Large-scale simulations of fluctuating biological membranes

Journal of Chemical Physics

Volumn 132, Issue 15, 2010, Pages

  Pasqua, Andrea ^a   Maibaum, Lutz ^a,b   Oster, George ^c   Fletcher, Daniel A ^b,d   Geissler, Phillip L ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c University of California Berkeley   (United States)

^d University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BI-LAYER; COARSE GRAINED MODELS; CRYSTALLINE ORDER; HYDROPHOBIC ASSOCIATION; IMPLICIT SOLVENTS; LARGE SCALE SIMULATIONS; MICRON SCALE; MULTI-PARTICLE INTERACTIONS; NATURAL LIPIDS; SPHERICAL PARTICLE; TWO-DIMENSIONAL STRUCTURES;

ASSOCIATION REACTIONS; BIOLOGICAL MEMBRANES; CYTOLOGY; LIPID BILAYERS; NANORODS;

COMPUTER SIMULATION;

NANOTUBE;

ALGORITHM; ARTICLE; ARTIFICIAL MEMBRANE; CHEMISTRY; COMPUTER SIMULATION; ELASTICITY; HYDROPHOBICITY; LIPID BILAYER; PARTICLE SIZE;

ALGORITHMS; COMPUTER SIMULATION; ELASTICITY; HYDROPHOBICITY; LIPID BILAYERS; MEMBRANES, ARTIFICIAL; NANOTUBES; PARTICLE SIZE;

EID: 77951674735     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3382349     Document Type: Article

References (36)

