Spatially resolved simulations of membrane reactions and dynamics: Multipolar reaction DPD

European Physical Journal E

Volumn 29, Issue 4, 2009, Pages 431-448

  Fuchslin R M ^a   Maeke, T ^a   McCaskill, J S ^b  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CELL BIOLOGY; COLLECTIVE DYNAMICS; DIFFERENT LENGTH SCALE; DIRECT LINKS; DISSIPATIVE PARTICLE DYNAMICS; DYNAMIC REACTIONS; EXPERIMENTAL DATA; FLUORESCENCE IMAGE; HIGH-THROUGHPUT; KINETIC STUDY; LOCAL COMPOSITIONS; LOCAL INTERACTIONS; MECHANICAL PROCESS; MEMBRANE FLUIDITY; MEMBRANE STRUCTURES; MESO-SCALE SYSTEMS; MESOSCALE; MULTIPOLAR INTERACTION; PROTEIN SORTING; QUANTITATIVE MODELING; SCALING BEHAVIOR; SELF ORGANIZING; SELF-ORGANIZED; SIMULATION METHODOLOGY; SPATIALLY RESOLVED; STRUCTURAL SYSTEMS; SYSTEMS BIOLOGY;

CYTOLOGY; FLEXIBLE STRUCTURES; IMAGE PROCESSING; MECHANICAL STABILITY; PARTICLE INTERACTIONS; REACTION KINETICS; VIBRATIONS (MECHANICAL);

CELL MEMBRANES;

ARTICLE; CELL MEMBRANE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; KINETICS;

CELL MEMBRANE; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 70349312359     PISSN: 12928941     EISSN: 1292895X     Source Type: Journal    
DOI: 10.1140/epje/i2009-10482-x     Document Type: Article

References (51)

1. J.E. Rothmann, F.T. Wieland, Science 272, 227 (1996).
2. R. Scheckmann, L. Orci, Science 271, 1526 (1996).
3. C. Barlowe, Traffic 1, 1371 (2000).
4. P.J. Hoogerbrugge, J.M.V.A. Koelman, Europhys. Lett. 19, 155 (1992).
5. P. Español, P. Warren, Europhys. Lett. 30, 191 (1995).
6. R.D. Groot, P.D. Warren, J. Chem. Phys. 107, 4423 (1997).
7. P.B. Warren, Curr. Opin. Colloid. Sci. 3, 620 (1998).
8. J.C. Shillcock, R. Lipowsky, J. Chem. Phys. 117, 3048 (2002).
9. V. Ortiz, S.O. Nielsen, D.E. Discher, M.L. Klein, R. Lipowsky, J. Shillcock, J. Phys. Chem. B 109, 17708 (2005).
10. D.W. Li, X.Y. Liu, J. Chem. Phys. 122, 174909 (2005).
11. A.F. Jakobsen, O.G. Mouritsen, M. Weiss, J. Phys.: Condens. Matter 17, S4015 (2005).
12. B.P. Jena, S.J. Cho, Atomic Force Microscopy in Cell Biology, edited by B.P. Je, J.K. Heinrich Hörber, L. Wilson, P.T. Matsudaire, Methods Cell Biol. 68, 33 (2002).
13. J.W. Murray, A.W. Wolkoff, Adv. Drug Del. Rev. 55, 1385 (2003).
14. R.D. Groot, K.L. Rabone, Biophys. J. 81, 725 (2001).
15. R.M. Füchslin, H. Fellermann, A. Eriksson, H.J. Ziock, J. Chem. Phys. 130, 214102 (2009).
16. C. Thieulot, L. Janssen, P. Español, Phys. Rev. E 72, 16714 (2005).
17. S.Y. Trofimov, E.L.F. Nies, M.A.J. Michels, J. Chem. Phys. 117, 9383 (2002).
18. C. Thieulot, Thermodynamically consistent fluid particle modelling of phase separating mixtures, PhD Thesis (2004).
19. K. Tucci, R. Kapral, J. Chem. Phys. 120, 8262 (2004)
20. I.O. Götze, H. Noguchi, G. Gompper, Phys. Rev. E 76, 046705 (2007).
21. I. Vattulainen, M. Karttunen, G. Besold, J.M. Polson, J. Chem. Phys. 116, 3967 (2002).
22. H. Noguchi, M. Takasu, Phys. Rev. E 65, 051907 (2002).
23. J.B. Gibson, K. Chen, J. Mod. Phys. C 10, 241 (1999).
24. M. Turelli, Theor. Popul. Biol. 12, 140 (1977).
25. P.B.S. Kumar, G. Gompper, R. Lipowsky, Phys. Rev. Lett. 86, 3911 (2001).
26. K.A. Dawson, Z. Kurtovic, J. Chem. Phys. 92, 5473 (1990).
27. G. Brannigan, F.L.H. Brown, J. Chem. Phys. 120, 1059 (2004).
28. I. Pagonabarraga, D. Frenkel, J. Chem. Phys. 115, 5015 (2001).
29. P.B. Warren, Phys. Rev. E 68, 066702 (2003).
30. L. Gao, J. Shilcock, R. Lipowsky, J. Chem. Phys. 126, 015101 (2007).
31. D.B. Hill, M.J. Plaza, K. Bonin, G. Holzwarth, Eur. Biophys. J. 33, 623 (2004).
32. I.R. Cooke, K. Kremer, M. Deserno, Phys. Rev. E 72, 011506 (2005).
33. P. Del Conte Zerial, L. Brusch, A. Deutsch, preprint (2005).
34. B.J. Reynwar, G. Illya, V.A. Harmandaris, M.M. Müller, K. Kremer, M. Deserno, Nature 447, 461 (2007).
35. R. Kupfermann, P.P. Mitra, P.C. Hohenberg, S.S. Wang, Biophys. J. 72, 2430 (1997).
36. D. Frenkel, B. Smit, Understanding Molecular Simulations: From Algorithms to Applications, 2nd edition (Academic Press Inc., 2002).
37. R. Goetz, R. Lipowsky, J. Chem. Phys. 108, 7397 (1998).
38. B.M. Slepchenko, J.C. Schaff, I. Macara, L.M. Loew, Trends Cell. Biol. 13, 570 (2003).
39. www.sbml.org, the Systems Biology Markup Language.
40. J. Gao, W. Shi, L.B. Freund, Proc. Natl. Acad. Sci. U.S.A. 102, 9469 (2005).
41. G.M. Whitesides, M. Boncheva, Proc. Natl. Acad. Sci. U.S.A. 99, 4769 (2002).
42. H. Noguchi, G. Gompper, Phys. Rev. E 73, 021903 (2006).
43. H. Noguchi, G. Gompper, J. Chem. Phys. 125, 164908 (2006).
44. P. Español, Phys. Rev. E 57, 2930 (1998).
45. G. De Fabritiis, P.V. Coveney, E.G. Flekkoy, Philos. Trans. R. Soc. London, Ser. A 360, 317 (2002).
46. A. Harmandarisa, M. Deserno, J. Chem. Phys. 125, 204905 (2006).
47. H. Noguchi, G. Gompper, Proc. Natl. Acad. Sci. U.S.A. 102, 14159 (2005).
48. J.J. Monaghan, Rep. Prog. Phys. 68, 1703 (2005).
49. W. Dzwinel, D. Yuen, K. Boryczko, J. Mol. Model. 8, 33 (2002).
50. S.D. Stoyanov, R.D. Groot, J. Chem. Phys. 122, 114112 (2005).
51. L.A. Harris, P. Clancy, J. Chem. Phys. 125, 144107 (2006).