Effect of confinement on dynamics and rheology of dilute DNA solutions. I. Entropic spring force under confinement and a numerical algorithm

Journal of Rheology

Volumn 48, Issue 2, 2004, Pages 281-298

  Woo, Nathanael J ^a   Shaqfeh, Eric S G ^a   Khomami, Bamin ^b  

^a Stanford University   (United States)

^b WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEAD-SPRINGS MODELS; MICROCHANNELS; MULTISCALE SIMULATION;

ALGORITHMS; COMPUTER SIMULATION; CONFINED FLOW; ENTROPY; HYDRODYNAMICS; MATHEMATICAL MODELS; MICROELECTROMECHANICAL DEVICES; RHEOLOGY; SOLUTIONS;

DNA;

EID: 1642303150     PISSN: 01486055     EISSN: None     Source Type: Journal    
DOI: 10.1122/1.1648642     Document Type: Article

References (47)

1. Abramowitz, M., and I. A. Stegun, Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables (Wiley-Interscience, New York, 1984).
2. Allegra, G., and E. Colombo, "Polymer chain between attractive walls: A second-order transition," J. Chem. Phys. 98, 7398-7404 (1993).
3. Aubert, J. H., and M. Tirrel, "Effective viscosity of dilute polymer solutions near confining boundaries," J. Chem. Phys. 77, 553-561 (1982).
4. Ausserre, D., J. Edwards, J. Lecourtier, H. Hervet, and F. Rondelez, "Hydrodynamic thickening of depletion layers in colloidal solutions," Europhys. Lett. 14, 33-38 (1991).
5. Babcock, H. P., D. E. Smith, J. S. Hur, E. S. G. Shaqfeh, and S. Chu, "Relating the microscopic response of a polymeric fluid in a shear flow," Phys. Rev. Lett. 85, 2018-2021 (2000).
6. Bakajin, O. B., T. A. J. Duke, C. F. Chou, S. S. Chan, R. H. Austin, and E. C. Cox, "Electrohydrodynamic stretching of DNA in confined environments," Phys. Rev. Lett. 80, 2737-2740 (1998).
7. Brenner, H., "The slow motion of a sphere through a viscous fluid towards a plane surface," Chem. Eng. Sci. 16, 242-251 (1961).
8. Brunn, P. O., "The effect of a solid wall for the flow of dilute macromolecular solutions," Rheol. Acta 15, 23-29 (1976).
9. Brunn, P. O., and S. Grisafi, "Wall effects in simple shear of dilute polymer solutions: Exact results for very narrow and very wide channels," J. Non-Newtonian Fluid Mech. 24, 343-363 (1987).
10. Carslaw, H. S., and J. C. Jaeger, Conduction of Heat in Solids, 2nd ed. (Clarendon, New York, 1959).
11. Chopra, M., and R. G. Larson, "Brownian dynamics simulations of isolated polymer molecules in shear flow near adsorbing and nonadsorbing surfaces," J. Rheol. 46, 831-862 (2002).
12. de Pablo, J. J., H. C. Öttinger, and Y. Rabin, "Hydrodynamic changes of the depletion layer of dilute polymer solutions near a wall," AIChE J. 38, 273-283 (1992).
13. DiMarzio, E. A., "Proper accounting of conformations of a polymer near a surface," J. Chem. Phys. 42, 2101-2104 (1965).
14. Doi, M., and S. F. Edwards, The Theory of Polymer Dynamics (Oxford University Press, New York, 1986).
15. Doyle, P. S., E. S. G. Shaqfeh, and A. P. Gast, "Dynamic simulation of freely-draining, flexible polymers in steady linear flows," J. Fluid Mech. 334, 251-291 (1997a).
16. Doyle, P. S., E. S. G. Shaqfeh, and A. P. Gast, "Rheology of "wet" polymer brushes via Brownian dynamics simulation: Steady vs oscillatory shear," Phys. Rev. Lett. 78, 1182-1185 (1997b).
17. Duering, E., and Y. Rabin, "Polymers in shear flow near repulsive boundaries," Macromolecules 23, 2232-2237 (1990).
18. Duering, E., and Y. Rabin, "Polymers in plane Poiseuille flow: Dynamic Monte Carlo simulation," J. Rheol. 35, 213-219 (1991).
19. Feller, W., An Introduction to Probability Theory and Its Applications, 2nd ed. (Wiley, New York, 1961).
20. Graessley, M. W., R. L. Hayward, and G. S. Grest, "Excluded-volume effects in polymer solutions. 2. Comparison of experimental results with simulation data," Macromolecules 32, 3510-3517 (1999).
21. Grasselli, Y., and L. Lobry, "Hydrodynamic interactions between a particle and two rigid walls: Effect of surface roughness and many-body hydrodynamic interactions," Phys. Fluids 9, 3929-3931 (1997).
