Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations

Pure and Applied Chemistry

Volumn 86, Issue 2, 2014, Pages 215-222

  Shinoda, Wataru ^a   Klein, Michael L ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Temple University   (United States)

Author keywords

Computer simulation; Lipids; Liposomes; Membranes; Molecular dynamics; Self assembly; Vesicles

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; LIPIDS; LIPOSOMES; MEMBRANES; MOLECULES; SELF ASSEMBLY; SYNCHROTRONS;

COARSE-GRAINED FORCE FIELDS; COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; EFFECTIVE INTERACTIONS; MOLECULAR DYNAMICS SIMULATIONS; PHOSPHATIDYLETHANOLAMINE; REPULSIVE INTERACTIONS; SMALL UNILAMELLAR VESICLE; VESICLES;

MOLECULAR DYNAMICS;

EID: 84907216639     PISSN: 00334545     EISSN: 13653075     Source Type: Journal    
DOI: 10.1515/pac-2014-5023     Document Type: Conference Paper

References (43)

1. T. M. Allen, P. R. Cullis. Adv. Drug. Deliv. Rev. 65, 36 (2013).
2. T. M. Allen, P. R. Cullis. Science 303, 1818 (2004).
3. T. Lian, R. Ho. J. Pharm. Sci. 90, 667 (2001).
4. A. Samad, Y. Sultana, M. Aqil. Curr. Drug. Deliv. 4, 297 (2007).
5. J. de Leeuw, H. C. de Vijlder, P. Bjerring, H. A. M. Neumann. J. Eur. Acad. Dermatol. Venereol. 23, 505 (2009).
6. C. R. Safnya, K. K. Ewert. Nature 489, 372 (2012).
7. D. Lasic, D. Needham. Chem. Rev. 95, 2601 (1995).
8. M. L. Klein, W. Shinoda. Science 321, 798 (2008).
9. W. Shinoda, R. DeVane, M. L. Klein. Curr. Opin. Struct. Biol. 22, 175 (2012).
10. W. Shinoda, R. Devane, M. L. Klein. Mol. Simulat. 33, 27 (2007).
11. W. Shinoda, R. DeVane, M. L. Klein. Sof Matter 4, 2454 (2008).
12. W. Shinoda, R. DeVane, M. L. Klein. J. Phys. Chem. B 114, 6836 (2010).
13. W. Shinoda, R. DeVane, M. L. Klein. Sof Matter 7, 6178 (2011).
14. A. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus. J. Phys. Chem. B 102, 3586 (1998).
15. J. Klauda, B. Brooks, A. MacKerell, R. Venable, R. Pastor. J. Phys. Chem. B 109, 5300 (2005).
16. S. J. Marrink, H. J. Risselada, S. Yefmov, D. P. Tieleman, A. H. de Vries. J. Phys. Chem. B 111, 7812 (2007).
17. Z. Wu, Q. Cui, A. Yethiraj. J. Chem. Theory Comput. 7, 3793 (2011).
18. M. Venturoli, M. M. Sperotto, M. Kranenburg, B. Smit. Phys. Rep. 437, 1 (2006).
19. R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein. J. Chem. Theory Comput. 5, 2115 (2009).
20. R. DeVane, M. L. Klein, C.-C. Chiu, S. O. Nielsen, W. Shinoda, P. B. Moore. J. Phys. Chem. B 114, 6386 (2010).
21. C.-C. Chiu, R. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, S. O. Nielsen. J. Phys. Chem. B 114, 6394 (2010).
22. C.-C. Chiu, W. Shinoda, R. H. DeVane, S. O. Nielsen. Sof Matter 8, 9610 (2012).
23. B. G. Levine, D. N. LeBard, R. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein. J. Chem. Theory Comput. 7, 4135 (2011).
24. W. Shinoda, T. Nakamura, S. O. Nielsen. Sof Matter 7, 9012 (2011).
25. T. Nakamura, W. Shinoda, T. Ikeshoji. J. Chem. Phys. 135, 094106 (2011).
26. T. Nakamura, W. Shinoda. J. Chem. Phys. 138, 124903 (2013).
27. K. Shuhei, T. Nakamura, S. O. Nielsen, W. Shinoda. J. Chem. Phys. 139, 034108 (2013).
28. S. Nosé, M. L. Klein. Mol. Phys. 50, 1055 (1983).
29. W. Hoover. Phys. Rev. A 31, 1695 (1985).
30. M. Parrinello, A. Rahman. J. Appl. Phys. 52, 7182 (1981).
31. R. W. Hockney, J. W. Eastwood. Computer Simulation Using Particles, Taylor & Francis, New York (1988).
32. S. Plimpton. J. Comput. Phys. 117, 1 (1995).
33. nd ed., Academic Press (2001).
34. S. Marrin, A. Mark. J. Am. Chem. Soc. 125, 11144 (2003).
35. M. Stevens, J. Hoh, T. Woolf. Phys. Rev. Lett. 91, 188102 (2003).
36. S. J. Marrink, M. Fuhrmans, H. J. Risselada, X. Periole. In Coarse-Graining of Condensed Phase and Biomolecular Systems, G. A. Voth (Ed.), pp. 5-19, CRC Press, Boca Raton (2008).
37. T. C. Sudhof, J. E. Rothman. Science 323, 474 (2009).
38. J. Rizo, C. Rosenmund. Nat. Struct. Mol. Biol. 15, 665 (2008).
39. M. A. Brindley, M. Takeda, P. Plattet, R. K. Plemper. Proc. Natl. Acad. Sci. USA 109, E3018 (2012).
40. H. J. Risselada, C. Kutzner, H. Grubmüller. ChemBioChem 12, 1049 (2011).
41. Y. Sakuma, M. Imai, M. Yanagisawa, S. Komura. Eur. Phys. J. E 25, 403 (2008).
42. S. W. Hui, T. P. Stewart, L. T. Boni, P. L. Yeagle. Science 212, 921 (1981).
43. D. P. Siegel. Biophys. J. 65, 2124 (1993).