Recent progress in adaptive multiscale molecular dynamics simulations of soft matter

Physical Chemistry Chemical Physics

Volumn 12, Issue 39, 2010, Pages 12401-12414

  Nielsen, Steven O ^a   Bulo, Rosa E ^b   Moore, Preston B ^c   Ensing, Bernd ^d  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c UNIVERSITY OF THE SCIENCES   (United States)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957897253     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/c004111d     Document Type: Article

References (75)

1. P. K. Jain, X. Huang, I. H. El-Sayed, M. A. El-Sayed Acc. Chem. Res., 2008, 41, 1578.
2. Y. Yang, U. Khoe, X. Wang, A. Horii, H. Yokoi, S. Zhang Nano Today, 2009, 4, 269.
3. A. Guskov, A. Gabdulkhakov, M. Broser, C. Glöckner, J. Hellmich, J. Kern, J. Frank, F. Müh, W. Saenger, A. Zouni ChemPhysChem, 2010, 11, 1160.
4. K. Shirasu Annu. Rev. Plant Biol., 2009, 60, 139.
5. R. B. Schoch, J. Han, P. Renaud Rev. Mod. Phys., 2008, 80, 839.
6. M. Liu, N. A. Amro, G. Liu Annu. Rev. Phys. Chem., 2008, 59, 367.
7. O. E. Andreikiv, R. M. Lesiv, N. M. Levyts’ka Mater. Sci., 2009, 45, 1.
8. J. Peet, A. J. Heeger, G. C. Bazan Acc. Chem. Res., 2009, 42, 1700.
9. W. L. Jorgensen Acc. Chem. Res., 2009, 42, 724.
10. M. L. Klein, W. Shinoda Science, 2008, 321, 798.
11. C. Peter, K. Kremer Soft Matter, 2009, 5, 4357.
12. F. Müller-Plathe ChemPhysChem, 2002, 3, 754.
13. G. Tabacchi, C. Mundy, J. Hutter, M. Parrinello J. Chem. Phys., 2002, 117, 1416.
14. D. Paschek, R. Krishna Langmuir, 2001, 17, 247.
15. R. E. Miller, E. B. Tadmor Modell. Simul. Mater. Sci. Eng., 2009, 17, 053001.
16. H. Hu, W. Yang Annu. Rev. Phys. Chem., 2008, 59, 573.
17. I. G. Kevrekidis, G. Samaey Annu. Rev. Phys. Chem., 2009, 60, 321.
18. W. E. B. Engquist, X. Li, W. Ren, E. Vanden-Eijnden Commun. Comput. Phys., 2007, 2, 367.
19. V. Tozzini Acc. Chem. Res., 2010, 43, 220.
20. M. Tuckerman J. Phys.: Condens. Matter, 2002, 14, R1297.
21. W. Wang, O. Donini, C. Reyes, P. Kollman Annu. Rev. Biophys. Biomol. Struct., 2001, 30, 211.
22. S. O. Nielsen, C. F. Lopez, S. Srinivas, M. L. Klein J. Phys.: Condens. Matter, 2004, 16, R481.
23. M. J. Alava, P. K. V. V. Nukalaz, S. Zapperi Adv. Phys., 2006, 55, 349.
24. J. Stickel, R. Powell Annu. Rev. Fluid Mech., 2005, 37, 129.
25. G. Ciccotti, R. Kapral, E. Vanden-Eijnden ChemPhysChem, 2005, 6, 1809.
26. H. Lin, D. G. Truhlar Theor. Chem. Acc., 2007, 117, 185.
27. Q. Shi, S. Izvekov, G. Voth J. Phys. Chem. B, 2006, 110, 15045.
28. M. Neri, C. Anselmi, V. Carnevale, A. V. Vargiu, P. Carloni J. Phys.: Condens. Matter, 2006, 18, S347.
29. J. Michel, M. Orsi, J. W. Essex J. Phys.Chem. B, 2008, 112, 657.
30. M. Orsi, W. E. Sanderson, J. W. Essex J. Phys. Chem. B, 2009, 113, 12019.
31. K. M. Mohamed, A. A. Mohamad Microfluid. Nanofluid., 2010, 8, 283.
32. M. Praprotnik, L. Delle Site, K. Kremer Annu. Rev. Phys. Chem., 2008, 59, 545.
33. R. Kapral Annu. Rev. Phys. Chem., 2006, 57, 129.
34. P. Pechukas Phys. Rev., 1969, 181, 174.
35. J. J. de Pablo, W. A. Curtin MRS Bulletin, 2007, 32, 905.
36. M. Praprotnik, L. Delle Site, K. Kremer J. Chem. Phys., 2005, 123, 224106.
37. A. Heyden, D. G. Truhlar J. Chem. Theory Comput., 2008, 4, 217.
38. B. Ensing, S. O. Nielsen, P. B. Moore, M. L. Klein, M. Parrinello J. Chem. Theory Comput., 2007, 3, 1100.
39. C. Abrams J. Chem. Phys., 2005, 123, 234101.
40. J. H. Park, A. Heyden Mol. Simul., 2009, 35, 962.
41. M. Praprotnik, S. Matysiak, L. Delle Site, K. Kremer, C. Clementi J. Phys.: Condens. Matter, 2007, 19, 292201.
42. S. Matysiak, C. Clementi, M. Praprotnik, K. Kremer, L. Delle Site J. Chem. Phys., 2008, 128, 024503.
