Coarse-grain simulations of active molecular machines in lipid bilayers

Journal of Chemical Physics

Volumn 138, Issue 19, 2013, Pages

  Huang, Mu Jie ^a   Kapral, Raymond ^b   Mikhailov, Alexander S ^c   Chen, Hsuan Yi ^a,d,e  

^a NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^b UNIVERSITY OF TORONTO   (Canada)

^c FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

^d INSTITUTE OF PHYSICS   (Taiwan)

^e NATIONAL CENTER FOR THEORETICAL SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ASYMMETRIC PERTURBATIONS; COARSE-GRAIN METHOD; CONFORMATIONAL CHANGE; HYBRID SIMULATION; MEMBRANE FLUCTUATIONS; MOLECULAR MACHINES; MULTI-PARTICLE COLLISION DYNAMICS; PERIPHERAL MEMBRANES;

CYTOLOGY; LIPID BILAYERS; MOLECULAR DYNAMICS; REACTION KINETICS;

PROTEINS;

LIPID; LIPID BILAYER;

CHEMICAL STRUCTURE; CHEMISTRY; HYDRODYNAMICS; LIPID BILAYER; MOLECULAR DYNAMICS; ARTICLE;

HYDRODYNAMICS; LIPID BILAYERS; LIPIDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION;

EID: 84878352127     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4803507     Document Type: Article

References (53)

