Nonperiodic stochastic boundary conditions for molecular dynamics simulations of materials embedded into a continuum mechanics domain

Journal of Chemical Physics

Volumn 134, Issue 15, 2011, Pages

  Rahimi, Mohammad ^a   Karimi Varzaneh, Hossein Ali ^a   Böhm, Michael C ^a   Müller Plathe, Florian ^a   Pfaller, Sebastian ^b   Possart, Gunnar ^b   Steinmann, Paul ^b  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANCHOR POINT; BOUNDARY REGIONS; COARSE-GRAINED; DISSIPATIVE PARTICLE DYNAMICS; DYNAMIC PROPERTY; EQUILIBRIUM POSITIONS; FINITE ELEMENT; MOLECULAR DYNAMICS SIMULATIONS; PARTICLE DOMAINS; PERIODIC BOUNDARY CONDITIONS; POLYSTYRENE MELTS; STOCHASTIC BOUNDARY CONDITIONS;

BOUNDARY CONDITIONS; CONTINUUM MECHANICS; DYNAMICS; ELASTICITY; POLYSTYRENES; STOCHASTIC SYSTEMS;

MOLECULAR DYNAMICS;

EID: 79955417786     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3576122     Document Type: Article

References (49)

1. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford, Clarendon, 1987).
2. G. King and A. Warshel, J. Chem. Phys. 91, 3647 (1989). 10.1063/1.456845
3. A. H. Juffer and H. C. J. Berendsen, Mol. Phys. 79, 623 (1993). 10.1080/00268979300101501
4. D. Beglov and B. Roux, J. Chem. Phys. 100, 9050 (1994). 10.1063/1.466711
5. V. Lounnas, S. K. Ldemann, and R. C. Wade, Biophys. Chem. 78, 157 (1999). 10.1016/S0301-4622(98)00237-3 (Pubitemid 29206664)
6. G. Petraglio, M. Ceccarelli, and M. Parrinello, J. Chem. Phys. 123, 044103 (2005). 10.1063/1.1955449 (Pubitemid 41164715)
7. G. Brancato, A. D. Nola, V. Barone, and A. Amadei, J. Chem. Phys. 122, 154109 (2005). 10.1063/1.1877172 (Pubitemid 40858256)
8. G. Brancato, N. Rega, and V. Barone, Chem. Phys. Lett. 483, 177 (2009). 10.1016/j.cplett.2009.10.069
9. M. Berkowitz and J. A. McCammon, Chem. Phys. Lett. 90, 215 (1982). 10.1016/0009-2614(82)80028-6
10. C. L. Brooks and M. Karplus, J. Chem. Phys. 79, 6312 (1983). 10.1063/1.445724
11. A. Brnger, C. L. Brooks, and M. Karplus, Chem. Phys. Lett. 105, 495 (1984). 10.1016/0009-2614(84)80098-6
12. M. J. Mandell, J. Stat. Phys. 15, 299 (1976). 10.1007/BF01023055
13. L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1864 (1981). 10.1063/1.441276
14. L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1873 (1981). 10.1063/1.441277
15. B. Dnweg and K. Kremer, Phys. Rev. Lett. 66, 2996 (1991). 10.1103/PhysRevLett.66.2996
16. I.-C. Yeh and G. Hummer, J. Chem. Phys. B 108, 15873 (2004). 10.1021/jp0477147
17. M. Gonzlez-Melchor, P. Orea, J. Lpez-Lemus, F. Bresme, and J. Alejandre, J. Chem. Phys. 122, 094503 (2005). 10.1063/1.1854625 (Pubitemid 41042153)
18. P. E. Smith and B. M. Pettitt, J. Chem. Phys. 105, 4289 (1996). 10.1063/1.472246
19. P. H. Hnenberger and J. A. McCammon, J. Chem. Phys. 110, 1856 (1999). 10.1063/1.477873
20. P. Wriggers, Nonlinear Finite Element Methods (Springer, Heidelberg, 2008).
21. K. M. Mohamed and A. A. Mohamad, Microfluid. Nanofluid. 8, 283 (2010). 10.1007/s10404-009-0529-z
22. Multiscale Modeling and Simulation, Lecture Notes in Computational Science and Engineering, edited by, S. Attinger, and, P. Koumoutsakos, (Springer, Heidelberg, 2004), Vol. 39.
23. S. T. O'Connell and P. A. Thompson, Phys. Rev. E 52, R5792 (1995). 10.1103/PhysRevE.52.R5792
