko, D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000).Google Scholar
  5. 5.
    A. Meller, L. Nivon, D. Branton, Phys. Rev. Lett. 86, 3435 (2001).Google Scholar
  6. 6.
    A. Meller, D. Branton, Electrophoresis 23, 2583 (2002).Google Scholar
  7. 7.
    M. Wanunu, A. Meller, Nano Lett. 7, 1580 (2007).Google Scholar
  8. 8.
    S.M. Iqbal, D. Akin, R. Bashir, Nat. Nanotech. 2, 243 (2007).Google Scholar
  9. 9.
    A.F. Sauer-Budge, J.A. Nyamwanda, D.K. Lubensky, D. Branton, Phys. Rev. Lett. 90, 238101 (2003).Google Scholar
  10. 10.
    J. Mathe, H. Visram, V. Viasnoff, Y. Rabin, A. Meller, Biophys. J. 87, 3205 (2004).Google Scholar
  11. 11.
    S.E. Henrickson, M. Misakian, B. Robertson, J.J. Kasianowicz, Phys. Rev. Lett. 85, 3057 (2000).Google Scholar
  12. 12.
    J.L. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz, J.A. Golovchenko, Nature (London) 412, 166 (2001)Google Scholar
  13. 13.
    D. Fologea, J. Uplinger, B. Thomas, D.S. McNabb, J.L. Li, Nano Lett. 2, 611 (2005).Google Scholar
  14. 14.
    H. Peng, S. Wu, S.R. Park, A. Potter, X.S. Ling, http:// meetings.aps.org/link/BAPS.2006.MAR.N26.10Google Scholar
  15. 15.
    U.F. Keyser, J.B.M. Koelman, S. van Dorp, D. Krapf, R.M.M. Smeets, S.G. Lemay, N.H. Dekker, C. Dekker, Nat. Phys. 2, 473 (2006).Google Scholar
  16. 16.
    U.F. Keyser, J. van der Does, C. Dekker, N.H. Dekker, Rev. Sci. Instrum. 77, 105105 (2006).Google Scholar
  17. 17.
    E.H. Trepagnier, A. Radenovic, D. Sivak, P. Geissler, J. Liphardt, Nano Lett. 7, 2824 (2007).Google Scholar
  18. 18.
    A.J. Storm, J.H. Chen, X.S. Ling, H.W. Zandbergen, C. Dekker, Nat. Mater. 2, 537 (2003).Google Scholar
  19. 19.
    A.J. Storm, C. Storm, J. Chen, H. Zandbergen, J.-F. Joanny, C. Dekker, Nano Lett. 5, 1193 (2005)Google Scholar
  20. 20.
    S.M. Simon, C.S. Peskin, G.F. Oster, Proc. Natl. Acad. Sci. U.S.A. 89, 3770 (1992).Google Scholar
  21. 21.
    W. Sung, P.J. Park, Phys. Rev. Lett. 77, 783 (1996)Google Scholar
  22. 22.
    E.A. diMarzio, A.L. Mandell, J. Chem. Phys. 107, 5510 (1997).Google Scholar
  23. 23.
    M. Muthukumar, J. Chem. Phys. 111, 10371 (1999)Google Scholar
  24. 24.
    D.K. Lubensky, D.R. Nelson, Biophys. J. 77, 1824 (1999).Google Scholar
  25. 25.
    Y. Kafri, D.K. Lubensky, D.R. Nelson, Biophys. J. 86, 3733 (2004).Google Scholar
  26. 26.
    E. Slonkina, A.B. Kolomeisky, J. Chem. Phys. 118, 7112 (2003).Google Scholar
  27. 27.
    T. Ambjornsson, S.P. Apell, Z. Konkoli, E.A. DiMarzio, J.J. Kasianowicz, J. Chem. Phys. 117, 4063 (2002)Google Scholar
  28. 28.
    R. Metzler, J. Klafter, Biophys. J. 85, 2776 (2003).Google Scholar
  29. 29.
    A. Baumgartner, J. Skolnick, Phys. Rev. Lett. 74, 2142 (1995).Google Scholar
  30. 30.
    J. Chuang, Y. Kantor, M. Kardar, Phys. Rev. E 65, 011802 (2002).Google Scholar
  31. 31.
    Y. Kantor, M. Kardar, Phys. Rev. E 69, 021806 (2004).Google Scholar
  32. 32.
    A. Milchev, K. Binder, A. Bhattacharya, J. Chem. Phys. 121, 6042 (2004).Google Scholar
  33. 33.
    A. Aksimentiev, J.B. Heng, G. Timp, K. Schulten, Biophys. J. 87, 2086 (2004).Google Scholar
  34. 34.
