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Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions

J. Chem. Phys. 116, 7752 (2002); doi:10.1063/1.1466831

Issue Date: 1 May 2002

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Richard M. Jendrejack, Juan J. de Pablo, and Michael D. Graham
Department of Chemical Engineering and Rheology Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706-1691
We present a fully parametrized bead–spring chain model for stained lambda-phage DNA. The model accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating hydrodynamic interactions (HI). Parameters are determined from equilibrium experimental data for 21 µm stained lambda-phage DNA, and are shown to quantitatively predict the non-equilibrium behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium behavior of DNA molecules up to 126 µm. In particular, the HI model gives results that are in quantitative agreement with experimental diffusivity data over a wide range of molecular weights. When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining or HI model at that molecular weight, although the fitted bead friction coefficients for the two models differ significantly. In shear flow, we find two regimes at high shear rate (gamma-dot) that follow different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly as gamma-dot–6/11 and gamma-dot–14/11, respectively. At higher shear rates, these become gamma-dot–2/3 and gamma-dot–4/3. These regimes are found for both free-draining and HI models and can be understood based on scaling arguments for the diffusion of chain ends. ©2002 American Institute of Physics.
History: Received 15 May 2001; accepted 8 February 2002
Permalink: http://link.aip.org/link/?JCPSA6/116/7752/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.14.Gg
    Biological and medical physics Biomolecules: types DNA, RNA
  • 87.15.Kg
    Biological and medical physics Biomolecules: structure and physical properties Molecular interactions; membrane-protein interactions
  • 36.20.Ey
    Exotic atoms and molecules; macromolecules; clusters Macromolecules and polymer molecules Conformation (statistics and dynamics)
  • 87.15.Ya
    Biological and medical physics Biomolecules: structure and physical properties Fluctuations
  • 87.19.-j
    Biological and medical physics Properties of higher organisms
  • 87.15.Aa
    Biological and medical physics Biomolecules: structure and physical properties Theory and modeling; computer simulation
  • 47.50.+d
    Fluid dynamics Non-Newtonian fluid flows
  • YEAR: 2002

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (36)
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  1. J. Han and H. G. Craighead, Science 288, 1026 (2000).
  2. D. E. Smith, H. P. Babcock, and S. Chu, Science 283, 1724 (1999).
  3. D. E. Smith, T. T. Perkins, and S. Chu, Macromolecules 29, 1372 (1996).
  4. S. B. Smith, L. Finzi, and C. Bustamante, Science 258, 1122 (1992).
  5. D. E. Smith and S. Chu, Science 281, 1335 (1998).
  6. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science 265, 1600 (1994).
  7. T. T. Perkins, D. E. Smith, and S. Chu, Science 276, 2016 (1997).
  8. R. G. Larson, T. T. Perkins, D. E. Smith, and S. Chu, Phys. Rev. E 55, 1794 (1997).
  9. J. S. Hur, E. S. G. Shaqfeh, and R. G. Larson, J. Rheol. 44, 713 (2000).
  10. R. G. Larson, H. Hu, D. E. Smith, and S. Chu, J. Rheol. 43, 267 (1999).
  11. J. S. Hur, E. S. G. Shaqfeh, H. P. Babcock, D. E. Smith, and S. Chu, J. Rheol. 45, 421 (2001).
  12. H. Jian, A. V. Vologodskii, and T. Schlick, J. Comput. Phys. 136, 168 (1997).
  13. H. Jian, T. Schlick, and A. Vologodskii, J. Mol. Biol. 284, 287 (1998).
  14. T. Schlick, D. A. Beard, J. Huang, D. A. Strahs, and X. Qian, Comput. Sci. Eng. 2, 38 (2000).
  15. R. M. Jendrejack, J. J. de Pablo, and M. D. Graham, to appear in "Technical Proceedings of the 2002 International Conference on Modeling and Simulation of Microsystems" (Applied Computational Research Society, Cambridge, 2002).
  16. R. M. Jendrejack, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 113, 2894 (2000).
  17. J. Rotne and S. Prager, J. Chem. Phys. 50, 4831 (1969).
  18. In a previous paper (Ref. 16), we also used the RPY tensor, but omitted the divergence term without comment.
  19. J. G. Kirkwood and J. Riseman, J. Chem. Phys. 16, 565 (1948).
  20. R. B. Bird, C. F. Curtiss, R. C. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids (Wiley, New York, 1987), Vol. 2.
  21. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Clarendon, Oxford, 1986).
  22. H.-C. Öttinger, Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996).
  23. J. F. Marko and E. D. Siggia, Macromolecules 27, 981 (1994).
  24. J. F. Marko and E. D. Siggia, Macromolecules 28, 8759 (1995).
  25. B. Ladoux and P. S. Doyle, Europhys. Lett. 52, 511 (2000).
  26. G. R. Strobl The Physics of Polymers (Springer, Berlin, 1997).
  27. B. Farnoux, F. Bou, J. P. Cotton, M. Daoud, G. Jannink, M. Nierlich, and P. G. de Gennes, J. Phys. (Paris) 39, 77 (1978).
  28. S. Kumar and R. G. Larson, J. Chem. Phys. 114, 6937 (2001).
  29. S. Sorlie and R. Pecora, Macromolecules 23, 487 (1990).
  30. J. W. Hatfield and S. R. Quake, Phys. Rev. Lett. 82, 3548 (1999).
  31. M. Fixman, Macromolecules 19, 1204 (1986).
  32. D. Petera and M. Muthukumar, J. Chem. Phys. 111, 7614 (1999).
  33. P. S. Doyle, E. S. G. Shaqfeh, and A. P. Gast, J. Fluid Mech. 334, 251 (1997).
  34. P. Grassia and E. J. Hinch, J. Fluid Mech. 308, 255 (1996).
  35. W. M. Deen, Analysis of Transport Phenomena (Oxford, New York, 1998).
  36. L. E. Wedgewood, D. N. Ostrov, and R. B. Bird, J. Non-Newtonian Fluid Mech. 40, 119 (1991).

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