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Coarse-Grained Modeling for Macromolecular Chemistry

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References

  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

    Google Scholar 

  2. Martonak R, Paul W, Binder K (1997) J Chem Phys 106:8918

    CAS  Google Scholar 

  3. Goldstein H, Poole C, Safko J (2002) Classical mechanics. Addison Wesley, San Francisco

    Google Scholar 

  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

    Google Scholar 

  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

    CAS  Google Scholar 

  6. Binder K (1995) Monte Carlo and molecular dynamics simulations in polymer science. Oxford University Press, New York

    Google Scholar 

  7. Theodorou DN (2010) Ind Eng Chem Res 49:3047

    CAS  Google Scholar 

  8. Mavrantzas VG, Boone TD, Zervopoulou E, Theodorou DN (1999) Macromolecules 32:5072

    CAS  Google Scholar 

  9. Karayiannis NC, Giannousaki AE, Mavrantzas VG, Theodorou DN (2002) J Chem Phys 117:5465

    CAS  Google Scholar 

  10. Kremer K, Grest GS (1990) J Chem Phys 92:5057

    CAS  Google Scholar 

  11. Muller M, Katsov K, Schick M (2006) Phys Rep 434:113

    Google Scholar 

  12. Reynwar BJ, Illya G, Harmandaris VA, Müller MM, Kremer K, Deserno M (2007) Nature 447:461

    CAS  Google Scholar 

  13. Auhl R, Everaers R, Grest GS, Kremer K, Plimpton SJ (2003) J Chem Phys 119:12718

    CAS  Google Scholar 

  14. Grest GS, Kremer K (1986) Phys Rev A 33:3628

    CAS  Google Scholar 

  15. Carbone P, Karimi-Varzaneh HA, Chen X, Müller-Plathe F (2008) J Chem Phys 128:064904

    Google Scholar 

  16. Karimi-Varzaneh HA, Carbone P, Müller-Plathe F (2008) J Chem Phys 129:154904

    Google Scholar 

  17. Milano G, Müller-Plathe F (2005) J Phys Chem B 109:18609

    CAS  Google Scholar 

  18. Qian H-J, Carbone P, Chen X, Karimi-Varzaneh HA, Liew CC, Müller-Plathe F (2008) Macromolecules 41:9919

    CAS  Google Scholar 

  19. Karimi-Varzaneh HA, Müller-Plathe F, Balasubramanian S, Carbone P (2010) Phys Chem Chem Phys 12:4714

    CAS  Google Scholar 

  20. Carbone P, Negri F, Müller-Plathe F (2007) Macromolecules 40:7074

    Google Scholar 

  21. Harmandaris VA, Reith D, van der Vegt NFA, Kremer K (2007) Macromol Chem Phys 208:2109

    CAS  Google Scholar 

  22. Harmandaris VA, Adhikari NP, van der Vegt NFA, Kremer K (2007) Macromolecules 40:7026

    CAS  Google Scholar 

  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

    CAS  Google Scholar 

  24. Lopes J, Padua AAH (2006) J Phys Chem B 110:3330

    Google Scholar 

  25. Bhargava BL, Devane R, Klein ML, Balasubramanian S (2007) Soft Matter 3:1395

    CAS  Google Scholar 

  26. Urahata SM, Ribeiro MCC (2004) J Chem Phys 120:1855

    CAS  Google Scholar 

  27. Praprotnik M, Delle Site L, Kremer K (2008) Annu Rev Phys Chem 59:545

    CAS  Google Scholar 

  28. Izvekov S, Parrinello M, Burnham CJ, Voth GA (2004) J Chem Phys 120:10896

