Journal of Chemical Physics
Feedback | Help | Exit
The Journal of Chemical Physics
   
 
 
 
Previous Article
Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction ensemble Monte Carlo. I. Polydispersed polymer systems
We present a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics (RxDPD) method, for studying reaction equilibrium of polymer systems. The RxDPD method combines ...
Next Article
Coarse grained model of entangled polymer melts
A coarse graining procedure aimed at reproducing both the chain structure and dynamics in melts of linear monodisperse polymers is presented. The reference system is a bead-spring-type representation ...

N  log  N method for hydrodynamic interactions of confined polymer systems: Brownian dynamics

J. Chem. Phys. 125, 164906 (2006); doi:10.1063/1.2358344

Published 26 October 2006

You are not logged in to this journal. Log in

Juan P. Hernández-Ortiz, Juan J. de Pablo, and Michael D. Graham
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691
A Brownian dynamics simulation technique is presented where a Fourier-based N  log  N approach is used to calculate hydrodynamic interactions in confined flowing polymer systems between two parallel walls. A self-consistent coarse-grained Langevin description of the polymer dynamics is adopted in which the polymer beads are treated as point forces. Hydrodynamic interactions are therefore included in the diffusion tensor through a Green's function formalism. The calculation of Green's function is based on a generalization of a method developed for sedimenting particles by Mucha et al. [J. Fluid Mech. 501, 71 (2004)]. A Fourier series representation of the Stokeslet that satisfies no-slip boundary conditions at the walls is adopted; this representation is arranged in such a way that the total O(N2) contribution of bead-bead interactions is calculated in an O(N  log  N) algorithm. Brownian terms are calculated using the Chebyshev polynomial approximation proposed by Fixman [Macromolecules 19, 1195 (1986); 19, 1204 (1986)] for the square root of the diffusion tensor. The proposed Brownian dynamics simulation methodology scales as O(N1.25  log  N). Results for infinitely dilute systems of dumbbells are presented to verify past predictions and to examine the performance and numerical consistency of the proposed method. ©2006 American Institute of Physics
History: Received 17 May 2006; accepted 6 September 2006; published 26 October 2006
Permalink: http://link.aip.org/link/?JCPSA6/125/164906/1
BUY THIS ARTICLE   (US$28)
Download HTML Download Sectioned HTML Download PDF (241 kB) View Cart

KEYWORDS and PACS

Keywords
PACS
  • 61.20.Gy
    Theory and models of liquid structure
  • 61.25.Hq
    Structure of macromolecular and polymer solutions, and polymer melts; swelling
  • 66.10.Cb
    Diffusion and thermal diffusion in liquids
  • YEAR: 2006

RELATED DATABASES


To view database links for this article,
you need to log in.
To view database links for this article,
you need to log in.

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (37)
View in Separate Window/Tab
For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. O. S. Andersen, Biophys. J. 77, 2899 (1999).
  2. 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. Han, and S. Turner, Electrophoresis 21, 81 (2000).
  3. M. Sauer, B. Angerer, W. Ankenbauer, Z. Földes-Papp, F. Göbel, K. Han, R. Rigler, A. Schultz, J. Wolfrum, and C. Zander, J. Biotechnol. 86, 281 (2001).
  4. J. O. Tegenfeldt, C. Prinz, H. Cao, R. L. Huang, R. H. Austin, S. Y. Chou, E. C. Cox, and J. C. Sturm, Anal. Bioanal. Chem. 378, 1678 (2004).
  5. L. Fang, H. Hu, and R. G. Larson, J. Rheol. 49, 127 (2005).
  6. R. M. Jendrejack, E. T. Dimalanta, D. C. Schwartz, M. D. Graham, and J. de Pablo, Phys. Rev. Lett. 91, 038102 (2003).
  7. R. M. Jendrejack, D. C. Schwartz, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 119, 1165 (2003).
  8. R. M. Jendrejack, D. C. Schwartz, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 120, 2513 (2004).
  9. Y.-L. Chen, M. D. Graham, J. J. de Pablo, G. C. Randall, M. Gupta, and P. S. Doyle, Phys. Rev. E 70, 060901 (2004).
  10. H. B. Ma and M. D. Graham, Phys. Fluids 17, 083103 (2005).
  11. J. Blake, Proc. Cambridge Philos. Soc. 70, 30 (1971).
  12. N. Liron and S. Mochon, J. Eng. Math. 10, 287 (1976).
  13. J. Happel and H. Brenner, Low Reynolds Number Hydrodynamics (Kluwer, Dordrecht, 1991).
  14. C. Pozrikidis, Boundary Integral and Singularity Methods for Linearized Viscous Flow (Cambridge University Press, Cambridge, 1992).
  15. R. Jendrejack, M. Graham, and J. J. de Pablo, J. Chem. Phys. 113, 2894 (2000).
  16. M. Fixman, Macromolecules 19, 1195 (1986).
  17. M. Fixman, Macromolecules 19, 1204 (1986).
  18. O. Usta, A. Ladd, and J. Butler, J. Chem. Phys. 122, 4902 (2005).
  19. X. Fan, N. Phan-Thien, N. T. Yong, X. Wu, and D. Xu, Phys. Fluids 15, 11 (2003).
  20. C. Stoltz, J. de Pablo, and M. Graham, J. Rheol. 50, 137 (2006).
  21. P. J. Mucha, S.-Y. Tee, D. A. Weitz, B. I. Shraiman, and M. P. Brenner, J. Fluid Mech. 501, 71 (2004).
  22. R. B. Bird, C. Curtiss, F. R. C. Armstrong, and O. Hassager, Dynamics of Polymer Liquids: Kinetic Theory, 2nd ed. (Wiley, New York, 1987), Vol. 2.
  23. H.-C. Öttinger, Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996).
  24. C. Gardiner, Handbook of Stochastic Methods (Springer, Berlin, 1985).
  25. H. Risken, The Fokker-Planck Equation (Springer, Berlin, 1989).
  26. L. Landau and E. Lifshitz, Fluid Mechanics, 2nd ed. (Butterworth-Heinemann, Oxford, 1987).
  27. H.-C. Öttinger, Beyond Equilibrium Thermodynamics (Wiley-Interscience, New York, 2005).
  28. L. Reichl, A Modern Course in Statistical Physics 2nd ed. (Wiley-Interscience, New York, 1998).
  29. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, Oxford, 2001).
  30. S. Kim and S. Karrila, Microhydrodynamics: Principles and Selected Applications (Butterworth-Heinemann, Boston, 1991).
  31. H. Power and L. C. Wrobel, Boundary Integral Methods in Fluid Mechanics (Computational Mechanics, Southampton, 1995).
  32. J. Rotne and S. Prager, J. Chem. Phys. 50, 4831 (1969).
  33. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran 77, 2nd ed. (Cambridge University Press, Cambridge, 1992).
  34. I. Bronstein, K. Semendjajew, G. Musiol, and H. Muehlig, Taschenbuch der Mathematik (Verlag Harri-Deutsch, Frankfurt am Main, 2001).
  35. C. Canuto, M. Hussaini, A. Quarteroni, and T. Zang, Spectral Methods in Fluid Dynamics (Springer-Verlag, Berlin, 1988).
  36. J. Hernández-Ortiz, C. Stoltz, and M. Graham, Phys. Rev. Lett. 95, 204501 (2005).
  37. www.nsec.wisc.edu

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.


Copyright © American Institute of Physics