A family of time-staggered schemes for integrating hybrid DPD models for polymers: Algorithms and applications

Journal of Computational Physics

Volumn 218, Issue 1, 2006, Pages 82-101

  Symeonidis, Vasileios ^a   Karniadakis, George Em ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

DNA; Hard potentials; Multi scale modeling; Non Newtonian fluids

Indexed keywords

NON NEWTONIAN FLOW; NON NEWTONIAN LIQUIDS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

DILUTE POLYMER SOLUTIONS; DISSIPATIVE PARTICLE DYNAMICS; DISSIPATIVE PARTICLE DYNAMICS MODEL; HARD POTENTIAL; MICROSCOPIC DYNAMICS; MULTISCALE MODELING; NON-NEWTONIAN FLUIDS; SOFT POTENTIALS; STAGGERED SCHEMES; STOCHASTIC DIFFERENTIAL EQUATIONS;

DISSIPATIVE PARTICLE DYNAMICS;

EID: 33748574244     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2006.01.043     Document Type: Article

References (41)

1. de Gennes P.-G. Scaling Concepts in Polymer Physics (1979), Cornell University Press, Ithaca, NY
2. Ahlrichs P., and Dünweg B. Simulation of a single polymer chain in solution by combining Boltzmann and molecular dynamics. J. Chem. Phys. 111 17 (1999) 8225-8239
3. Malevanets A., and Kapral R. Mesoscopic model for solvent dynamics. J. Chem. Phys. 110 17 (1999) 8605
4. Malevanets A., and Kapral R. Solute molecular dynamics in a mesoscale solvent. J. Chem. Phys. 112 16 (2000) 7260
5. Malevanets A., and Yeomans J. Dynamics of short polymer chains in solution. Europhys. Lett. 52 (2000) 231
6. Falck E., Punkkinen O., Vattulainen I., and Ala-Nissila T. Dynamics and scaling of two-dimensional polymers in a dilute solution. Phys. Rev. E 68 (2003) 050102
7. Noguchi H., and Gompper G. Fluid vesicles with viscous membranes in shear flow. Phys. Rev. Lett. 93 (2004) 258102
8. Hoogerbrugge P.J., and Koelman J.M. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys. Lett. 19 3 (1992) 155-160
9. Español P., and Warren P. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 30 4 (1995) 191-196
10. Schlijper A., Hoogerbrugge P., and Manke C. Computer simulation of dilute polymer solutions with the dissipative particle dynamics method. J. Rheol. 39 3 (1995) 567
11. Groot R.D., and Warren P.B. Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 107 11 (1997) 4423-4435
12. Pierleoni C., and Ryckaert J.-P. Molecular dynamics investigation of dynamic scaling for dilute polymer solutions in good solvent conditions. J. Chem. Phys. 96 11 (1992) 8539-8551
13. Pagonabarraga I., Hagen M.H.J., and Frenkel D. Self-consistent dissipative particle dynamics algorithm. Europhys. Lett. 42 (1998) 377
14. den Otter W., and Clarke J. The temperature in dissipative particle dynamics. Europhys. Lett. 53 (2001) 426-431
15. Lowe C.P. An alternative approach to dissipative particle dynamics. Europhys. Lett. 47 2 (1999) 145-151
16. Shardlow T. Splitting for dissipative particle dynamics. SIAM J. Sci. Comput. 24 4 (2003) 1267-1282
17. Peters E. Elimination of time step effects in DPD. Europhys. Lett. 66 3 (2004) 311-317
18. Besold G., Vattulainen I., Karttunen M., and Polson J. Towards better integrators for dissipative particle dynamics simulations. Phys. Rev. E 62 6 (2000) R7611
19. Nikunen P., Karttunen M., and Vattulainen I. How would you integrate the equations of motion in dissipative particle dynamic simulations?. Comput. Phys. Commun. 153 (2003) 407-423
20. Karniadakis G.E., and Sherwin S.J. Spectral/hp Element Methods for Computational Fluid Dynamics. second ed. (2005), Oxford University Press, Oxford
21. Bishop T., Skeel R.D., and Schulten K. Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics. J. Comput. Chem. 18 14 (1997) 1785-1791
22. Verlet L. Computer 'experiments' on classical fluids. I: Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159 (1967) 98-103
23. Jakobsen A., Mouritsen O., and Besold G. Artifacts in dynamical simulations of coarse-grained model lipid bilayers. J. Chem. Phys. 122 (2005) 204901
24. Forrest B.M., and Suter U.W. Accelerated equilibration of polymer melts by time-coarse-graining. J. Chem. Phys. 102 18 (1995) 7256-7266
25. Jendrejack R.M., de Pablo J.J., and Graham M.D. Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions. J. Chem. Phys. 116 (2002) 7752-7759
26. Kratky O., and Porod G. Röntgenuntersuchung gelöster fadenmoleküle. Rec. Trav. Chim. 68 (1949) 1106-1115
27. Yamakawa H. Modern Theory of Polymer Solutions (1971), Harper and Row, New York
28. Sun S.F. Physical Chemistry of Macromolecules (1994), Wiley, New York
29. Marko J.F., and Siggia E.D. Stretching DNA. Macromolecules 28 (1995) 8759-8770
30. Larson R.G., Perkins T.T., Smith D.E., and Chu S. Hydrodynamics of a DNA molecule in a flow field. Phys. Rev. E 55 2 (1997) 1794-1797
31. Underhill P.T., and Doyle P.S. On the coarse-graining of polymers into bead-spring chains. J. Non-Newtonian Fluid Mech. 122 1 (2004) 3-31
32. Andersen H.C. Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72 4 (1980) 2384-2396
33. Ma Q., Izaguirre J.A., and Skeel R.D. Verlet-I/R-RESPA/Impulse is limited by nonlinear instabilities. SIAM J. Sci. Comput. 24 6 (2003) 1951-1973
34. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1989), Oxford University Press, Oxford
35. Larson R.G. The Structure and Rheology of Complex Fluids (1999), Oxford University Press, Oxford
36. Kong Y., Manke C.W., Maddenand W.G., and Schlijper A.G. Effect of solvent quality on the conformation and relaxation of polymers via dissipative particle dynamics. J. Chem. Phys. 107 2 (1997) 592-602
37. Bouchiat C., Wang M.D., Allemand J.-F., Strick T., Block S.M., and Croquette V. Estimating the persistence length of a worm-like-chain molecule from force-extension measurements. Biophys. J. 76 (1999) 409-413
38. Smith D.E., Babcock H.P., and Chu S. Single polymer dynamics in steady shear flow. Science 283 (1999) 1724
39. Hur J.S., Shaqfeh E.S.G., and Larson R.G. Brownian dynamics simulations of single DNA molecules in shear flow. J. Rheol. 44 4 (2000) 713-742
40. Lees A.W., and Edwards S.F. The computer study of transport processes under extreme conditions. J. Phys. C 5 (1972) 1921
41. V. Symeonidis, Numerical methods for multi-scale modeling of non-Newtonian flows, Ph.D. Thesis, Brown University, 2006.