Validation of a hybrid MD-SCF coarse-grained model for DPPC in non-lamellar phases

Theoretical Chemistry Accounts

Volumn 131, Issue 3, 2012, Pages 1-16

  de Nicola, Antonio ^a,b   Zhao, Ying ^a   Kawakatsu, Toshihiro ^c   Roccatano, Danilo ^d   Milano, Giuseppe ^a,b  

^a UNIVERSITY OF SALERNO   (Italy)

^b IMAST Scarl Technological District in Polymer and Composite Engineering   (Italy)

^c TOHOKU UNIVERSITY   (Japan)

^d JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

Coarse graining; Lipids; Molecular dynamics; Self consistent field theory

Indexed keywords

EID: 84862823327     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-012-1167-1     Document Type: Article

References (64)

1. Bandyopadhyay S, Tarek M, Klein ML (1999) Molecular dynamics study of a lipid-DNA complex. J Phys Chem B 103(46): 10075-10080. doi: 10. 1021/jp9927496.
2. Saiz L, Klein ML (2002) Computer simulation studies of model biological membranes. Acc Chem Res 35(6): 482-489. doi: 10. 1021/ar010167c.
3. Faller R, Marrink S-J (2004) Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir 20(18): 7686-7693. doi: 10. 1021/la0492759.
4. Pal S, Milano G, Roccatano D (2006) Synthetic polymers and biomembranes. How do they interact?: Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer. J Phys Chem B 110(51): 26170-26179. doi: 10. 1021/jp063418d.
5. Bennett WFD, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP (2009) Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. J Am Chem Soc 131(35): 12714-12720. doi: 10. 1021/ja903529f.
6. Katsaras J, Tristram-Nagle S, Liu Y, Headrick RL, Fontes E, Mason PC, Nagle JF (2000) Revisiting the ripple phase using fully hydrated, aligned DPPC multibilayers. Biophys J 78(1): 20A.
7. Ayton G, Smondyrev AM, Bardenhagen SG, McMurtry P, Voth GA (2002) Calculating the bulk modulus for a lipid bilayer with non-equilibrium molecular dynamics simulation. Biophys J 82: 1226-1238.
8. Ayton G, Voth GA (2004) Mesoscopic lateral diffusion in lipid bilayers. Biophys J 87(5): 3299-3311.
9. Ayton G, Voth GA (2007) Multiscale simulation of transmembrane proteins. J Struct Biol 157(3): 570-578.
10. Gurtovenko AA, Anwar J, Vattulainen I (2010) Defect-mediated trafficking across cell membranes: insights from in silico modeling. Chem Rev 110(10): 6077-6103. doi: 10. 1021/cr1000783.
11. Izvekov S, Voth GA (2006) Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J Chem Theory Comput 2(3): 637-648. doi: 10. 1021/ct050300c.
12. Shi Q, Voth GA (2005) Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys J 89(4): 2385-2394.
13. Tepper HL, Voth GA (2006) Mechanisms of passive ion permeation through lipid bilayers: insights from simulations. J Phys Chem B 110(42): 21327-21337. doi: 10. 1021/jp064192h.
14. Venturoli M, Sperotto MM, Kranenburg M, Smit B (2006) Mesoscopic models of biological membranes. Phys Rep Rev Sect Phys Lett 437(1-2): 1-54. doi: 10. 1016/j. physrep. 2006. 07. 006.
15. Marrink SJ, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta 1788(1): 149-168. doi: 10. 1016/j. bbamem. 2008. 10. 006.
16. Psachoulia E, Marshall DP, Sansom MSP (2010) Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. Acc Chem Res 43(3): 388-396. doi: 10. 1021/ar900211k.
17. Lyubartsev AP, Rabinovich AL (2011) Recent development in computer simulations of lipid bilayers. Soft Matter 7(1): 25-39. doi: 10. 1039/c0sm00457j.
18. Burkett SL, Mann S (1996) Spatial organization and patterning of gold nanoparticles on self-assembled biolipid tubular templates. Chem Commun 3: 321-322.
19. Bhattacharya S, Srivastava A (2003) Synthesis and characterization of novel cationic lipid and cholesterol-coated gold nanoparticles and their interactions with dipalmitoylphosphatidylcholine membranes. Langmuir 19(10): 4439-4447. doi: 10. 1021/la0269513.