    CAS  Google Scholar 

  29. Luybartsev AP, Laaksonen A (1995) Phys Rev E 52:3730

    Google Scholar 

  30. Spyriouni T, Tzoumanekas C, Theodorou D, Müller-Plathe F, Milano G (2007) Macromolecules 40:3876

    CAS  Google Scholar 

  31. Nielsen SO, Srinivas G, Klein M (2005) J Chem Phys 123:124907

    Google Scholar 

  32. Marrink SJ, Vries AHd, Mark AE (2004) J Phys Chem B 108:750

    CAS  Google Scholar 

  33. Padding JT, Briels WJ (2002) J Chem Phys 117:925

    CAS  Google Scholar 

  34. Li XJ, Kou DZ, Rao SL, Liang H (2006) J Chem Phys 124:204909

    Google Scholar 

  35. Haliloglou T, Mattice WL (1998) J Chem Phys 108:6989

    Google Scholar 

  36. Sun Q, Faller R (2006) Macromolecules 39:812

    CAS  Google Scholar 

  37. Harmandaris VA, Adhikari NP, van der Vegt NFA, Kremer K (2006) Macromolecules 39:6708

    CAS  Google Scholar 

  38. Larson RG (2004) Mol Phys 102:341

    CAS  Google Scholar 

  39. Fukunaga H, Takimoto J, Doi M (2002) J Chem Phys 116:8183

    CAS  Google Scholar 

  40. Reith D, Meyer H, Müller-Plathe F (2001) Macromolecules 34:2335

    CAS  Google Scholar 

  41. Reith D, Pütz M, Müller-Plathe F (2003) J Comput Chem 24:1624

    CAS  Google Scholar 

  42. Tschöp KKW, Batoulis J, Bürger T, Hahn O (1998) Acta Polym 49:61

    Google Scholar 

  43. Paul W, Binder K, Kremer K, Heermann D (1991) Macromolecules 24:6332

    CAS  Google Scholar 

  44. Abrams C, Kremer K (2003) Macromolecules 36:260

    CAS  Google Scholar 

  45. Milano G, Goudeau S, Müller-Plathe F (2005) J Polym Sci Pol Phys 43:871

    CAS  Google Scholar 

  46. Queyroy S, Neyertz S, Brown D, Müller-Plathe F (2004) Macromolecules 37:7338

    CAS  Google Scholar 

  47. Meyer H, Müller-Plathe F (2002) Macromolecules 35:1241

    CAS  Google Scholar 

  48. Peter C, Delle Site L, Kremer K (2008) Soft Matter 4:859

    CAS  Google Scholar 

  49. Faller R, Schmitz H, Biermann O, Müller-Plathe F (1999) J Comput Chem 20:1009

    CAS  Google Scholar 

  50. Meyer H, Biermann O, Faller R, Reith D, Müller-Plathe F (2000) J Chem Phys 113:6264

    CAS  Google Scholar 

  51. Soper AK (1996) Chem Phys 202:295

    CAS  Google Scholar 

  52. Reith D, Meyer H, Müller-Plathe F (2002) Comput Phys Commun 148:299

    CAS  Google Scholar 

  53. Henderson RL (1974) Phys Lett A 49:197

    Google Scholar 

  54. Karimi-Varzaneh HA, Qian H-J, Chen X, Carbone P, Müller-Plathe F (2011) J Comput Chem. DOI: 10.1002/jcc.21717

    Google Scholar 

  55. Groot RD, Warren PB (1997) J Chem Phys 107:4423

    CAS  Google Scholar 

  56. Lowe CP (1999) Europhys Lett 47:145

    CAS  Google Scholar 

  57. Qian H-J, Liew CC, Müller-Plathe F (2009) Phys Chem Chem Phys 11:1962

    CAS  Google Scholar 

  58. Bordat P, Müller-Plathe F (2002) J Chem Phys 116:3362

    CAS  Google Scholar 

  59. Vettorel T, Meyer H (2006) J Chem Theory Comput 2:616

    CAS  Google Scholar 

  60. Ghosh J, Faller R (2007) Mol Simul 33:759

    CAS  Google Scholar 

