Simulation approaches to soft matter: Generic statistical properties vs. chemical details

Computer Physics Communications

Volumn 179, Issue 1-3, 2008, Pages 51-60

  Praprotnik, Matej ^a   Junghans, Christoph ^a   Delle Site, Luigi ^a   Kremer, Kurt ^a  

^a MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

Author keywords

Adaptive resolution simulation; Multiscale modeling; Scale bridging; Soft matter; Transverse DPD thermostat

Indexed keywords

COMPUTER SIMULATION; MOLECULAR MODELING; MOLECULAR STRUCTURE; MOLECULAR WEIGHT; NANOSTRUCTURED MATERIALS; THERMOSTATS;

ADAPTIVE RESOLUTION SIMULATION; MULTISCALE MODELING; SCALE BRIDGING; SOFT MATTER; TRANSVERSE DPD THERMOSTATS;

MATERIALS SCIENCE;

EID: 44649198783     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2008.01.018     Document Type: Article

References (66)

1. Flory P.J. Principles of Polymer Chemistry (1953), Cornell University Press, Ithaca
2. Flory P.J. Statistical Mechanics of Chain Molecules (1969), Interscience Publishers, New York
3. de Gennes P.-G. Scaling Concept in Polymer Physics (1979), Cornell University, Ithaca
4. Doi M., and Edwards S.F. The Theory of Polymer Dynamics (1986), Clarendon, Oxford
5. In: Binder K. (Ed). Monte Carlo and Molecular Dynamics Simulation in Polymer Science (1995), Clarendon, Oxford
6. Tschöp W., Kremer K., Batoulis J., Bürger T., and Hahn O. Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates. Acta Polym. 49 (1998) 61-74
7. Tschöp W., Kremer K., Hahn O., Batoulis J., and Bürger T. Simulation of polymer melts. II. From coarse-grained models back to atomistic description. Acta Polym. 49 (1998) 75-79
8. Kremer K. Computer simulations in soft matter science. In: Cates M.E., and Evans M.R. (Eds). Soft and Fragile Matter, Nonequilibrium Dynamics, Metastability and Flow, Proceedings of NATO ASI Workshop. St. Andrews, Summer 1999 (2000), Inst. of Physics, Bristol
9. Eilhard J., Zirkel A., Tschöp W., Hahn O., Kremer K., Scharpf O., Richter D., and Buchenau U. Spatial correlations in polycarbonates: Neutron scattering and simulation. J. Chem. Phys. 110 (1999) 1819-1830
10. Abrams C.F., and Kremer K. Combined coarse-grained and atomistic simulation of liquid bisphenol-a-polycarbonate: Liquid packing and intramolecular structure. Macromolecules 36 (2003) 260-267
11. In: Ferraio M., Ciccotti G., and Binder K. (Eds). Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, vol. 1. Lecture Notes Phys. vol. 703 (2006), Springer, Berlin/Heidelberg
12. In: Ferraio M., Ciccotti G., and Binder K. (Eds). Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, vol. 2. Lecture Notes Phys. vol. 704 (2006), Springer, Berlin/Heidelberg
13. van der Vegt N.F.A., Peter C., and Kremer K. Structure-based coarse- and fine-graining in soft matter simulations. In: Voth G. (Ed). Coarse-Graining of Condensed Phase and Biomolecular Systems (2007), Chapman and Hall/CRC Press, Taylor and Francis Group
14. Praprotnik M., Delle Site L., and Kremer K. Multiscale simulation of soft matter: From scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 59 (2008) 545-571
15. Delle Site L., Leon S., and Kremer K. BPA-PC on a Ni(111) surface: The interplay between adsorption energy and conformational entropy for different chain-end modifications. J. Amer. Chem. Soc. 126 (2004) 2944-2955
16. Harmandaris V., Reith D., van der Vegt N.F., and Kremer K. Comparison between coarse-graining models for polymers systems: Two mapping schemes for polystyrene. Macromol. Chem. Phys. 208 (2007) 2109-2120