20. Wallace EJ, Sansom MSP (2009) Carbon nanotube self-assembly with lipids and detergent: a molecular dynamics study. Nanotechnology 20(4): 045101. doi: 10. 1088/0957-4484/20/4/045101.
21. Lian T, Ho RJY (2001) Trends and developments in liposome drug delivery systems. J Pharm Sci 90(6): 667-680.
22. Bolinger PY, Stamou D, Vogel H (2004) Integrated nanoreactor systems: triggering the release and mixing of compounds inside single vesicles. J Am Chem Soc 126(28): 8594-8595. doi: 10. 1021/ja049023u.
23. Jang J, Yoon H (2005) Formation mechanism of conducting polypyrrole nanotubes in reverse micelle systems. Langmuir 21(24): 11484-11489. doi: 10. 1021/la051447u.
24. Müller M, Katsov K, Schick M (2006) Biological and synthetic membranes: what can be learned from a coarse-grained description? Phys Rep 434(5-6): 113-176.
25. Sintes T, Baumgaertner A (1998) Interaction of wedge-shaped proteins in flat bilayer membranes. J Phys Chem B 102(36): 7050-7057.
26. Lenz O, Schmid F (2005) A simple computer model for liquid lipid bilayers. J Mol Liq 117(1-3): 147-152. doi: 10. 1016/j. molliq. 2004. 08. 008.
27. Marrink SJ, de Vries AH, Mark AE (2003) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108(2): 750-760. doi: 10. 1021/jp036508g.
28. Marrink S-J, Mark AE (2004) Molecular view of hexagonal phase formation in phospholipid membranes. Biophys J 87(6): 3894-3900.
29. Marrink SJ, Mark AE (2003) The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J Am Chem Soc 125(37): 11144-11145. doi: 10. 1021/ja036138+.
30. Kawakatsu T (2004) Statistical physics of polymers. Springer, Berlin.
31. Matsen MW, Schick M (1994) Stable and unstable phases of a diblock copolymer melt. Phys Rev Lett 72(16): 2660-2663.
32. Drolet F, Fredrickson GH (1999) Combinatorial screening of complex block copolymer assembly with self-consistent field theory. Phys Rev Lett 83(21): 4317-4320.
33. Fredrickson GH, Ganesan V, Drolet F (2002) Field-theoretic computer simulation methods for polymers and complex fluids. Macromolecules 35(1): 16-39. doi: 10. 1021/ma011515t.
34. Lauw Y, Leermakers FAM, Stuart MAC (2006) Self-consistent-field analysis of the micellization of carboxy-modified poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymers. J Phys Chem B 110(1): 465-477.
35. Ly DQ, Honda T, Kawakatsu T, Zvelindovsky AV (2008) Hexagonally perforated lamella-to-cylinder transition in a diblock copolymer thin film under an electric field. Macromolecules 41(12): 4501-4505.
36. Dickinson E, Pinfield VJ, Home DS, Leermakers FAM (1997) Self-consistent-field modelling of adsorbed casein interaction between two protein-coated surfaces. J Chem Soc, Faraday Trans 93(9): 1785-1790.
37. Balazs AC, Singh C, Zhulina E (1998) Modeling the interactions between polymers and clay surfaces through self-consistent field theory. Macromolecules 31(23): 8370-8381.
38. Roan JR, Kawakatsu T (2002) Self-consistent-field theory for interacting polymeric assemblies. I. Formulation, implementation, and benchmark tests. J Chem Phys 116(16): 7283-7294.
39. Roan JR, Kawakatsu T (2002) Self-consistent-field theory for interacting polymeric assemblies. II. Steric stabilization of colloidal particles. J Chem Phys 116(16): 7295-7310.
40. Marcelja S (1973) Molecular model for phase transition in biological membranes. Nature 241(5390): 451-453.
41. Leermakers FAM, Rabinovich AL, Balabaev NK (2003) Self-consistent-field modeling of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to molecular dynamics simulations. Phys Rev E 67(1): 011910.
