52. Brannigan G, Lin L, Brown F (2006) Implicit solvent simulation models for biomembranes.
Eur Biophys J 35(2):104–124
53. Marrink Siewert J, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of
membrane pores, domains, stalks and curves. Biochim Biophys Acta Biomembr 1788
(1):149–168
54. Bennun SV, Hoopes MI, Xing C, Faller R (2009) Coarse-grained modeling of lipids. Chem
Phys Lipids 159(2):59–66
55. Deserno M (2009) Mesoscopic membrane physics: concepts, simulations, and selected
applications. Macromol Rapid Comm 30(9–10):752–771
56. Noguchi H (2009) Membrane simulation models from nanometer to micrometer scale. J Phys
Soc Jpn 78(4):041007
57. Schmid F (2009) Toy amphiphiles on the computer: What can we learn from generic models?
Macromol Rapid Comm 30:741–751
58. Mu ¨ller-Plathe F (2002) Coarse-graining in polymer simulation: from the atomistic to the
mesoscopic scale and back. Chem Phys Chem 3(9):754–769
59. Izvekov S, Both GA (2005) Multiscale coarse graining of liquid-state systems. J Chem Phys
123(13):134105
60. Praprotnik M, Delle Site L, Kremer K (2005) Adaptive resolution molecular-dynamics
simulation: changing the degrees of freedom on the fly. J Chem Phys 123(22):224106
61. Praprotnik M, Delle Site L, Kremer K (2007) A macromolecule in a solvent: adaptive
resolution molecular dynamics simulation. J Chem Phys 126(13):134902
62. Praprotnik M, Site LD, Kremer K (2008) Multiscale simulation of soft matter: from scale
bridging to adaptive resolution. Ann Rev Phys Chem 59(1):545–571
63. Delgado-Buscalioni R, Kremer K, Praprotnik M (2008) Concurrent triple-scale simulation of
molecular liquids. J Chem Phys 128(11):114110
64. Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC (2008)
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarsegrained models. J Chem Phys 128(24):244114
65. Noid WG, Liu P, Wang Y, Chu JW, Ayton GS, Izvekov S, Andersen HC, Voth GA (2008)
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained
molecular models. J Chem Phys 128(24):244115
66. Das A, Andersen HC (2009) The multiscale coarse-graining method. III. A test of pairwise
additivity of the coarse-grained potential and of new basis functions for the variational
calculation. J Chem Phys 131(3):034102
67. Delgado-Buscalioni R, Kremer K, Praprotnik M (2009) Coupling atomistic and continuum
hydrodynamics through a mesoscopic model: application to liquid water. J Chem Phys
131(24):244107
68. Peter C, Kremer K (2009) Multiscale simulation of soft matter systems – from the atomistic to
the coarse-grained level and back. Soft Matter 5:4357–4366
69. Poblete S, Praprotnik M, Kremer K, Delle Site L (2010) Coupling different levels of
resolution in molecular simulations. J Chem Phys 132(11):114101
70. Voth GA (ed) (2008) Coarse-graining of condensed phase and biomolecular systems, 1st edn.
CRC, Boca Raton
71. Ru ¨hle V, Junghans C, Lukyanov A, Kremer K, Andrienko D (2009) Versatile object-oriented
toolkit for coarse-graining applications. J Chem Theory Comput 5(12):3211–3223
72. Lu L, Voth GA (2012) The multiscale coarse-graining method. In: Rice SA, Dinner AR (eds)
Advances in chemical physics, vol 149. Wiley, Hoboken, pp 47–81 doi: 10.1002/
9781118180396.ch2
73. Cooke IR, Kremer K, Deserno M (2005) Tunable generic model for fluid bilayer membranes.
Phys Rev E 72(1):011506
74. Cooke IR, Deserno M (2005) Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials. J Chem Phys
123(22):224710
Computational Studies of Biomembrane Systems: Theoretical Considerations. . .
273
Eur Biophys J 35(2):104–124
53. Marrink Siewert J, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of
membrane pores, domains, stalks and curves. Biochim Biophys Acta Biomembr 1788
(1):149–168
54. Bennun SV, Hoopes MI, Xing C, Faller R (2009) Coarse-grained modeling of lipids. Chem
Phys Lipids 159(2):59–66
55. Deserno M (2009) Mesoscopic membrane physics: concepts, simulations, and selected
applications. Macromol Rapid Comm 30(9–10):752–771
56. Noguchi H (2009) Membrane simulation models from nanometer to micrometer scale. J Phys
Soc Jpn 78(4):041007
57. Schmid F (2009) Toy amphiphiles on the computer: What can we learn from generic models?
Macromol Rapid Comm 30:741–751
58. Mu ¨ller-Plathe F (2002) Coarse-graining in polymer simulation: from the atomistic to the
mesoscopic scale and back. Chem Phys Chem 3(9):754–769
59. Izvekov S, Both GA (2005) Multiscale coarse graining of liquid-state systems. J Chem Phys
123(13):134105
60. Praprotnik M, Delle Site L, Kremer K (2005) Adaptive resolution molecular-dynamics
simulation: changing the degrees of freedom on the fly. J Chem Phys 123(22):224106
61. Praprotnik M, Delle Site L, Kremer K (2007) A macromolecule in a solvent: adaptive
resolution molecular dynamics simulation. J Chem Phys 126(13):134902
62. Praprotnik M, Site LD, Kremer K (2008) Multiscale simulation of soft matter: from scale
bridging to adaptive resolution. Ann Rev Phys Chem 59(1):545–571
63. Delgado-Buscalioni R, Kremer K, Praprotnik M (2008) Concurrent triple-scale simulation of
molecular liquids. J Chem Phys 128(11):114110
64. Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC (2008)
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarsegrained models. J Chem Phys 128(24):244114
65. Noid WG, Liu P, Wang Y, Chu JW, Ayton GS, Izvekov S, Andersen HC, Voth GA (2008)
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained
molecular models. J Chem Phys 128(24):244115
66. Das A, Andersen HC (2009) The multiscale coarse-graining method. III. A test of pairwise
additivity of the coarse-grained potential and of new basis functions for the variational
calculation. J Chem Phys 131(3):034102
67. Delgado-Buscalioni R, Kremer K, Praprotnik M (2009) Coupling atomistic and continuum
hydrodynamics through a mesoscopic model: application to liquid water. J Chem Phys
131(24):244107
68. Peter C, Kremer K (2009) Multiscale simulation of soft matter systems – from the atomistic to
the coarse-grained level and back. Soft Matter 5:4357–4366
69. Poblete S, Praprotnik M, Kremer K, Delle Site L (2010) Coupling different levels of
resolution in molecular simulations. J Chem Phys 132(11):114101
70. Voth GA (ed) (2008) Coarse-graining of condensed phase and biomolecular systems, 1st edn.
CRC, Boca Raton
71. Ru ¨hle V, Junghans C, Lukyanov A, Kremer K, Andrienko D (2009) Versatile object-oriented
toolkit for coarse-graining applications. J Chem Theory Comput 5(12):3211–3223
72. Lu L, Voth GA (2012) The multiscale coarse-graining method. In: Rice SA, Dinner AR (eds)
Advances in chemical physics, vol 149. Wiley, Hoboken, pp 47–81 doi: 10.1002/
9781118180396.ch2
73. Cooke IR, Kremer K, Deserno M (2005) Tunable generic model for fluid bilayer membranes.
Phys Rev E 72(1):011506
74. Cooke IR, Deserno M (2005) Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials. J Chem Phys
123(22):224710
Computational Studies of Biomembrane Systems: Theoretical Considerations. . .
273