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Progress in Chemistry 2007, Vol. 19 Issue (9): 1249-1257 Previous Articles   Next Articles

• Review •

Molecular Dynamics Simulations of Self-Assembling

Deng Pingye 1,2;Zhang Donghai 1; Tian Yajun 1; Chen Yunfa 1*; Ding Hui 3   

  1. 1. Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100080 China;
    2. Beijing center for Physical and Chemical Analysis , Beijing 100089 China;
    3. Beijing Academy of Science and Technology, Beijing 100089 China
  • Received: Revised: Online: Published:
  • Contact: Chen Yunfa
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The current research about self-assembly by the means of molecular dynamics simulations is briefly reviewed in this paper. Both the methods of computational modeling, and the visual representation of simulating results are briefly described respectively, coupling with their applications in certain topics. Based on the analyzing and discussing of the contributions of previous research，unclosed problems of molecular dynamics simulating self-assembly are proposed. The natural linkage of self-assembly with phase transition or with fluctuation indeed gives the clue of heading path, and consequently, the reports of oscillation in self-assembly and study of frequency depend specific heat are also presented in this paper. Therefore the idea that inspecting the oscillating parameters with respect to frequency depend specific heat in self-assembly might be helpful to understand the process of self–assembly and computational simulations is proposed.
Key words: molecular dynamics simulation, self-assembly, frequency dependent specific heat