42. Leermakers FAM, Scheutjens J (1988) Statistical thermodynamics of association colloids. 1. Lipid bilayer-membranes. J Chem Phys 89(5): 3264-3274.
43. Ayton G, McWhirter JL, Voth GA (2006) A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics. J Chem Phys 124(6): 12. doi: 10. 1063/1. 2165194.
44. Muller M, Smith GD (2005) Phase separation in binary mixtures containing polymers: a quantitative comparison of single-chain-in-mean-field simulations and computer simulations of the corresponding multichain systems. J Polym Sci, Part B: Polym Phys 43(8): 934-958.
45. Daoulas KC, Muller M, Stoykovich MP, Park SM, Papakonstantopoulos YJ, de Pablo JJ, Nealey PF, Solak HH (2006) Fabrication of complex three-dimensional nanostructures from self-assembling block copolymer materials on two-dimensional chemically patterned templates with mismatched symmetry. Phys Rev Lett 96(3): 036104.
46. Detcheverry FA, Kang HM, Daoulas KC, Muller M, Nealey PF, de Pablo JJ (2008) Monte Carlo simulations of a coarse grain model for block copolymers and nanocomposites. Macromolecules 41(13): 4989-5001.
47. Detcheverry FA, Pike DQ, Nealey PF, Müller M, de Pablo J (2010) Simulations of theoretically informed coarse grain models of polymeric systems. Faraday Discuss 144: 111-125.
48. Milano G, Kawakatsu T (2009) Hybrid particle-field molecular dynamics simulations for dense polymer systems. J Chem Phys 130(21): 214106.
49. Milano G, Kawakatsu T (2010) Pressure calculation in hybrid particle-field simulations. J Chem Phys 133(21): 214102. doi: 10. 1063/1. 3506776.
50. De Nicola A, Zhao Y, Kawakatsu T, Roccatano D, Milano G (2011) Hybrid particle-field coarse-grained models for biological phospholipids. J Chem Theory Comput 7(9): 2947.
51. Schmid F (1998) Self-consistent-field theories for complex fluids. J Phys: Condens Matter 10(37): 8105-8138. doi: 10. 1088/0953-8984/10/37/002.
52. Matsen MW (2002) The standard Gaussian model for block copolymer melts. J Phys Condens Matter 14(2): R21. doi: 10. 1088/0953-8984/14/2/201.
53. Fredrickson GH (2005) The equilibrium theory of inhomogeneous polymers, vol 1. Oxford University Press, Oxford.
54. Helfand E, Tagami J (1972) Theory of the interface between immiscible polymers. II. J Chem Phys 56(7): 10. doi: 10. 1063/1. 1677735.
55. Eastwood JW, Hockney RW, Lawrence DN (1980) P3M3DP-the three-dimensional periodic particle-particle/particle-mesh program. Comput Phys Commun 19(2): 215.
56. Deserno M, Holm C (1998) How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J Chem Phys 109(12): 7678.
57. Norizoe Y, Daoulas KC, Muller M (2010) Measuring excess free energies of self-assembled membrane structures. Faraday Discuss 144: 369-391.
58. Daoulas KC, Muller M (2006) Single chain in mean field simulations: Quasi-instantaneous field approximation and quantitative comparison with Monte Carlo simulations. J Chem Phys 125(18): 184904.
59. Marrink S-J, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27): 7812-7824. doi: 10. 1021/jp071097f.
60. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16): 1701-1718.
61. Zhao Y, De Nicola A, Kawakatsu T, Milano G (2012) Hybrid particle-field molecular dynamics simulations: parallelization and benchmarks. J Comput Chem 33: 868-880. doi: 10. 1002/jcc. 22883.
62. Carbone P, Varzaneh HAK, Chen X, Muller-Plathe F (2008) Transferability of coarse-grained force fields: the polymer case. J Chem Phys 128(6): 064904-064911.
63. Tuckerman ME, Glenn JM, Bruce JB (1990) Molecular dynamics algorithm for condensed systems with multiple time scales. J Chem Phys 93(2): 5. doi: 10. 1063/1. 459140.
64. Moroi Y (1992) Micelles. Theoretical and applied aspects. Springer, Berlin.