Coarse-grained modeling for macromolecular chemistry

Topics in Current Chemistry

Volumn 307, Issue , 2012, Pages 295-322

  Karimi Varzaneh, Hossein Ali ^a   Müller Plathe, Florian ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Atomistic simulation; Coarse graining simulation; Computational chemistry; Multiscale modeling

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MACROMOLECULE; PHYSICAL CHEMISTRY; QUANTUM THEORY; THERMODYNAMICS; TIME;

CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; QUANTUM THEORY; THERMODYNAMICS; TIME FACTORS;

EID: 81855185392     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2010_122     Document Type: Article

References (122)

1. Kremer K (2006) Polymer dynamics: long time simulations and topological constraints. In: Ferrario M, Ciccoti G, Binder K (eds) Computer simulations in condensed matter systems: from materials to chemical biology, vol 2. Lecture notes in physics, vol 704. Springer, Berlin, Heidelberg, p 341
2. Martonak R, Paul W, Binder K (1997) J Chem Phys 106:8918
3. Goldstein H, Poole C, Safko J (2002) Classical mechanics. Addison Wesley, San Francisco
4. Harmandaris VA, Mavrantzas V (2004) Molecular dynamic simulations of polymers. In: Theodorou DN, Kotelyanski M (eds) Simulation methods for polymers. Marcel Dekker, New York
5. Baschnagel J, Binder K, Doruker P, Gusev AA, Hahn O, Kremer K, Mattice WL, Müller-Plathe F, Murat M, Paul W, Santos S, Suter UW, Tries V (2000) Adv Polym Sci 152:41
6. Binder K (1995) Monte Carlo and molecular dynamics simulations in polymer science. Oxford University Press, New York
7. Theodorou DN (2010) Ind Eng Chem Res 49:3047
8. Mavrantzas VG, Boone TD, Zervopoulou E, Theodorou DN (1999) Macromolecules 32:5072
9. Karayiannis NC, Giannousaki AE, Mavrantzas VG, Theodorou DN (2002) J Chem Phys 117:5465
10. Kremer K, Grest GS (1990) J Chem Phys 92:5057
11. Muller M, Katsov K, Schick M (2006) Phys Rep 434:113
12. Reynwar BJ, Illya G, Harmandaris VA, Müller MM, Kremer K, Deserno M (2007) Nature 447:461
13. Auhl R, Everaers R, Grest GS, Kremer K, Plimpton SJ (2003) J Chem Phys 119:12718
14. Grest GS, Kremer K (1986) Phys Rev A 33:3628
15. Carbone P, Karimi-Varzaneh HA, Chen X,Müller-Plathe F (2008) J Chem Phys 128:064904
16. Karimi-Varzaneh HA, Carbone P, Müller-Plathe F (2008) J Chem Phys 129:154904
17. Milano G, Müller-Plathe F (2005) J Phys Chem B 109:18609
18. Qian H-J, Carbone P, Chen X, Karimi-Varzaneh HA, Liew CC, Müller-Plathe F (2008) Macromolecules 41:9919
19. Karimi-Varzaneh HA, Müller-Plathe F, Balasubramanian S, Carbone P (2010) Phys Chem Chem Phys 12:4714
20. Carbone P, Negri F, Müller-Plathe F (2007) Macromolecules 40:7074
21. Harmandaris VA, Reith D, van der Vegt NFA, Kremer K (2007) Macromol Chem Phys 208:2109
22. Harmandaris VA, Adhikari NP, van der Vegt NFA, Kremer K (2007) Macromolecules 40:7026
23. Triolo A, Mandanici A, Russina O, Rodriguez-Mora V, Cutroni M, Hardacre C, Nieuwenhuyzen M, Bleif HJ, Keller L, Ramos MA (2006) J Phys Chem B 110:21357
24. Lopes J, Padua AAH (2006) J Phys Chem B 110:3330
25. Bhargava BL, Devane R, Klein ML, Balasubramanian S (2007) Soft Matter 3:1395
26. Urahata SM, Ribeiro MCC (2004) J Chem Phys 120:1855
27. Praprotnik M, Delle Site L, Kremer K (2008) Annu Rev Phys Chem 59:545
28. Izvekov S, Parrinello M, Burnham CJ, Voth GA (2004) J Chem Phys 120:10896
29. Luybartsev AP, Laaksonen A (1995) Phys Rev E 52:3730