24. E. M. Kotsalis, J. H. Walther, and P. Koumoutsakos, Phys. Rev. E 76, 016709 (2007). 10.1103/PhysRevE.76.016709 (Pubitemid 47208430)
25. T. Werder, J. H. Walther, and P. Koumoutsakos, J. Comput. Phys. 205, 373 (2005). 10.1016/j.jcp.2004.11.019
26. R. Delgado-Buscalioni, K. Kremer, and M. Praprotnik, J. Chem. Phys. 131, 244107 (2009). 10.1063/1.3272265
27. E. G. Flekky, R. Delgado-Buscalioni, and P. V. Coveney, Phys. Rev. E 72, 026703 (2005). 10.1103/PhysRevE.72.026703 (Pubitemid 41520810)
28. E. B. Tadmor, M. Ortiz, and R. Phillips, Philos. Mag. A 73, 1529 (1996). 10.1080/01418619608243000
29. R. Miller, M. Ortiz, R. Phillips, V. Shenoy, and E. B. Tadmor, Eng. Frac. Mech. 61, 1899 (1998). 10.1016/S0013-7944(98)00047-2 (Pubitemid 29085496)
30. J. Knap and M. Ortiz, J. Mech. Phys. Solids 49, 1899 (2001). 10.1016/S0022-5096(01)00034-5 (Pubitemid 32768095)
31. L. E. Shilkrot, W. A. Curtin, and R. E. Miller, J. Mech. Phys. Solids 50, 2085 (2002). 10.1016/S0022-5096(02)00017-0 (Pubitemid 34803079)
32. L. E. Shilkrot, R. E. Miller, and W. A. Curtin, J. Mech. Phys. Solids 52, 755 (2004). 10.1016/j.jmps.2003.09.023
33. T. Belytschko and S. P. Xiao, Int. J. Multiscale Comp. Eng. 1, 115 (2003). 10.1615/IntJMultCompEng.v1.i1.100
34. P. T. Bauman, H. B. Dhia, N. Elkhodja, J. T. Oden, and S. Prudhomme, Comput. Mech. 42, 511 (2008). 10.1007/s00466-008-0291-1
35. S. Pfaller, G. Possart, P. Steinmann, M. Rahimi, F. Møller-Plathe, and M. C. Bhm, A comparison of staggered solution schemes for coupled particle-continuum systems modeled with the Arlequin method., Comput. Mech. (submitted).
36. F. Møller-Plathe, Chem. Phys. Chem. 3, 754 (2002). 10.1002/1439-7641(20020916)3:9754::AID-CPHC7543.0.CO;2-U
37. R. Delgado-Buscalioni, K. Kremer, and M. Praprotnik, J. Chem. Phys. 128, 114110 (2008). 10.1063/1.2890729 (Pubitemid 351423189)
38. R. D. Groot and P. B. Warren, J. Chem. Phys. 107, 4423 (1997). 10.1063/1.474784
39. H. Meyer, O. Biermann, R. Faller, D. Reith, and F. Møller-Plathe, J. Chem. Phys. 113, 6265 (2000). 10.1063/1.1308542
40. F. Møller-Plathe, Soft Mater. 1, 1 (2003). 10.1081/SMTS-120016739
41. T. Spyriouni, C. Tzoumanekas, D. Theodorou, F. Møller-Plathe, and G. Milano, Macromolecules 40, 3876 (2007). 10.1021/ma0700983 (Pubitemid 46841951)
42. P. Espaol and P. Warren, Europhys. Lett. 30, 191 (1995). 10.1209/0295-5075/30/4/001
43. H.-J. Qian, C. C. Liew, and F. Møller-Plathe, Phys. Chem. Chem. Phys. 11, 1962 (2009). 10.1039/b817584e
44. I. Vattulainen, M. Karttunen, G. Besold, and J. M. Polson, J. Chem. Phys. 116, 3967 (2002). 10.1063/1.1450554 (Pubitemid 34459312)
45. H. Qian, P. Carbone, X. Chen, H. A. Karimi-Varzaneh, and F. Møller-Plathe, Macromolecules 41, 9919 (2008). 10.1021/ma801910r
46. G. Milano and F. Møller-Plathe, J. Chem. Phys. B 109, 18609 (2005). 10.1021/jp0523571 (Pubitemid 41464198)
47. H. A. Karimi-Varzaneh, H.-J. Qian, X. Chen, P. Carbone, and F. Møller-Plathe, J. Comput. Chem. 32, 1475 (2011). 10.1002/jcc.21717
48. H. J. C. Berendsen, J. P. M. Postma, W. F. v. Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984). 10.1063/1.448118
49. H. Heinz, W. Paul, and K. Binder, Phys. Rev. E 72, 066704 (2005). 10.1103/PhysRevE.72.066704 (Pubitemid 43272997)