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Molecular-dynamics simulations with explicit hydrodynamics I: On the friction coefficients of deformed polymers

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Abstract.

We implement large-scale Molecular-Dynamics (MD) simulations which incorporate hydrodynamic interactions via the inclusion of explicit Lennard-Jones solvent to examine the behaviour of polymer chains in sieving media. We begin by examining the friction coefficients of polymers in long-lived states responsible for inducing length-dependent mobility, i.e., allowing separation of polymers (or polyelectrolytes) by molecular weight. In particular, the conformations we examine occur in devices which utilize arrays of molecular obstacles or dilute solutions of polymers. We compare the results from our MD simulations with expressions from macroscopic hydrodynamics for four specific cases: i) a random coil excluded-volume Zimm polymer, ii) a rigid polymer moving perpendicular to its major axis iii) a rigid polymer moving parallel to its major axis and iv) a rigid polymer, folded at different points along its contour. We also examine the behaviour of the friction coefficient of a fully flexible molecule pulled by its middle monomer as a function of an applied force F and show that there are several distinct frictional regimes.

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References

  1. M. Doi, S.F. Edwards, The Theory of Polymer Dynamics (Oxford University Press, 1986).

  2. M.E. Starkweather, D.A. Hoagland, M. Muthukumar, Macromolecules 33, 1245 (2000).

    Article  Google Scholar 

  3. P.S. Doyle, J. Bibette, A. Bancaud, J. Viovy, Science 295, 2237 (2002).

    Article  Google Scholar 

  4. A.E. Barron, H.W. Blanch, D.S. Soane, Electrophoresis 15, 597 (1994).

    Google Scholar 

  5. P. Andre, D. Long, A. Ajdari, Eur. Phys. J. B 4, 307 (1998).

    Article  Google Scholar 

  6. S. Hubert, G.W. Slater, J. Viovy, Macromolecules 29, 1006 (1996).

    Article  MATH  Google Scholar 

  7. H. Noguchi, M. Takasu, J. Phys. Soc. Jpn. 69, 3729 (2000).

    Google Scholar 

  8. P. Munk, Introduction to Macromolecular Science (Wiley Interscience, Oxford, 1989).

  9. G.I. Nixon, G.W. Slater, Phys. Rev. E 50, 5033 (1994).

    Article  Google Scholar 

  10. E.M. Sevick, D.R.M. Williams, Europhys. Lett. 56, 529 (2001).

    Article  Google Scholar 

  11. A. Ortega, G. de la Torre, J. Chem. Phys. 119, 9914 (2003).

    Article  Google Scholar 

  12. W. Eimer, R. Pecora, J. Chem. Phys. 94, 2324 (1991).

    Article  Google Scholar 

  13. B.U. Felderhof, J.M. Deutch, J. Chem. Phys. 62, 2391 (1975).

    Article  Google Scholar 

  14. J.M. Deutch, B.U. Felderhof, J. Chem. Phys. 62, 2398 (1975).

    Article  Google Scholar 

  15. B. Carrasco, J.G. de la Torre, J. Chem. Phys. 111, 4817 (1999).

    Article  Google Scholar 

  16. K. Kremer, G.S. Grest, I. Carmesian, Phys. Rev. Lett. 61, 566 (1988).

    Article  Google Scholar 

  17. K. Kremer, G.S. Grest, J. Chem. Phys. 92, 5057 (1990).

    Article  Google Scholar 

  18. M.P. Allen, D.J. Tildesley, Computer Simulations of Liquids, fourth edition (Oxford Science Publications, Oxford, 1987).

  19. D.C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, 1995).

  20. D. Levesque, L. Verlet, Phys. Rev. A 2, 2514 (1970).

    Article  Google Scholar 

  21. M. Cheong, J. Chang, J. Koplik, J.R. Banavar, Europhys. Lett. 58, 215 (2002).

    Article  Google Scholar 

  22. M. Tanaka, A.Y. Grosberg, Eur. Phys. J. E 7, 371 (2002).

    Google Scholar 

  23. D.M. Heyes, The Liquid State: Application of Molecular Simulations (John Wiley and Sons, 1988).

  24. Openmp, http://www.openmp.org/.

  25. K. Meier, A. Laesecke, S. Kabelac, Int. J. Thermophys. 22, 161 (2001).

    Article  Google Scholar 

  26. A.M. Bazhenov, D.M. Heyes, J. Chem. Phys. 92, 1106 (1990).

    Article  Google Scholar 

  27. B. Dunweg, J. Chem. Phys. 99, 6977 (1993).

    Article  Google Scholar 

  28. B. Dunweg, K. Kremer, J. Chem. Phys. 99, 6983 (1993).

    Article  Google Scholar 

  29. B. Dunweg, K. Kremer, Phys. Rev. Lett. 66, 2996 (1991).

    Article  Google Scholar 

  30. C. Pierleoni, J.P. Ryckaert, J. Chem. Phys. 96, 8539 (1992).

    Article  Google Scholar 

  31. C. Pierleoni, J.P. Ryckaert, Phys. Rev. Lett. 66, 2992 (1991).

    Article  Google Scholar 

  32. C.F. Abrams, N.K. Lee, S.P. Obukhov, Europhys. Lett. 59, 391 (2002).

    Article  Google Scholar 

  33. M.L. Adams, M. Enzelberger, S. Quake, A. Scherer, Sens. Actuator A-Phys. 104, 25 (2003).

    Article  Google Scholar 

  34. B. Ilic, D. Czaplewski, M. Zalalutdinov, B. Schmidt, H.G. Craighead, J. Vac. Sci. Technol. B 20, 2459 (2002).

    Article  Google Scholar 

  35. H. Cao, J.O. Tegenfeldt, R.H. Austin, S.Y. Chou, Appl. Phys. Lett. 81, 3058 (2002).

    Article  Google Scholar 

  36. H.G. Craighead, Abstr. pap. - Am. Chem. Soc., 222, 160-ANYL (2001).

  37. S.R. Quake, A. Scherer, Science 290, 1536 (2000).

    Article  Google Scholar 

  38. C.F. Chou, R.H. Austin, O. Bakajin, J.O. Tegenfeldt, J.A. Castelino, S.S. Chan, E.C. Cox, H. Craighead, N. Darnton, T. Duke, J.Y. Han, S. Turner, Electrophoresis 21, 81 (2000).

    Article  Google Scholar 

  39. G.K. Batchelor, J. Fluid Mech. 44, 410 (1970).

    Google Scholar 

  40. A. Meunier, J. Phys. II 4, 561 (1994).

    Article  Google Scholar 

  41. C.-Y. Shew, J. Chem. Phys. 119, 10428 (2003).

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Physics, University of Ottawa, 150 Louis-Pasteur, K1N 6N5, Ottawa, Ontario, Canada

    M. Kenward & G. W. Slater

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  1. M. Kenward
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  2. G. W. Slater
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Correspondence to G. W. Slater.

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PACS:

83.10.Mj Molecular dynamics, Brownian dynamics - 61.41. + e Polymers, elastomers, and plastics - 82.20.Wt Computational modeling; simulation

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Kenward, M., Slater, G.W. Molecular-dynamics simulations with explicit hydrodynamics I: On the friction coefficients of deformed polymers. Eur. Phys. J. E 14, 55–65 (2004). https://doi.org/10.1140/epje/i2004-10006-4

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  • DOI: https://doi.org/10.1140/epje/i2004-10006-4

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