30. Spyriouni T, Tzoumanekas C, Theodorou D, Müller-Plathe F, Milano G (2007) Macromolecules 40:3876
31. Nielsen SO, Srinivas G, Klein M (2005) J Chem Phys 123:124907
32. Marrink SJ, Vries AHd, Mark AE (2004) J Phys Chem B 108:750
33. Padding JT, Briels WJ (2002) J Chem Phys 117:925
34. Li XJ, Kou DZ, Rao SL, Liang H (2006) J Chem Phys 124:204909
35. Haliloglou T, Mattice WL (1998) J Chem Phys 108:6989
36. Sun Q, Faller R (2006) Macromolecules 39:812
37. Harmandaris VA, Adhikari NP, van der Vegt NFA, Kremer K (2006) Macromolecules 39:6708
38. Larson RG (2004) Mol Phys 102:341
39. Fukunaga H, Takimoto J, Doi M (2002) J Chem Phys 116:8183
40. Reith D, Meyer H, Müller-Plathe F (2001) Macromolecules 34:2335
41. Reith D, Pütz M, Müller-Plathe F (2003) J Comput Chem 24:1624
42. Tschöp KKW, Batoulis J, Bürger T, Hahn O (1998) Acta Polym 49:61
43. Paul W, Binder K, Kremer K, Heermann D (1991) Macromolecules 24:6332
44. Abrams C, Kremer K (2003) Macromolecules 36:260
45. Milano G, Goudeau S, Müller-Plathe F (2005) J Polym Sci Pol Phys 43:871
46. Queyroy S, Neyertz S, Brown D, Müller-Plathe F (2004) Macromolecules 37:7338
47. Meyer H, Müller-Plathe F (2002) Macromolecules 35:1241
48. Peter C, Delle Site L, Kremer K (2008) Soft Matter 4:859
49. Faller R, Schmitz H, Biermann O, Müller-Plathe F (1999) J Comput Chem 20:1009
50. Meyer H, Biermann O, Faller R, Reith D, Müller-Plathe F (2000) J Chem Phys 113:6264
51. Soper AK (1996) Chem Phys 202:295
52. Reith D, Meyer H, Müller-Plathe F (2002) Comput Phys Commun 148:299
53. Henderson RL (1974) Phys Lett A 49:197
54. Karimi-Varzaneh HA, Qian H-J, Chen X, Carbone P, Müller-Plathe F (2011) J Comput Chem. DOI: 10.1002/jcc.21717
55. Groot RD, Warren PB (1997) J Chem Phys 107:4423
56. Lowe CP (1999) Europhys Lett 47:145
57. Qian H-J, Liew CC, Müller-Plathe F (2009) Phys Chem Chem Phys 11:1962
58. Bordat P, Müller-Plathe F (2002) J Chem Phys 116:3362
59. Vettorel T, Meyer H (2006) J Chem Theory Comput 2:616
60. Ghosh J, Faller R (2007) Mol Simul 33:759
61. Karimi-Varzaneh HA, Carbone P, Müller-Plathe F (2008) Macromolecules 41:7211
62. Steiner T (2002) Angew Chem Int Ed 41:48
63. Sancho DD, Rey A (2007) J Comput Chem 28:1187
64. Murthy NS (2006) J Polym Sci B Polym Phys 44:1763
65. Garcia D, Starkweather HW (1985) J Polym Sci Polym Phys Ed 23:537
66. Bessler E, Bier G (1969) Makromol Chem 122:30
67. Trifan DS, Terenzi JF (1958) J Polym Sci 28:443
68. Schroeder LR, Cooper SL (1976) J Appl Phys 47:4310
69. Waldman M, Hagler AT (1993) J Comput Chem 14:1077
70. Chen X, Carbone P, Cavalcanti WL, Milano G, Müller-Plathe F (2007) Macromolecules 40:8087
71. Izvekov S, Voth GA (2006) J Chem Phys 125:151101
72. Leon S, van der Vegt NFA, Delle Site L, Kremer K (2005) Macromolecules 38:8078
73. Harmandaris VA, Kremer K (2009) Macromolecules 42:791
74. Sun Q, Faller R (2006) J Chem Theory Comput 2:607
75. Villa A, van der Vegt NFA, Peter C (2009) Phys Chem Chem Phys 11:2068
76. Villa A, Peter C, van der Vegt NFA (2009) Phys Chem Chem Phys 11:2077
77. Fritz D, Harmandaris VA, Kremer K, van der Vegt NFA (2009) Macromolecules 42:7579
78. Izvekov S, Voth GA (2005) J Chem Phys B 109:2469
79. Izvekov S, Voth GA (2005) J Chem Phys 123:134105
80. Noid WG, Chu J-W, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC (2008) J Chem Phys 128:244114
81. Noid WG, Chu JW, Ayton GS, Voth GA (2007) J Phys Chem B 111:4116