    K.F. Luo, T. Ala-Nissila, S.C. Ying, J. Chem. Phys. 124, 034714 (2006).Google Scholar
  35. 35.
    K.F. Luo, I. Huopaniemi, T. Ala-Nissila, S.C. Ying, J. Chem. Phys. 124, 114704 (2006).Google Scholar
  36. 36.
    I. Huopaniemi, K.F. Luo, T. Ala-Nissila, S.C. Ying, J. Chem. Phys. 125, 124901 (2006).Google Scholar
  37. 37.
    I. Huopaniemi, K.F. Luo, T. Ala-Nissila, S.C. Ying, Phys. Rev. E 75, 061912 (2007).Google Scholar
  38. 38.
    K.F. Luo, T. Ala-Nissila, S.C. Ying, A. Bhattacharya, J. Chem. Phys. 126, 145101 (2007).Google Scholar
  39. 39.
    K.F. Luo, T. Ala-Nissila, S.C. Ying, A. Bhattacharya, Phys. Rev. Lett. 99, 148102 (2007)Google Scholar
  40. 40.
    K.F. Luo, T. Ala-Nissila, S.C. Ying, A. Bhattacharya, Phys. Rev. Lett. 100, 058101 (2008)Google Scholar
  41. 41.
    S.-S. Chern, A.E. Cardenas, R.D. Coalson, J. Chem. Phys. 115, 7772 (2001).Google Scholar
  42. 42.
    H.C. Loebl, R. Randel, S.P. Goodwin, C.C. Matthai, Phys. Rev. E 67, 041913 (2003).Google Scholar
  43. 43.
    R. Randel, H.C. Loebl, C.C. Matthai, Macromol. Theory Simul. 13, 387 (2004).Google Scholar
  44. 44.
    Y. Lansac, P.K. Maiti, M.A. Glaser, Polymer 45, 3099 (2004).Google Scholar
  45. 45.
    C.Y. Kong, M. Muthukumar, Electrophoresis 23, 2697 (2002).Google Scholar
  46. 46.
    Z. Farkas, I. Derenyi, T. Vicsek, J. Phys.: Condens. Matter 15, S1767 (2003).Google Scholar
  47. 47.
    P. Tian, G.D. Smith, J. Chem. Phys. 119, 11475 (2003).Google Scholar
  48. 48.
    R. Zandi, D. Reguera, J. Rudnick, W.M. Gelbart, Proc. Natl. Acad. Sci. U.S.A. 100, 8649 (2003).Google Scholar
  49. 49.
    S. Kotsev, A.B. Kolomeisky, J. Chem. Phys. 125, 084906 (2006).Google Scholar
  50. 50.
    S. Tsuchiya, A. Matsuyama, Phys. Rev. E 76, 011801 (2007).Google Scholar
  51. 51.
    D. Wei, W. Yang, X. Jin, Q. Liao, J. Chem. Phys. 126, 204901 (2007)Google Scholar
  52. 52.
    J.K. Wolterink, G.T. Barkema, D. Panja, Phys. Rev. Lett. 96, 208301 (2006)Google Scholar
  53. 53.
    J.L.A. Dubbeldam, A. Milchev, V.G. Rostiashvili, T.A. Vilgis, Phys. Rev. E 76, 010801(R) (2007)Google Scholar
  54. 54.
    S. Guillouzic, G.W. Slater, Phys. Lett. A 359, 261 (2006)Google Scholar
  55. 55.
    D. Panja, G.T. Barkema, e-print arXiv:0706.3969v3.Google Scholar
  56. 56.
    M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids (Oxford University Press, 1987).Google Scholar
  57. 57.
    P.G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).Google Scholar
  58. 58.
    P. Pincus, Macromolecules 9, 386 (1976).Google Scholar
  59. 59.
    T. Soddemann, H. Schiessel, A. Blumen, Phys. Rev. E 57, 2081 (1998).Google Scholar
  60. 60.
    D.L. Ermak, H. Buckholz, J. Comput. Phys. 35, 169 (1980).Google Scholar
  61. 61.
    J.F. Kenney, E.S. Keeping, Mathematics of Statistics, Pt. 2, 2nd edition (Princeton, NJ, 1951).Google Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • S. T. T. Ollila
    • 1
  • K. F. Luo
    • 1
  • T. Ala-Nissila
    • 1
    • 2
  • S. -C. Ying
    • 2
  1. 1.Department of Applied PhysicsHelsinki University of TechnologyEspooFinland
  2. 2.Department of PhysicsBrown UniversityProvidenceUSA

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