Effect of confinement on DNA dynamics in microfluidic devices

Journal of Chemical Physics

Volumn 119, Issue 2, 2003, Pages 1165-1173

  Jendrejack, Richard M ^a   Schwartz, David C ^b   Graham, Michael D ^a   De Pablo, Juan J ^a  

^a University of Wisconsin Madison   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFUSION; FLUIDIC DEVICES; MACROMOLECULES; RELAXATION PROCESSES;

MICROFLUIDIC DEVICES;

DNA;

EID: 0042992582     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1575200     Document Type: Article

References (49)

1. O. S. Andersen, Biophys. J. 77, 2899 (1999).
2. C. F. Chou, R. H. Austin, O. Bakajin et al., Electrophoresis 21, 81 (2000).
3. A. Lim, E. T. Dimalanta, K. D. Potamousis et al., Genome Res. 11, 1584 (2001).
4. N. Perna, G. Plunkett III, V. Burland et al., Nature (London) 409, 529 (2001).
5. M. Sauer, B. Angerer, W. Ankenbauer, Z. Földes-Papp, F. Göbel, K. T. Han, R. Rigler, A. Schultz, J. Wolfrum, and C. Zander, J. Biotechnol. 86, 181 (2001).
6. M. Hinz, S. Gura, B. Nitzan, S. Margel, and H. Seliger, J. Biotechnol. 86, 281 (2001).
7. J. Stephan, K. Dörre, S. Brakmann, T. Winkler et al., J. Biotechnol. 86, 255 (2001).
8. F. T. Wall, W. A. Seitz, J. C. Chin, and P. G. de Gennes, Proc. Natl. Acad. Sci. U.S.A. 75, 2069 (1978).
9. J. H. van Vliet and G. ten Brinke, J. Chem. Phys. 93, 1436 (1990).
10. D. C. Schwartz and C. R. Cantor, Cell 37, 67 (1984).
11. D. C. Schwartz and M. Koval, Nature (London) 338, 520 (1989).
12. J. L. Viovy, Rev. Mod. Phys. 72, 813 (2000).
13. R. M. Kantor, X. H. Guo, E. J. Huff, and D. C. Schwartz, Biochem. Biophys. Res. Commun. 258, 102 (1999).
14. P. J. Shrewsbury, D. Liepmann, and S. J. Muller, Biomed. Microdevices 4, 17 (2002).
15. P. J. Shrewsbury, S. J. Muller, and D. Liepmann, Biomed. Microdevices 3, 225 (2001).
16. F. Brochard and P. G. de Gennes, J. Chem. Phys. 67, 52 (1977).
17. J. L. Harden and M. Doi, J. Phys. Chem. 96, 4046 (1992).
18. M. Fixman, J. Chem. Phys. 69, 1527 (1978).
19. R. B. Bird, C. F. Curtiss, R. C. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids (Wiley, New York, 1987), Vol. 2.
20. M. Chopra and R. G. Larson, J. Rheol. 46, 831 (2002).
21. R. M. Jendrejack, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 116, 7752 (2002).
22. H.-C. Öttinger, Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996).
23. R. M. Jendrejack, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 113, 2894 (2000).
24. C. Pozrikidis, Introduction to Theoretical and Computational Fluid Dynamics (Oxford University Press, New York, 1997).
25. M. Fixman, Macromolecules 19, 1204 (1986).
26. R. M. Jendrejack, J. J. de Pablo, and M. D. Graham, J. Non-Newtonian Fluid Mech. 108, 123 (2002).
27. J. Rotne and S. Prager, J. Chem. Phys. 50, 4831 (1969).
28. J. F. Marko and E. D. Siggia, Macromolecules 27, 981 (1994).
29. J. F. Marko and E. D. Siggia, Macromolecules 28, 8759 (1995).
30. R. M. Jendrejack, J. J. de Pablo, and M. D. Graham, Technical Proceedings of the Fifth International Conference on Modeling and Simulation of Microsystems (Applied Computational Research Society, San Juan, Puerto Rico, 2002), pp. 88-91.
31. R. G. Larson, T. T. Perkins, D. E. Smith, and S. Chu, Phys. Rev. E 55, 1794 (1997).
32. J. S. Hur, E. S. G. Shaqfeh, and R. G. Larson, J. Rheol. 44, 713 (2000).
33. R. G. Larson, H. Hua, D. E. Smith, and S. Chu, J. Rheol. 43, 267 (1999).
34. B. Ladoux and P. S. Doyle, Europhys. Lett. 52, 125 (2000).
35. J. Happel and H. Brenner, Low Reynolds Number Hydrodynamics (Kluwer, Dordrecht, 1991).
36. C. Pozrikidis, Boundary Integral and Singularity Methods for Linearized Viscous Flow (Cambridge University Press, Cambridge, 1992).
37. E. R. Dufresne, T. M. Squires, M. P. Brenner, and D. G. Grier, Phys. Rev. Lett. 85, 3317 (2000).
38. C. K. Colton, C. N. Satternfield, and C.-J. Lai, AIChE J. 21, 289 (1975).
39. 3D quadratic interpolation functions are used.
40. B. U. Felderhof, Physica A 89, 373 (1977).
41. C. W. J. Beenakker, J. Chem. Phys. 85, 1581 (1986).
42. K. R. Hase and R. L. Powell, Phys. Fluids 13, 32 (2001).
43. H. Faxen, Arch. Mat. Astron. Fys. 17, 27 (1923).
44. C. N. Satterfield, C. K. Colton, and W. H. Pitcher, AIChE J. 19, 628 (1973).
45. D. S. Cannell and F. Rondelez, Macromolecules 13, 1599 (1980).
46. E. M. Renkin, J. Gen. Physiol. 38, 225 (1953).
47. J. D. Ferry, J. Gen. Physiol. 20, 95 (1936).
48. O. B. Bakajin, T. A. J. Duke, C. F. Chou, S. S. Chan, R. H. Austin, and E. C. Cox, Phys. Rev. Lett. 80, 2737 (1998).
49. We used a quadratic velocity, linear pressure formulation. The resultant sparse, symmetric system of equations was solved using GMRES with a partial LU decomposition preconditioner.