17. Abrams C.F., Delle Site L., and Kremer K. Dual-resolution coarse-grained simulation of the bisphenol-a-polycarbonate/nickel interface. Phys. Rev. E 67 (2003) 021807
18. Lyubartsev A.P., and Laaksonen A. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. Phys. Rev. E 52 (1995) 3730-3737
19. Reith D., Pütz M., and Müller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 24 (2003) 1624-1636
20. Leon S., Delle Site L., van der Vegt N.F.A., and Kremer K. Bisphenol-a-polycarbonate: Entanglement analysis from coarse-grained MD simulations. Macromolecules 38 (2005) 8078-8092
21. Hess B., Leon S., Van der Vegt N., and Kremer K. Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-a-polycarbonate. Soft Matter 2 (2006) 409-414
22. Heath A.P., Kavraki L.E., and Clementi C. From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes. Proteins Struct. Funct. Bioinf. 68 (2007) 646-661
23. Hahn O., Mooney D.A., Müller-Plathe F., and Kremer K. A new mechanism for penetrant diffusion in amorphous polymers: Molecular dynamics simulations of phenol diffusion in bisphenol-a-polycarbonate. J. Chem. Phys. 111 (1999) 6061-6068
24. Harmandaris V.A., Adhikari N.P., Van der Vegt N.F.A., and Kremer K. Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations. Macromolecules 39 (2006) 6708-6719
25. Delle Site L., Abrams C.F., Alavi A., and Kremer K. Polymers near metal surfaces: Selective adsorption and global conformations. Phys. Rev. Lett. 89 (2002) 156103
26. Zhou X., Andrienko D., Delle Site L., and Kremer K. Dynamics surface decoupling in a sheared polymer melt. Europhys. Lett. 70 (2005) 264-270
27. Zhou X., Andrienko D., Delle Site L., and Kremer K. Flow boundary conditions for chain-end adsorbing polymer melts. J. Chem. Phys. 123 (2005) 104904
28. Andrienko D., Leon S., Delle Site L., and Kremer K. Adhesion of polycarbonate blends on a nickel surface. Macromolecules 38 (2005) 5810-5816
29. Delle Site L., Leon S., and Kremer K. Specific interaction of polymers with surface defects: Structure formation of polycarbonate on nickel. J. Phys.: Condens. Matter 17 (2005) L53-L60
30. Malevanets A., and Kapral R. Solute molecular dynamics in a mesoscale solvent. J. Chem. Phys. 112 (2000) 7260-7269
31. Villa E., Balaeff A., Mahadevan L., and Schulten K. Multiscale method for simulating protein-DNA complexes. Multiscale Model. Simul. 2 (2004) 527-553
32. Neri M., Anselmi C., Cascella M., Maritan A., and Carloni P. Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett. 95 (2005) 218102
33. Laio A., VandeVondele J., and Röthlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J. Chem. Phys. 116 (2002) 6941
34. Praprotnik M., Delle Site L., and Kremer K. Adaptive resolution molecular dynamics simulation: Changing the degrees of freedom on the fly. J. Chem. Phys. 123 (2005) 224106
35. Praprotnik M., Kremer K., and Delle Site L. Adaptive molecular resolution via a continuous change of the phase space dimensionality. Phys. Rev. E 75 (2007) 017701
36. Praprotnik M., Kremer K., and Delle Site L. Fractional dimensions of phase space variables: A tool for varying the degrees of freedom of a system in a multiscale treatment. J. Phys. A: Math. Theor. 40 (2007) F281-F288
37. Goldstein H. Classical Mechanics. second ed. (1980), Addison-Wesley Publishing Company
38. Praprotnik M., and Janežič D. Molecular dynamics integration meets standard theory of molecular vibrations. J. Chem. Inf. Model 45 (2005) 1571-1579
39. Soddemann T., Dünweg B., and Kremer K. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E 68 (2003) 046702
40. Ensing B., Nielsen S.O., Moore P.B., Klein M.L., and Parrinello M. Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics. J. Chem. Theory Comput. 3 (2007) 1100-1105