1. R. Phillips, J. Kondev, and J. Theriot, Physical Biology of the Cell (Garland Science, 2009).
2. A. Arkhipov, Y. Yin, and K. Schulten, Biophys. J. 95, 2806 (2008). 10.1529/biophysj.108.132563
3. A. Callan-Jones and P. Bassereau, Dev. Cell 22, 691 (2012). 10.1016/j.devcel.2012.04.001
4. H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher, H. Ploegh, and P. Matsudaira, Molecular Cell Biology, 6th ed. (W. H. Freeman, 2007).
5. M. D. El Alaoui Faris, D. Lacoste, J. Pécréaux, J.-F. Joanny, J. Prost, and P. Bassereau, Phys. Rev. Lett. 102, 038102 (2009). 10.1103/PhysRevLett.102.038102
6. N. Gov, Phys. Rev. Lett. 93, 268104 (2004). 10.1103/PhysRevLett.93.268104
7. D. Lacoste and A. W. C. Lau, Europhys. Lett. 70, 418 (2005). 10.1209/epl/i2004-10494-8
8. L.-L. Lin, N. Gov, and F. L. Brown, J. Chem. Phys. 124, 074903 (2006). 10.1063/1.2166383
9. H.-Y. Chen and A. S. Mikhailov, Phys. Rev. E 81, 031901 (2010). 10.1103/PhysRevE.81.031901
10. A. Alonso, H.-Y. Chen, M. Bär, and A. S. Mikhailov, Eur. Phys. J. Spec. Top. 191, 131 (2010). 10.1140/epjst/e2010-01346-4
11. B. L. de Groot and H. Grubmuller, Science 294, 2353 (2001). 10.1126/science.1062459
12. G. Portella, T. Polupanow, F. Zocher, D. A. Boytsov, P. Pohl, U. Diederichsen, and B. L. de Groot, Biophys. J. 103, 1698 (2012). 10.1016/j.bpj.2012.08.059
13. N. Go, Annu. Rev. Biophys. Bioeng. 12, 183 (1983). 10.1146/annurev.bb.12. 060183.001151
14. M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996). 10.1103/PhysRevLett.77. 1905
15. T. Haliloglu, I. Bahar, and B. Erman, Phys. Rev. Lett. 79, 3090 (1997). 10.1103/PhysRevLett.79.3090
16. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, and O. Keskin, Biophys. J. 80, 505 (2001). 10.1016/S0006-3495(01)76033-X
17. Y. Togashi and A. S. Mikhailov, Proc. Natl. Acad. Sci. U.S.A. 104, 8697 (2007). 10.1073/pnas.0702950104
18. H. Flechsig and A. S. Mikhailov, Proc. Natl. Acad. Sci. U.S.A. 107, 20875 (2010). 10.1073/pnas.1014631107
19. M. Düttmann, M. Mittnenzweig, Y. Togashi, T. Yanagida, and A. Mikhailov, PLoS ONE 7, e45859 (2012). 10.1371/journal.pone.0045859
20. M. Düttmann, Y. Togashi, T. Yanagida, and A. Mikhailov, Biophys. J. 102, 542 (2012). 10.1016/j.bpj.2011.12.013
21. I. Bahar, A. R. Atilgan, and B. Erman, Folding Des. 2, 173 (1997). 10.1016/S1359-0278(97)00024-2
22. A. Cressman, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Rev. E 77, 050901 (2008). 10.1103/PhysRevE.77.050901
23. C. Echeverria, Y. Togashi, A. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys. 13, 10527 (2011). 10.1039/c1cp00003a
24. I. R. Cooke, K. Kremer, and M. Deserno, Phys. Rev. E 72, 011506 (2005). 10.1103/PhysRevE.72.011506
25. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, " Coarse grain models and the computer simulation of soft materials.," J. Phys.: Condens. Matter 16, R481 (2004). 10.1088/0953-8984/16/15/R03
26. M. Venturoli, M. M. Sperotto, M. Kranenburg, and B. Smit, Phys. Rep. 437, 1 (2006). 10.1016/j.physrep.2006.07.006
27. J. C. Shillcock and R. Lipowsky, J. Chem. Phys. 117, 5048 (2002). 10.1063/1.1498463
28. M. Laradji and P. S. Kumar, Phys. Rev. Lett. 93, 198105 (2004). 10.1103/PhysRevLett.93.198105
29. L. Gao, J. Shillcock, and R. Lipowsky, J. Chem. Phys. 126, 015101 (2007). 10.1063/1.2424698
30. N. Malevanets and R. Kapral, J. Chem. Phys. 110, 8605 (1999). 10.1063/1.478857
31. N. Malevanets and R. Kapral, J. Chem. Phys. 112, 7260 (2000). 10.1063/1.481289
32. R. Kapral, Adv. Chem. Phys. 140, 89 (2008). 10.1002/9780470371572.ch2
33. G. Gompper, T. Ihle, D. M. Kroll, and R. G. Winkler, Adv. Polym. Sci. 221, 1 (2009). 10.1007/12-2008-5
34. M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys. 137, 055101 (2012). 10.1063/1.4736414
35. U. Schmidt, G. Guigas, and M. Weiss, Phys. Rev. Lett. 101, 128104 (2008). 10.1103/PhysRevLett.101.128104
36. F. J.-M. de Meyer, M. Venturoli, and B. Smit, Biophys. J. 95, 1851 (2008). 10.1529/biophysj.107.124164
37. S. Li, X. Zhang, and W. Wang, Biophys. J. 98, 2554 (2010). 10.1016/j.bpj.2010.02.032
38. D. Morozova, G. Guigas, and M. Weiss, PLoS Comput. Biol. 7, e1002067 (2011). 10.1371/journal.pcbi.1002067
39. K. Balali-Mood, P. J. Bond, and M. S. P. Sansom, Biochemistry 48, 2135 (2009). 10.1021/bi8017398
40. M.-J. Huang, H.-Y. Chen, and A. S. Mikhailov, Eur. Phys. J. E 35, 119 (2012). 10.1140/epje/i2012-12119-5
41. P. Maragakis and M. Karplus, J. Mol. Biol. 352, 807 (2005). 10.1016/j.jmb.2005.07.031
42. K. Okazaki, N. Koga, S. Takada, J. Onuchic, and P. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 103, 11844 (2006). 10.1073/pnas.0604375103
43. K. Kremer and G. S. Grest, J. Chem. Phys. 92, 5057 (1990). 10.1063/1.458541
44. T. Ihle and D. M. Kroll, Phys. Rev. E 63, 020201 (2001). 10.1103/PhysRevE.63.020201
45. T. Ihle and D. M. Kroll, Phys. Rev. E 67, 066705 (2003). 10.1103/PhysRevE.67.066705
46. D. Reeves, T. Ursell, P. Sens, J. Kondev, and R. Phillips, Phys. Rev. E 78, 041901 (2008). 10.1103/PhysRevE.78.041901
47. c. 10.1016/j.bpj.2012.07.053
48. H. Diamant, J. Phys. Soc. Jpn. 78, 041002 (2009). 10.1143/JPSJ.78.041002
49. P. G. Saffman and M. Delbrück, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 (1975). 10.1073/pnas.72.8.3111
50. J. S. Guasto, K. A. Johnson, and J. P. Gollub, Phys. Rev. Lett. 105, 168102 (2010). 10.1103/PhysRevLett.105.168102
51. I. B. Bischofs, S. A. Safran, and U. S. Schwarz, Phys. Rev. E 69, 021911 (2004). 10.1103/PhysRevE.69.021911
52. J. M. Schofield, P. Inder, and R. Kapral, J. Chem. Phys. 136, 205101 (2012). 10.1063/1.4719539
53. J. Dursi, L. Groer, D. Gruner, C. Loken, S. Northrup, S. Ross, R. Sobie, and C. Yip, " High performance computing symposium (hpcs2010).," J. Phys.: Conf. Ser. 256, 011001 (2010). 10.1088/1742-6596/256/1/011001