Multiscale modeling of lipids and lipid bilayers

European Biophysics Journal

Volumn 35, Issue 1, 2005, Pages 53-61

  Lyubartsev, Alexander P ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Lipids; Membranes; Molecular dynamics; Multiscale modeling

Indexed keywords

LIPID; WATER;

ARTICLE; LIPID BILAYER; MEMBRANE VESICLE; MOLECULAR DYNAMICS; MOLECULAR MODEL; MONTE CARLO METHOD; SIMULATION;

COMPUTER SIMULATION; LIPID BILAYERS; LIPIDS; MEMBRANE LIPIDS; MODELS, BIOLOGICAL; MOLECULAR CONFORMATION; MONTE CARLO METHOD; WATER;

EID: 27944495588     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-005-0005-y     Document Type: Article

References (29)

1. Feller SE, MacKerell AD (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B 104:7510-7515
2. Goetz R, Gompper G, Lipowsky R (1999) Mobility and elasticity of self-assembled membranes. Phys Rev Lett 82:221-224
3. Kranenburg M, Venturoli M, Smit B (2003) Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. J Phys Chem B 107:11491-11501
4. Kranenburg M, Nicolas J-P, Smit B (2004) Comparison of mesoscopic phospholipid - water models. Phys Chem Chem Phys 6(16):4142-4151
5. Lindahl E, Edholm O (2000) Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys J 79:426-433
6. Lobaskin V, Lyubartsev AP, Linse P (2001) Effective macroion-macroion potentials in assymmetric electrolytes. Phys Rev E 63:020401
7. Lowe CP (1999) An alternative approach to dissipative particle dynamics. Europhys Lett 47:145-151
8. Lyubartsev AP, Laaksonen A (1995) Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. Phys Rev E 52(4):3730-3737
9. Lyubartsev AP, Laaksonen A (1997) Osmotic and activity coefficients from effective potentials for hydrated ions. Phys Rev E 55(5):5689-5696
10. Lyubartsev AP, Laaksonen A (1999) Effective potentials for ion - DNA interactions. J Chem Phys 111(24):11207-11215
11. Lyubartsev AP, Laaksonen A (2000) A general and scalable parallel software package for arbitrary mixtures of molecules. Comput Phys Commun 128:565-589
12. Lyubartsev AP, Laaksonen A (2004) On the reduction of molecular degrees of freedom in computer simulations. Lect Notes Phys 640:219-244
13. Marrink SJ, Berendsen HJC (1994) Simulation of water transport through a lipid membrane. J Phys Chem 98:4155-4168
14. Marrink SJ, Mark AE (2003) Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J Am Chem Soc 125(49):15233-15242
15. Marrink SJ, de Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108:750-760
16. Martyna GJ, Tuckerman ME, Tobias DJ, Klein ML (1996) Explicit reversible integrators for extended systems dynamics. Mol Phys 87(5):1117-1157
17. Noguchi H, Takasu M (2001) Self-assembly of amphiphiles into vesicles: a brownian dynamics simulation. Phys Rev E 64:041913
18. Norberg J, Nilsson L (2003) Advances in biomolecular simulations: methodology and recent applications. Quart Rev Biophys 36:257-306
19. Patra M, Karttunen M, Hyvönen MT, Falck E, Lindqvist P, Vattulainen I (2003) Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions. Biophys J 84:3636-3645
20. Reith D, Pütz M, Müller-Plathe F (2003) Deriving effective mesoscale potentials from atomistic simulations. J Comp Chem 24:1624-1636
21. Shelley JC, Shelley MY, Reeder RC, Bandyopadhyay S, Klein ML (2001) A coarse grained model for phospholipid simulations. J Phys Chem B 105:4464-4470
22. Soper AK (1996) Empirical potential Monte Carlo simulation of fluid structure. Chem Phys 202:295-306
23. Stevens MJ (2004) Coarse-grained simulations of lipid bilayers. J Chem Phys 121(23):11942-11948
24. Sum AK, Faller R, de Pablo JJ (2003) Molecular simulation study of phospholipid bilayers and insights of the interactions with disaccharides. Biophys J 85(5):2830-2844
25. Tieleman DP, Marrink SJ, Berendsen HJC (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235-270
26. Tielerman DP, Biggin PC, Smith GR, Sansom MSP (2001) Simulation approaches to ion channel structure-function relationships. Quart Rev Biophys 34:473-561
27. Toukan K, Rahman A (1985) Molecular dynamics study of atomic motions in water. Phys Rev B 31:2643-2648
28. Wang W, Donini O, Reyes CM, Kollman PA (2001) Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 30:211-243
29. Yamamoto S, Maruyama Y, Hyodo S (2002) Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules. J Chem Phys 116:5842-5849