41. Delle Site L. Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme. Phys. Rev. E 76 (2007) 047701
42. Praprotnik M., Delle Site L., and Kremer K. Adaptive resolution scheme (address) for efficient hybrid atomistic/mesoscale molecular dynamics simulations of dense liquids. Phys. Rev. E 73 (2006) 066701
43. Praprotnik M., Delle Site L., and Kremer K. A macromolecule in a solvent: Adaptive resolution molecular dynamics simulation. J. Chem. Phys. 126 (2007) 134902
44. Praprotnik M., Matysiak S., Delle Site L., Kremer K., and Clementi C. Adaptive resolution simulation of liquid water. J. Phys.: Condens. Matter 19 (2007) 292201
45. Limbach H.J., Arnold A., Mann B.A., and Holm C. Espresso-an extensible simulation package for research on soft matter systems. Comput. Phys. Comm. 174 (2006) 704-727. http://www.espresso.mpg.de
46. Abrams C.F. Concurrent dual-resolution Monte Carlo simulation of liquid methane. J. Chem. Phys. 123 (2005) 234101
47. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1987), Clarendon Press, Oxford
48. Henderson R.L. A uniqueness theorem for fluid pair correlation functions. Phys. Lett. A 49 (1974) 197-198
49. Izvekov S., and Voth G.A. Multiscale coarse graining of liquid-state systems. J. Chem. Phys. 123 (2005) 134105
50. Klapp S.H.L., Diestler D.J., and Schoen M. Why are effective potentials 'soft'?. J. Phys.: Condens. Matter 16 (2004) 7331-7352
51. Bock H., Gubbins K.E., and Klapp S.H.L. Coarse graining of nonbonded degrees of freedom. Phys. Rev. Lett. 98 (2007) 267801
52. Kremer K., and Grest G.S. Dynamics of entangled linear polymer melts: A molecular-dynamics simulation. J. Chem. Phys. 92 (1990) 5057-5086
53. Junghans C., Praprotnik M., and Kremer K. Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat. Soft Matter 4 (2008) 156-161
54. Neumann M. The dielectric constant of water. computer simulations with the MCY potential. Mol. Phys. 50 (1983) 841
55. Neumann M. The dielectric constant of water. Computer simulations with the MCY potential. J. Chem. Phys. 82 (1985) 5663-5672
56. Praprotnik M., Janežič D., and Mavri J. Temperature dependence of water vibrational spectrum: A molecular dynamics simulation study. J. Phys. Chem. A 108 (2004) 11056-11062
57. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys 79 (1983) 926-936
58. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Molecular dynamics simulations: The limits and beyond. In: Pullman B. (Ed). Intermolecular Forces (1981), Reidel, Dordrecht 331
59. Berendsen H.J.C., Grigera J.R., and Straatsma T.P. The missing term in effective pair potentials. J. Phys. Chem. 91 (1987) 6269-6271
60. Lawrence C.P., and Skinner J.L. Flexible TIP4P model for molecular dynamics simulation of liquid water. Chem. Phys. Lett. 372 (2003) 842-847
61. Johnson M.E., Head-Gordon T., and Louis A.A. Representability problems for coarse-grained water potentials. J. Chem. Phys. 126 (2007) 144509
62. Matysiak S., Clementi C., Praprotnik M., Kremer K., and Delle Site L. Modeling diffusive dynamics in adaptive resolution simulation of liquid water. J. Chem. Phys. 128 (2008) 024503
63. Hoogerbrugge P.J., and Koelman J.M.V.A. Simulating microscopic hydrodynamic phenomena with Dissipative particle dynamics. Europhys. Lett. 19 (1992) 155-160
64. Español P., and Warren P. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 30 (1995) 191-196
65. Groot R.D., and Warren P.B. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 107 (1997) 4423-4435
66. Español P. Fluid particle model. Phys. Rev. E 57 (1998) 2930-2948