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[ 1 ] Depero L E , Curri M L. Curr. Opin. Solid State Mater. Sci . ,2004 , 8 : 103 —109
[ 2 ] Soten I , Ozin G A. Curr. Opin. Coll . Interface Sci . , 1999 , 4 :325 - 337
[ 3 ] Corti M, Zemb T. Curr. Opin. Coll . Interface Sci . , 2000 , 5 :1 —4
[ 4 ] Karaborni S , Esselink K, Hilbers P A J . Science , 1994 , 266 :254 —256
[ 5 ] Hue Q S , Margolese D I , Ciesla U , et al . Nature , 1994 , 368 :317 —321
[ 6 ] Tanev P T , Pinnavaia T J . Science , 1995 , 267 : 865 —867
[ 7 ] Rajagopalan R. Curr. Opin. Coll . Interface Sci . , 2001 , 6 :357 —365
[ 8 ] Haile J N. Molecular Dynamics Simulation : Elementary Methods.New York : Wiley , 1992
[ 9 ] Rapaport D C. The Art of Molecular Dynamics Simulation , 2nd ed. Cambridge University Press , 2004
[10] Arya G, Panagiotopoulos A Z. Comput . Phys. Commun. , 2005 ,169 : 262 —266
[11] Groot R D , Warren P B. J . Chem. Phys. , 1997 , 107 : 4423 —4435
[12] Espanol P , Serrano M. Phys. Rev. E , 1999 , 59 : 6340 —6347
[13] Lowe C P. Europhys. Lett . , 1999 , 47 : 145 —151
[14] Pagonabarraga I , Frenkel D. J . Chem. Phys. , 1999 , 110 :8605 —8613
[15] Boek E S , Coveney P V , Lekkerkerker H N W. Phys. Rev. E ,1997 , 55 : 3124 —3133
[16] Warren P B. Curr. Opin. Coll . Interface Sci . , 1998 , 3 : 6206 —6224
[17] Boghosian B M. Coveney P V , Love P , Maillet J B. Mol .Simulat . , 2001 , 26 : 85 —100
[18] Ladd A J C. J . Fluid. Mech. , 1994 , 271 : 285 —309
[19] Ladd A J C. J . Fluid. Mech. , 1994 , 271 : 311 —339
[20] Chen H D , Boghosian B M, Coveney P V , Nekovee M. Proc. R.Soc. Lond. A , 2000 , 465 : 2043 —2057
[21] Nekovee M, Coveney P V , Chen H D , Boghosian B M. Phys.Rev. E , 2000 , 62 : 8282 —8294
[22] Chatterji A , Horbach J . J . Chem. , Phys. , 2005 , 122 :184903 —184914
[23] Balazs A C. Curr. Opin. Solid State Mater. Sci . , 2003 , 7 : 27 —33
[24] Thompson R , Ginzbug V , Masten M, Balazs A C. Science ,2001 : 292 : 2469 —2472
[25] Gao J , Ge W, Hu G H , Li J H. Langmuir 2005 , 21 : 5223 —5229
[26] Srinivas G, Discher D E , Klein M L. Nature Mater. , 2004 , 3 :638 —644
[27] Lopez C F , Nielsen S O , Moore P B , Shelley J C , Klein ML. J .Phys. Condens. Matter. , 2002 , 40 : 9431 —9444
[28] Maiti P K, Lansac Y, Glaser M A , Clark N A , Rouault Y.Langmuir , 2002 , 18 : 1908 —1918
[29] Zou J , Ji B , Feng X, Gao H. Nano Lett . , 2006 , 6 : 430 —434
[30] Bilalbegovic’　G. Comput . Mater. Sci . , 2004 , 31 : 181 —186
[31] Rapaport D C , Johnson J E , Skolnick J . Comput . Phys.Commun. , 1999 , 121/122 : 231 —235
[32] 王音(Wang Y) , 李鹏(Li P) , 宁西京(Ning X J ) . 物理学报(Acta Physica Sinica) , 2005 , 54 : 2847 —2852
[33] Izvekov S , Violi A. J . Chem. Theory Comput . , 2006 , 2 : 504 —512
[34] Cuny V , Antoni M, Arbelot M, Liggieri L. J . Phys. Chem. B ,2004 , 108 : 13353 —13363
[35] Heinz H , Castelijns H J , Suter U W. J . Am. Chem. Soc. ,2003 , 125 : 9500 —9510
[36] Luo M, Mazyar O A , Zhu Q , et al . Langmuir , 2006 , 22 :6385 —6390
[37] Lu L , Berkowitz M L. J . Am. Chem. Soc. , 2004 , 126 :10254 —10255
[38] Bogusz S , Venable RM, Pastor R W. J . Phys. Chem. B , 2001 ,105 : 8312 —8321
[39] Stephenson B C , Beers K, Blankschtein D. Langmuir , 2006 , 22 :1500 —1513
[40] Bond P J , Sansom M S P. J . Am. Chem. Soc. , 2006 , 128 :2697 —2704
[41] Khurana E , Nielsen S O , Ensing B , Klein M L. J . Phys. Chem.B , 2006 , 110 : 18965 —18972
[42] Elmahdy M M, Floudas G, Oldridge L. Chem. Phys. Chem. ,2006 , 7 : 1431 —1441
[43] Ghosh T , García A E , Garde S. J . Phys. Chem. B , 2003 , 107 :612 —617
[44] Ko M J , Kim S H , Jo W H. Macromol . Theory Simul . , 2001 ,10 : 381 —388
[45] 冯端(Feng D) ,师昌绪(Shi C X) , 刘治国(Liu Z G) ,材料科学导论( Introduction to Materials Science) . 北京: 化学工业出版社(Beijing , Chemical Industry Press) , 2002
[46] Gallagher K R , Sharp K A. J . Am. Chem. Soc. , 2003 , 125 :9853 —9860
[47] Birge N O , Nagel R. Phys. Rev. Lett . , 1985 , 54 : 2674 —2677
[48] Christensen T. J . Phys. (Paris) , Colloq. , 1985 , 46 : C8 —635
[49] Stillinger F H. Science , 1995 , 267 : 1935 —1939
[50] Chakrabarti D , Bagchi B. arXiv : cond2mat P0409467 v1 2004 ,17 Sep
[51] Nielsen J K, Dyre J C. Phys. Rev. B , 1996 , 54 : 15754 —15761
[52] Nielsen J K. Phys. Rev. E , 1999 , 60 : 471 —481
[53] Maillet J B , Lachet V , Coveney P V. Phys. Chem. Chem.Phys. , 1999 , 23 : 5277 —5290
[54] Hathorn B C , Sumpte B G, Noid D W, Barmes M D.Macromolecules , 2002 , 35 : 1102 —1108
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