22. Grassia, P. S., E. J. Hinch, and L. C. Nitsche, "Computer simulation of Brownian motion of complex systems," J. Fluid Mech. 282, 373-403 (1995).
23. Happel, J., and H. Brenner, Low Reynolds Number Hydrodynamics (Prentice-Hall, Englewood Cliffs, NJ, 1965).
24. Herrchen, M., and H. Öttinger, "A detailed comparison of various FENE dumbbell models," J. Non-Newtonian Fluid Mech. 68, 17-42 (1997).
25. Ho, C. M., and Y. C. Tai, "Review: MEMS and its applications for flow control," J. Fluids Eng. 118, 437-447 (1996).
26. Ho, C. M., and Y. C. Tai, "Micro-Electro-Mechanical-Systems (MEMS) and fluid flows," Annu. Rev. Fluid Mech. 30, 579-612 (1998).
27. Hur, J. S., E. S. G. Shaqfeh, and R. G. Larson, "Brownian dynamics simulations of single DNA molecules in shear flow," J. Rheol. 44, 713-742 (2000).
28. Hur, J. S., E. S. G. Shaqfeh, H. P. Babcock, D. E. Smith, and S. Chu, "Dynamics of dilute and semidilute DNA solutions in the startup of shear flow," J. Rheol. 45, 421-450 (2001).
29. Jendrejack, R. M., J. J. de Pablo, and M. D. Graham, "Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions," J. Chem. Phys. 116, 7752-7759 (2002).
30. Koch, D. L., and J. F. Brady, "The effective diffusivity of fibrous media," AIChE J. 32, 575-591 (1986).
31. Kuhn, W., and F. Grün, "Relationships between elastic constants and stretching double refraction of highly elastic substances," Kolloid-Z. 101, 248-253 (1942).
32. Lee, G. B., S. H. Chen, G. R. Huang, W. C. Sung, and Y. H. Lin, "Microfabricated plastic chips by hot embossing methods and their applications for DNA separation and detection," Sens. Actuators B 75, 142-148 (2001).
33. Lin, B., J. Yu, and S. Rice, "Direct measurements of constrained Bronwnian motion of an isolated sphere between two walls," Phys. Rev, E 62, 3909-3919 (2000).
34. Lobry, L., and N. Ostrowsky, "Diffusion of Brownian particles trapped between two walls: Theory and dynamic-light-scattering measurements," Phys. Rev. B 53, 12050-12056 (1996).
35. Maier, B., and J. O. Radler, "Conformation and self-diffusion of single DNA molecules confined to two dimensions," Phys. Rev. Lett. 82, 1911-1914 (1999).
36. Marko, J. F., and E. D. Siggia, "Stretching DNA," Macromolecules 28, 3427-3433 (1995).
37. Mavrantzas, V. G., and A. N. Beris, "Theoretical study of wall effects on the rheology of dilute polymer solutions," J. Rheol. 36, 175-213 (1992).
38. Mavrantzas, V. G., and A. N. Beris, "A hierarchical model for surface effects on chain conformation and rheology of polymer solutions. II. Application to a neutral surface," J. Chem. Phys. 110, 628-638 (1999).
39. Muller-Mohnssen, H., D. Weiss, and A. Tippe, "Concentration dependent changes of apparent slip in polymer solution flow," J. Rheol. 34, 223-244 (1990).
40. Muthukumar, M., "Brownian dynamics of polymer chains in membranes," J. Chem. Phys. 82, 5696-5706 (1999).
41. Öttinger, H. C., Stochastic Processes in Polymeric Fluids (Springer, New York, 1996).
42. Rowley, R. L., Statistical Mechanics for Thermophysical Property Calculations (Prentice-Hall, Englewood Cliffs, NJ, 1994).
43. Schiek, R. L., and E. S. G. Shaqfeh, "A nonlocal theory for stress in bound, Brownian suspensions of slender, rigid fibres," J. Fluid Mech. 296, 271-324 (1995).
44. Smith, D. E., H. P. Babcock, and S. Chu, "Single polymer dynamics in steady shear flow," Science 283, 1724-1727 (1999).
45. Smith, S. B., L. Finzi, and C. Bustamante, "Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads," Science 258, 1122-1126 (1992).
46. Somasi, M., B. Khomami, N. J. Woo, J. S. Hur, and E. S. G. Shaqfeh, "Brownian dynamics simulation of bead-rod and bead-spring chains: Numerical algorithms and coarse graining issues," J. Non-Newtonian Fluid Mech. 108, 227-255 (2002).
47. Woo, J. H., DNA chain dynamics and its applications to micro-devices and scission, Ph.D. thesis (Stanford University, Stanford, CA, 2003).