  61. Karimi-Varzaneh HA, Carbone P, Müller-Plathe F (2008) Macromolecules 41:7211

    CAS  Google Scholar 

  62. Steiner T (2002) Angew Chem Int Ed 41:48

    CAS  Google Scholar 

  63. Sancho DD, Rey A (2007) J Comput Chem 28:1187

    Google Scholar 

  64. Murthy NS (2006) J Polym Sci B Polym Phys 44:1763

    CAS  Google Scholar 

  65. Garcia D, Starkweather HW (1985) J Polym Sci Polym Phys Ed 23:537

    CAS  Google Scholar 

  66. Bessler E, Bier G (1969) Makromol Chem 122:30

    CAS  Google Scholar 

  67. Trifan DS, Terenzi JF (1958) J Polym Sci 28:443

    CAS  Google Scholar 

  68. Schroeder LR, Cooper SL (1976) J Appl Phys 47:4310

    CAS  Google Scholar 

  69. Waldman M, Hagler AT (1993) J Comput Chem 14:1077

    CAS  Google Scholar 

  70. Chen X, Carbone P, Cavalcanti WL, Milano G, Müller-Plathe F (2007) Macromolecules 40:8087

    CAS  Google Scholar 

  71. Izvekov S, Voth GA (2006) J Chem Phys 125:151101

    Google Scholar 

  72. Leon S, van der Vegt NFA, Delle Site L, Kremer K (2005) Macromolecules 38:8078

    CAS  Google Scholar 

  73. Harmandaris VA, Kremer K (2009) Macromolecules 42:791

    CAS  Google Scholar 

  74. Sun Q, Faller R (2006) J Chem Theory Comput 2:607

    CAS  Google Scholar 

  75. Villa A, van der Vegt NFA, Peter C (2009) Phys Chem Chem Phys 11:2068

    CAS  Google Scholar 

  76. Villa A, Peter C, van der Vegt NFA (2009) Phys Chem Chem Phys 11:2077

    CAS  Google Scholar 

  77. Fritz D, Harmandaris VA, Kremer K, van der Vegt NFA (2009) Macromolecules 42:7579

    CAS  Google Scholar 

  78. Izvekov S, Voth GA (2005) J Chem Phys B 109:2469

    CAS  Google Scholar 

  79. Izvekov S, Voth GA (2005) J Chem Phys 123:134105

    Google Scholar 

  80. Noid WG, Chu J-W, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC (2008) J Chem Phys 128:244114

    CAS  Google Scholar 

  81. Noid WG, Chu JW, Ayton GS, Voth GA (2007) J Phys Chem B 111:4116

    CAS  Google Scholar 

  82. Noid WG, Liu P, Wang Y, Chu J-W, Ayton GS, Izvekov S, Andersen HC, Voth GA (2008) J Chem Phys 128:244115

    CAS  Google Scholar 

  83. Liu P, Voth GA (2007) J Chem Phys 126:045106

    Google Scholar 

  84. Zhou J, Thorpe IF, Izvekov S, Voth GA (2007) Biophys J 92:4289

    CAS  Google Scholar 

  85. Izvekov S, Voth GA (2006) J Chem Theory Comput 2:637

    CAS  Google Scholar 

  86. Wang Y, Izvekov S, Yan T, Voth GA (2006) J Phys Chem B 110:3564

    CAS  Google Scholar 

  87. Wang Y, Voth GA (2005) J Am Chem Soc 127:12192

    CAS  Google Scholar 

  88. Izvekov S, Violi A, Voth GA (2005) J Phys Chem B 109:17019

    CAS  Google Scholar 

  89. Shi Q, Izvekov S, Voth GA (2006) J Phys Chem B 110:15045

    CAS  Google Scholar 

  90. Larini L, Lu L, Voth GA (2010) J Chem Phys 132:164107

    Google Scholar 

  91. Marrink SJ, Risselada HJ, Yefi mov S, Tieleman DP, de Vries AH (2007) J Phys Chem B 111:7812

    CAS  Google Scholar 

  92. Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF (2007) Chem Phys Chem 8:452