1. G. Brannigan, L. C.-L. Lin, and F. L. H. Brown, Eur. Biophys. J. EBJOE8 0175-7571 35, 104 (2006). 10.1007/s00249-005-0013-y (Pubitemid 43042770)
2. O. Edholm, in Computational Modeling of Membrane Bilayers, edited by, S. E. Feller, (Academic, New York, 2008).
3. J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, and M. L. Klein, J. Phys. Chem. B JPCBFK 1089-5647 105, 4464 (2001). 10.1021/jp010238p (Pubitemid 35381588)
4. S. J. Marrink, A. H. de Vries, and A. E. Mark, J. Phys. Chem. B JPCBFK 1089-5647 108, 750 (2004). 10.1021/jp036508g
5. G. S. Ayton and G. A. Voth, J. Phys. Chem. B JPCBFK 1089-5647 113, 4413 (2009). 10.1021/jp8087868
6. G. S. Ayton, E. Lyman, and G. A. Voth, Faraday Discuss. FDISE6 0301-7249 144, 347 (2010). 10.1039/b901996k
7. I. R. Cooke, K. Kremer, and M. Deserno, Phys. Rev. E PLEEE8 1063-651X 72, 011506 (2005). 10.1103/PhysRevE.72.011506 (Pubitemid 41521033)
8. G. Brannigan, P. F. Philips, and F. L. H. Brown, Phys. Rev. E PLEEE8 1063-651X 72, 011915 (2005). 10.1103/PhysRevE.72.011915 (Pubitemid 41521069)
9. M. Venturoli, M. M. Sperotto, M. Kranenburg, and B. Smit, Phys. Rep. PRPLCM 0370-1573 437, 1 (2006). 10.1016/j.physrep.2006.07.006
10. J. -M. Drouffe, A. C. Maggs, and S. Leibler, Science SCIEAS 0036-8075 254, 1353 (1991). 10.1126/science.1962193
11. G. Gompper and D. M. Kroll, J. Phys.: Condens. Matter JCOMEL 0953-8984 12, A29 (2000). 10.1088/0953-8984/12/8A/304
12. G. Ayton and G. A. Voth, Biophys. J. BIOJAU 0006-3495 83, 3357 (2002). 10.1016/S0006-3495(02)75336-8
13. H. Noguchi and G. Gompper, Phys. Rev. E PLEEE8 1063-651X 73, 021903 (2006). 10.1103/PhysRevE.73.021903 (Pubitemid 43287743)
14. G. S. Ayton, S. Izvekov, W. G. Noid, and G. A. Voth, Curr. Top. Membr. CTMEET 1063-5823 60, 181 (2008). 10.1016/S1063-5823(08)00007-0
15. T. Kohyama, Physica A PHYADX 0378-4371 388, 3334 (2009). 10.1016/j.physa.2009.05.011
16. W. Helfrich, Z. Naturforsch. C ZNFCAP 0341-0471 28, 693 (1973).
17. S. A. Safran, Statistical Thermodynamics of Surfaces, Interfaces and Membranes (Addison-Wesley, Reading, MA, 1994).
18. G. S. Ayton, P. D. Blood, and G. A. Voth, Biophys. J. BIOJAU 0006-3495 92, 3595 (2007). 10.1529/biophysj.106.101709 (Pubitemid 46698648)
19. G. S. Ayton, E. Lyman, V. Krishna, R. D. Swenson, C. Mim, V. M. Unger, and G. A. Voth, Biophys. J. BIOJAU 0006-3495 97, 1616 (2009). 10.1016/j.bpj.2009.06.036
20. G. Gompper and D. M. Kroll, J. Phys. (France) JOPQAG 0302-0738 6, 1305 (1996). 10.1051/jp1:1996246
21. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed. (Garland Science, New York, 2002).
22. D. Chandler, Nature (London) NATUAS 0028-0836 437, 640 (2005). 10.1038/nature04162 (Pubitemid 41486526)
23. BT.
24. W. Rawicz, K. C. Olbrich, T. McIntosh, D. Needham, and E. Evans, Biophys. J. BIOJAU 0006-3495 79, 328 (2000). 10.1016/S0006-3495(00)76295-3
25. J. -B. Fournier and C. Barbetta, Phys. Rev. Lett. PRLTAO 0031-9007 100, 078103 (2008). 10.1103/PhysRevLett.100.078103 (Pubitemid 351393546)
26. q. This procedure generates a systematic bias at large wavevectors (Ref.). Taking this bias into account does not change the value of κ for our model.
27. A. P. Liu, D. L. Richmond, L. Maibaum, S. Pronk, P. L. Geissler, and D. A. Fletcher, Nat. Phys. ZZZZZZ 1745-2473 4, 789 (2008). 10.1038/nphys1071
28. X. Chen, A. Kis, A. Zettl, and C. R. Bertozzi, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 104, 8218 (2007). 10.1073/pnas.0700567104 (Pubitemid 47175468)
29. I. Deŕnyi, F. Jülicher, and J. Prost, Phys. Rev. Lett. PRLTAO 0031-9007 88, 238101 (2002). 10.1103/PhysRevLett.88.238101
30. T. R. Powers, G. Huber, and R. E. Goldstein, Phys. Rev. E PLEEE8 1063-651X 65, 041901 (2002). 10.1103/PhysRevE.65.041901 (Pubitemid 40618856)
31. E. Atilgan, D. Wirtz, and S. X. Sun, Biophys. J. BIOJAU 0006-3495 90, 65 (2006). 10.1529/biophysj.105.071480
32. G. Koster, A. Cacciuto, I. Derenyi, D. Frenkel, and M. Dogterom, Phys. Rev. Lett. PRLTAO 0031-9007 94, 068101 (2005). 10.1103/PhysRevLett.94.068101 (Pubitemid 40620808)
33. I. R. Cooke and M. Deserno, J. Chem. Phys. JCPSA6 0021-9606 123, 224710 (2005). 10.1063/1.2135785 (Pubitemid 41816331)
34. K. A. Brakke, Exp. Math. ZZZZZZ 1058-6458 1, 141 (1992).
35. K. A. Brakke, Surface Evolver 2.30c. http://www.susqu.edu/brakke/evolver.
36. 2), where H is the local mean curvature. Calculation were performed using the Surface Evolver software package (Refs.), which employs discretized approximations for both the membrane shape and the operators in the energy functional. To mimic the geometry of our particle simulation as closely as possible, we constrained the membrane height to zero on a square frame of side length 60d, and set the Cartesian coordinates of a single vertex to (0,0,l). The force f (l) was computed as the derivative of the ground state energy with respect to l.