Development of bead-spring polymer models using the constant extension ensemble

Journal of Rheology

Volumn 49, Issue 5, 2005, Pages 963-987

  Underhill, Patrick T ^a   Doyle, Patrick S ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEAD-SPRING CHAINS; MOLECULAR MODEL; POLYMER MODELS; SPRING FORCE LAW;

BROWNIAN MOVEMENT; COMPUTER SIMULATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; PHASE TRANSITIONS;

POLYMERS;

EID: 30344473592     PISSN: 01486055     EISSN: None     Source Type: Journal    
DOI: 10.1122/1.2008294     Document Type: Article

References (27)

1. Baschnagel, J., K. Binder, P. Doruker, A. Guusev, O. Hahn, K. Kremer, W. Mattice, F. Müller-Plathe, M. Murat, W. Paul, S. Santos, U. Suter, and V. Tries, "Bridging the gap between atomistic and coarse-grained models of polymers: Status and perspectives," Adv. Polym. Sci., 152, 41-156 (2000).
2. Bird, R., C. Curtiss, R. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids, Volume 2: Kinetic Theory, 2nd ed. (Wiley, New York, 1987).
3. Bustamante, C., J. Marko, E. Siggia, and S. Smith, "Entropic elasticity of λ-phage DNA," Science 265, 1599-1600 (1994).
4. Cohen, A., "A Padé approximant to the inverse Langevin function," Rheol. Acta 30, 270-272 (1991).
5. Dhar, A., and D. Chaudhuri, "Triple minima in free energy of semiflexible polymers," Phys. Rev. Lett. 89, 065502 (2002).
6. Doyle, P., J. Bibette, A. Bancaud, and J.-L. Viovy, "Self-assembled magnetic matrices for DNA separation chips," Science 295, 2237 (2002).
7. Doyle, P., B. Ladoux, and J.-L. Viovy, "Dynamics of a tethered polymer in shear flow," Phys. Rev. Lett. 84, 4769-4772 (2000).
8. Flory, P., Statistical Mechanics of Chain Molecules (Oxford University Press, New York, 1989).
9. Foss, D., and J. Brady, "Brownian dynamics simulation of hard-sphere coloidal dispersions," J. Rheol. 44, 629-651 (2000).
10. Han, J., and H. Craighead, "Separation of long DNA molecules in a microfabricated entropie trap array," Science 288, 1026-1029 (2000).
11. Heyes, D., and J. Melrose, "Brownian dynamics simulations of model hard-sphere suspensions," J. Non-Newtonian Fluid Mech. 46, 1-28 (1993).
12. Hur, J., E. Shaqfeh, and R. Larson, "Brownian dynamics simulations of single DNA molecules in shear flow," J. Rheol. 44, 713-742 (2000).
13. Jendrejack, R., E. Dimalanta, D. Schwartz, M. Graham, and J. de Pablo, "DNA dynamics in a microchannel," Phys. Rev. Lett. 91, 038102 (2003).
14. Keller, D., D. Swigon, and C. Bustamante, "Relating single-molecule measurements to thermodynamics," Biophys. J. 84, 733-738 (2003).
15. Kratky, O., and G. Porod, "X-ray investigation of dissolved chain molecules," Recl. Trav. Chim. Pays-Bas 68, 1106-1022 (1949).
16. Larson, R., T. Perkins, D. Smith, and S. Chu, "Hydrodynamics of a DNA molecule in a flow field," Phys. Rev. E 55, 1794-1797 (1997).
17. Le Goff, L., O. Hallatschek, E. Prey, and F. Amblard, "Tracer studies of F-actin fluctuations," Phys. Rev. Lett. 89, 258101 (2002).
18. Marko, J., and E. Siggia, "Stretching DNA," Macromolecules 28, 8759-8770 (1995).
19. Öttinger, H., Stochastic Processes in Polymeric Fluids: Tools and Examples for Developing Simulation Algorithms (Springer, Berlin, 1996).
20. Pathria, R., Statistical Mechanics, 2nd ed. (Butterworth-Heinemann, Boston, 1996).
21. Rayleigh, Lord, "On the problem of random vibrations, and of random flights in one, two or three dimensions," Philos. Mag. 37, 321-347 (1919).
22. Samuel, J., and S. Sinha, "Elasticity of semiflexible polymers," Phys. Rev. E 66, 050801 (2002).
23. Somasi, M., B. Khomami, N. Woo, J. Hur, and E. Shaqfeh, "Brownian dynamics simulations of bead-rod and bead-spring chains: Numerical algorithms and coarse-graining issues," J. Non-Newtonian Fluid Mech. 108, 227-255 (2002).
24. Treloar, L., The Physics of Rubber Elasticity, 2nd ed. (Clarendon, Oxford, 1975).
25. Underhill, P., and P. Doyle, "On the coarse-graining of polymers into bead-spring chains," J. Non-Newtonian Fluid Mech. 122, 3-31 (2004).
26. Warner, H., "Kinetic theory and rheology of dilute suspensions of finitely extendible dumbbells," Ind. Eng. Chem. Fundam. 11, 379-387 (1972).
27. Wilhelm, J., and E. Frey, "Radial distribution function of semiflexible polymers," Phys. Rev. Lett. 77, 2581-2584 (1996).