    CAS  Google Scholar 

  93. Monticelli L, Kandasamy S, Periole X, Larson RG, Tieleman DP, Marrink SJ (2008) J Chem Theory Comp 4:819

    CAS  Google Scholar 

  94. Marrink SJ, Mark AE (2004) Biophys J 87:3894

    CAS  Google Scholar 

  95. Lee H, Vries AHd, Marrink S-J, Pastor RW (2009) J Phys Chem B 113:13186

    CAS  Google Scholar 

  96. Rossi G, Monticelli L, Puisto SR, Vattulainen I, Ala-Nissila T (2011) Soft Matter 7:698

    Google Scholar 

  97. Lyubartsev A, Mirzoev A, Chen L, Laaksonen A (2010) Faraday Discuss 144:43

    CAS  Google Scholar 

  98. Lyubartsev AP, Laaksonen A (1995) Phys Rev E 52:3730

    CAS  Google Scholar 

  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

    Google Scholar 

  100. Schneider J, Hess W, Klein R (1985) J Phys A 18:1221

    CAS  Google Scholar 

  101. Jiang W, Wang YT, Yan TY, Voth GA (2008) J Phys Chem C 112:1132

    CAS  Google Scholar 

  102. Abrams CF, Delle Site L, Kremer K (2003) Phys Rev E 67:021807

    Google Scholar 

  103. Delle Site L, Leon S, Kremer K (2004) J Am Chem Soc 126:2944

    CAS  Google Scholar 

  104. Praprotnik M, Delle Site L, Kremer K (2005) J Chem Phys 123:224106

    Google Scholar 

  105. Praprotnik M, Matysiak S, Delle Site L, Kremer K, Clementi C (2007) J Phys Condens Mater 19:292201

    Google Scholar 

  106. Praprotnik M, Delle Site L, Kremer K (2007) J Chem Phys 126:134902

    Google Scholar 

  107. Ensing B, Nielsen SO, Moore PB, Klein ML, Parrinello M (2007) J Chem Theory Comp 3:1100

    CAS  Google Scholar 

  108. Poblete S, Praprotnik M, Kremer K, Site LD (2010) J Chem Phys 132:114101

    Google Scholar 

  109. Matysiak S, Clementi C, Praprotnik M, Kremer K, Site LD (2008) J Chem Phys 128:024503

    Google Scholar 

  110. Poma AB, Site LD (2010) Phys Rev Lett 104:250201

    CAS  Google Scholar 

  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

    Google Scholar 

  112. Delgado-Buscalioni R, Kremer K, Praprotnik M (2008) J Chem Phys 128:114110

    Google Scholar 

  113. Violi A (2009) In: Voth GA (ed) Coarse-graining of condensed phase and biomolecular systems. CRC, Boca Raton, pp 433–448

    Google Scholar 

  114. Violi A (2004) Combust Flame 139:279

    CAS  Google Scholar 

  115. Santangelo G, Di Matteo A, Müller-Plathe F, Milano G (2007) J Phys Chem B 111:2765

    CAS  Google Scholar 

  116. Hess B, Leon S, van der Vegt NFA, Kremer K (2006) Soft Matter 2:409

    CAS  Google Scholar 

  117. Chen X, Carbone P, Santangelo G, Di Matteo A, Milano G, Müller-Plathe F (2009) Phys Chem Chem Phys 11:1977

    CAS  Google Scholar 

  118. Hess B, Peter C, Ozal T, van der Vegt NFA (2008) Macromolecules 41:2283

    CAS  Google Scholar 

  119. Ozal T, Peter C, Hess B, van der Vegt NFA (2008) Macromolecules 41:5055

    Google Scholar 

  120. Hess B, van der Vegt NFA (2008) Macromolecules 41:7281

    CAS  Google Scholar 

  121. Merkel TC, Bondar VI, Nagai K, Freeman BD, Pinnau I (2000) J Polym Sci B Polym Phys 38:415

    CAS  Google Scholar 

  122. Korsmeyer RW, Meerwall EV, Peppas NA (1986) J Polym Sci B Polym Phys 24:409

    CAS  Google Scholar 

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Acknowledgments

The authors thank Dr. V. Harmandaris and Dr. Qian for providing the data for RDFs of PS and EB in united atom and CG simulations.

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Correspondence to Hossein Ali Karimi-Varzaneh .

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Karimi-Varzaneh, H.A., Müller-Plathe, F. (2011). Coarse-Grained Modeling for Macromolecular Chemistry. In: Kirchner, B., Vrabec, J. (eds) Multiscale Molecular Methods in Applied Chemistry. Topics in Current Chemistry, vol 307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2010_122

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