43. M. Praprotnik, L. Delle Site, K. Kremer Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2006, 73, 066701.
44. M. Praprotnik, K. Kremer, L. Delle Site J. Phys. A: Math. Theor., 2007, 40, F281.
45. M. Praprotnik, K. Kremer, L. Delle Site Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2007, 75, 017701.
46. A. Heyden, H. Lin, D. G. Truhlar J. Phys. Chem. B, 2007, 111, 2231.
47. R. E. Bulo, B. Ensing, J. Sikkema, L. Visscher J. Chem. Theory Comput., 2009, 5, 2212.
48. S. O. Nielsen, B. Ensing, P. B. Moore, and M. L. Klein, Advances in Hierarchical and MultiScale Simulations of Materials, John Wiley & Sons Inc., Hoboken, NJ, USA, 2007, pp. 73-88
49. W. Tschöp, K. Kremer, O. Hahn, J. Batoulis, T. Bürger Acta Polym., 1998, 49, 75.
50. L.-J. Chen, H.-J. Qian, Z.-Y. Lu, Z.-S. Li, C.-C. Sun J. Phys. Chem. B, 2006, 110, 24093.
51. B. Hess, S. Leon, N. van der Vegt, K. Kremer Soft Matter, 2006, 2, 409.
52. G. Santangelo, A. D. Matteo, F. Müller-Plathe, G. Milano J. Phys. Chem. B, 2007, 111, 2765.
53. P. Liu, Q. Shi, E. Lyman, G. A. Voth J. Chem. Phys., 2008, 129, 114103.
54. P. Carbone, H. A. Karimi-Varzaneh, F. Müller-Plathe Faraday Discuss., 2010, 144, 25.
55. A. J. Rzepiela, L. V. Schafer, N. Goga, H. J. Risselada, A. H. D. Vries, S. J. Marrink J. Comp. Chem., 2010, 31, 1333.
56. J. Baschnagel, K. Binder, P. Doruker, A. A. Gusev, O. Hahn, K. Kremer, W. L. Mattice, F. Müller-Plathe, M. Murat, W. Paul, et al.Adv. Polym. Sci., 2000, 152, 41.
57. V. A. Harmandaris, N. P. Adhikari, N. F. A. van der Vegt, K. Kremer Macromolecules, 2006, 39, 6708.
58. A. P. Heath, L. E. Kavraki, C. Clementi Proteins: Struct., Funct., Bioinf., 2007, 68, 646.
59. C. J. Taylor, and D. J. Kriegman, Tech. Rep. 9405, Center for Systems Science, Dept. of Electrical Engineering, Yale University, New Haven, CT, 1994
60. A. MacKerel Jr., C. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus, in The Encyclopedia of Computational Chemistry, ed. P. V. R. Schleyer, P. R. Schreiner, N. L. Allinger, T. Clark, J. Gasteiger, P. Kollman, H. F. Schaefer III, John Wiley & Sons, Chichester, 1998, vol. 1, pp. 271-277
61. B. Ensing, and S. O. Nielsen, Multiscale molecular dynamics and the reverse mapping problem, In: Trends in Computational Nanomechanics (Challenges and Advances in Computational Chemistry and Physics, Volume 9), ed. T. Dumitrica, Springer, 2010, pp.25-60
62. P. Krysl, L. Endres Int. J. Numer. Methods Eng., 2005, 62, 2154.
63. E. Lyman, F. Ytreberg, D. Zuckerman Phys. Rev. Lett., 2006, 96, 028105.
64. E. Lyman, D. M. Zuckerman J. Chem. Theory Comput., 2006, 2, 656.
65. M. Christen, W. van Gunsteren J. Chem. Phys., 2006, 124, 154106.
66. P. Liu, G. A. Voth J. Chem. Phys., 2007, 126, 045106.
67. S. O. Nielsen, C. F. Lopez, G. Srinivas, M. L. Klein J. Chem. Phys., 2003, 119, 7043.
68. T. Kerdcharoen, K. R. Liedl, B. M. Rode Chem. Phys., 1996, 211, 313.
69. T. Kerdcharoen, K. Morokuma Chem. Phys. Lett., 2002, 355, 257.
70. G. Csányi, T. Albaret, M. C. Payne, A. DeVita Phys. Rev. Lett., 2004, 93, 175503.
71. M. Cascella, M. A. Neri, P. Carloni, M. D. Peraro J. Chem. Theory Comput., 2008, 4, 1378.
72. R. Delgado-Buscalioni, K. Kremer, M. Praprotnik J. Chem. Phys., 2008, 128, 114110.
73. F. Varnik, K. Binder Int. J. Mater. Res., 2009, 100, 1494.
74. R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein J. Chem. Theory Comput., 2009, 5, 2115.
75. Here and in the following we will refer to E as the total energy although this is in fact a fictitious augmented energy that includes the differences between T + V in the AA and CG representations