82. Noid WG, Liu P, Wang Y, Chu J-W, Ayton GS, Izvekov S, Andersen HC, Voth GA (2008) J Chem Phys 128:244115
83. Liu P, Voth GA (2007) J Chem Phys 126:045106
84. Zhou J, Thorpe IF, Izvekov S, Voth GA (2007) Biophys J 92:4289
85. Izvekov S, Voth GA (2006) J Chem Theory Comput 2:637
86. Wang Y, Izvekov S, Yan T, Voth GA (2006) J Phys Chem B 110:3564
87. Wang Y, Voth GA (2005) J Am Chem Soc 127:12192
88. Izvekov S, Violi A, Voth GA (2005) J Phys Chem B 109:17019
89. Shi Q, Izvekov S, Voth GA (2006) J Phys Chem B 110:15045
90. Larini L, Lu L, Voth GA (2010) J Chem Phys 132:164107
91. Marrink SJ, Risselada HJ, Yefi mov S, Tieleman DP, de Vries AH (2007) J Phys Chem B 111:7812
92. Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (2007) Chem Phys Chem 8:452
93. Monticelli L, Kandasamy S, Periole X, Larson RG, Tieleman DP, Marrink SJ (2008) J Chem Theory Comp 4:819
94. Marrink SJ, Mark AE (2004) Biophys J 87:3894
95. Lee H, Vries AHd, Marrink S-J, Pastor RW (2009) J Phys Chem B 113:13186
96. Rossi G, Monticelli L, Puisto SR, Vattulainen I, Ala-Nissila T (2011) Soft Matter 7:698
97. Lyubartsev A, Mirzoev A, Chen L, Laaksonen A (2010) Faraday Discuss 144:43
98. Lyubartsev AP, Laaksonen A (1995) Phys Rev E 52:3730
99. Lyubartsev AP, Laaksonen A (2004) On the reduction of molecular degrees of freedom in computer simulations. In: Karttunen M, Vattulainen I, Lukkarinen A (eds) Novel methods in soft matter simulations. Springer, Berlin, Heidelberg, pp 219-244
100. Schneider J, Hess W, Klein R (1985) J Phys A 18:1221
101. Jiang W, Wang YT, Yan TY, Voth GA (2008) J Phys Chem C 112:1132
102. Abrams CF, Delle Site L, Kremer K (2003) Phys Rev E 67:021807
103. Delle Site L, Leon S, Kremer K (2004) J Am Chem Soc 126:2944
104. Praprotnik M, Delle Site L, Kremer K (2005) J Chem Phys 123:224106
105. Praprotnik M, Matysiak S, Delle Site L, Kremer K, Clementi C (2007) J Phys Condens Mater 19:292201
106. Praprotnik M, Delle Site L, Kremer K (2007) J Chem Phys 126:134902
107. Ensing B, Nielsen SO, Moore PB, Klein ML, Parrinello M (2007) J Chem Theory Comp 3:1100
108. Poblete S, Praprotnik M, Kremer K, Site LD (2010) J Chem Phys 132:114101
109. Matysiak S, Clementi C, Praprotnik M, Kremer K, Site LD (2008) J Chem Phys 128:024503
110. Poma AB, Site LD (2010) Phys Rev Lett 104:250201
111. Junghans C, Praprotnik M, Site LD (2009) In: Grotendorst J, Attig N, Blügel S, Marx D (eds) Multiscale simulation methods in molecular sciences, NIC Series vol 42. Institute for Advanced Simulation, Forschungszentrum Jülich, Germany, p 359
112. Delgado-Buscalioni R, Kremer K, Praprotnik M (2008) J Chem Phys 128:114110
113. Violi A (2009) In: Voth GA (ed) Coarse-graining of condensed phase and biomolecular systems. CRC, Boca Raton, pp 433-448
114. Violi A (2004) Combust Flame 139:279
115. Santangelo G, Di Matteo A, Müller-Plathe F, Milano G (2007) J Phys Chem B 111:2765
116. Hess B, Leon S, van der Vegt NFA, Kremer K (2006) Soft Matter 2:409
117. Chen X, Carbone P, Santangelo G, Di Matteo A, Milano G, Müller-Plathe F (2009) Phys Chem Chem Phys 11:1977
118. Hess B, Peter C, Ozal T, van der Vegt NFA (2008) Macromolecules 41:2283
119. Ozal T, Peter C, Hess B, van der Vegt NFA (2008) Macromolecules 41:5055
120. Hess B, van der Vegt NFA (2008) Macromolecules 41:7281
121. Merkel TC, Bondar VI, Nagai K, Freeman BD, Pinnau I (2000) J Polym Sci B Polym Phys 38:415
122. Korsmeyer RW, Meerwall EV, Peppas NA (1986) J Polym Sci B Polym Phys 24:409