Calculating hydrodynamic interactions for membrane-embedded objects

Journal of Chemical Physics

Volumn 141, Issue 12, 2014, Pages

  Noruzifar, Ehsan ^a   Camley, Brian A ^b   Brown, Frank L H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFUSION IN LIQUIDS; LIPID BILAYERS; PROTEINS; SURFACE DIFFUSION;

ANALYTICAL PREDICTIONS; ANALYTICAL RESULTS; COUPLED DIFFUSION; HYDRODYNAMIC INTERACTION; LIPID BILAYER MEMBRANES; MULTIPLE OBJECTS; NUMERICAL SCHEME; SELF-DIFFUSION COEFFICIENTS;

HYDRODYNAMICS;

LIPID BILAYER; MEMBRANE PROTEIN;

ALGORITHM; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; DIFFUSION; DIMERIZATION; HYDRODYNAMICS; LIPID BILAYER; ROTATION; VALIDATION STUDY;

ALGORITHMS; COMPUTER SIMULATION; DIFFUSION; DIMERIZATION; HYDRODYNAMICS; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, CHEMICAL; ROTATION;

EID: 84907486146     PISSN: 00219606     EISSN: 10897690     Source Type: Journal    
DOI: 10.1063/1.4896180     Document Type: Article

References (73)

1. H. C. Berg and E. M. Purcell, Biophys. J. 20, 193 (1977). 10.1016/S0006-3495(77)85544-6
2. R. B. Gennis, Biomembranes: Molecular Structure and Function (Springer-Verlag, Berlin, 1989).
3. S. Ramadurai, A. Holt, V. Krasnikov, G. van den Bogaart, J. A. Killian, and B. Poolman, J. Am. Chem. Soc. 131, 12650 (2009). 10.1021/ja902853g
4. C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schonle, and S. W. Hell, Nature (London) 457, 1159 (2009). 10.1038/nature07596
5. D. Lingwood and K. Simons, Science 327, 46 (2010). 10.1126/science.1174621
6. M. Ott, Y. Shai, and G. Haran, J. Phys. Chem. B 117, 13308 (2013). 10.1021/jp4039418
7. M. J. Saxton and K. Jacobson, Annu. Rev. Biophys. Biomol. Struct. 26, 373 (1997). 10.1146/annurev.biophys.26.1.373
8. R. Lipowsky and E. Sackmann, Structure and Dynamics of Membranes (Elsevier Science, Amsterdam, 1995).
9. S. L. Veatch and S. L. Keller, Biochim. Biophys. Acta 1746, 172 (2005). 10.1016/j.bbamcr.2005.06.010
10. K. Simons and W. L. Vaz, Annu. Rev. Biophys. Biomol. Struct. 33, 269 (2004). 10.1146/annurev.biophys.32.110601.141803
11. F. L. Brown, Quart. Rev. Biophys. 44, 391 (2011). 10.1017/S0033583511000047
12. W. L. Ash, M. R. Zlomislic, E. O. Oloo, and D. P. Tieleman, Biochim. Biophys. Acta 1666, 158 (2004). 10.1016/j.bbamem.2004.04.012
13. N. Oppenheimer and H. Diamant, Biophys. J. 96, 3041 (2009). 10.1016/j.bpj.2009.01.020
14. P. G. Saffman and M. Delbrück, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 (1975). 10.1073/pnas.72.8.3111
15. B. Hughes, B. Pailthorpe, and L. White, J. Fluid Mech. 110, 349 (1981). 10.1017/S0022112081000785
16. R. Peters and R. J. Cherry, Proc. Natl. Acad. Sci. U.S.A. 79, 4317 (1982). 10.1073/pnas.79.14.4317
17. W. L. C. Vaz, M. Criado, V. M. C. Madeira, G. Schoellmann, and T. M. Jovin, Biochemistry 21, 5608 (1982). 10.1021/bi00265a034
18. P. Cicuta, S. L. Keller, and S. L. Veatch, J. Phys. Chem. B 111, 3328 (2007). 10.1021/jp0702088
19. E. P. Petrov and P. Schwille, Biophys. J. 94, L41 (2008). 10.1529/biophysj.107.126565
20. Z. H. Nguyen, M. Atkinson, C. S. Park, J. Maclennan, M. Glaser, and N. Clark, Phys. Rev. Lett. 105, 268304 (2010). 10.1103/PhysRevLett.105.268304
21. A. Eremin, S. Baumgarten, K. Harth, R. Stannarius, Z. H. Nguyen, A. Goldfain, C. S. Park, J. E. Maclennan, M. A. Glaser, and N. A. Clark, Phys. Rev. Lett. 107, 268301 (2011). 10.1103/PhysRevLett.107.268301
22. J. Kriegsmann, I. Gregor, I. Von Der Hocht, J. Klare, M. Engelhard, J. Enderlein, and J. Fitter, ChemBioChem 10, 1823 (2009). 10.1002/cbic.200900251
23. Y. Gambin, R. Lopez-Esparza, M. Reffay, E. Sierecki, N. S. Gov, M. Genest, R. S. Hodes, and W. Urbach, Proc. Natl. Acad. Sci. U.S.A. 103, 2098 (2006). 10.1073/pnas.0511026103
24. Y. Gambin, M. Reffay, E. Sierecki, F. Homblé, R. S. Hodges, N. S. Gov, N. Taulier, and W. Urbach, J. Phys. Chem. B 114, 3559 (2010). 10.1021/jp911354y
25. H. A. Stone and H. M. McConnell, Proc. R. Soc. London A 448, 97 (1995). 10.1098/rspa.1995.0007
26. B. A. Camley, C. Esposito, T. Baumgart, and F. L. H. Brown, Biophys. J. 99, L44 (2010). 10.1016/j.bpj.2010.07.007
27. B. A. Camley and F. L. H. Brown, Phys. Rev. Lett. 105, 148102 (2010). 10.1103/PhysRevLett.105.148102
28. B. A. Camley and F. L. Brown, J. Chem. Phys. 135, 225106 (2011). 10.1063/1.3662131
29. C. A. Stanich, A. R. Honerkamp-Smith, G. G. Putzel, C. S. Warth, A. K. Lamprecht, P. Mandal, E. Mann, T.-A. D. Hua, and S. L. Keller, Biophys. J. 105, 444 (2013). 10.1016/j.bpj.2013.06.013
30. A. R. Honerkamp-Smith, B. B. Machta, and S. L. Keller, Phys. Rev. Lett. 108, 265702 (2012). 10.1103/PhysRevLett.108.265702
31. M. Haataja, Phys. Rev. E 80, 020902 (2009). 10.1103/PhysRevE.80.020902
32. K. Inaura and Y. Fujitani, J. Phys. Soc. Jpn. 77, (2008). 10.1143/JPSJ.77.114603
33. A. J. Levine and F. C. MacKintosh, Phys. Rev. E 66, 061606 (2002). 10.1103/PhysRevE.66.061606
34. D. K. Lubensky and R. E. Goldstein, Phys. Fluids 8, 843 (1996). 10.1063/1.868893
35. V. Bloomfield, W. Dalton, and K. V. Holde, Biopolymers 5, 135 (1967). 10.1002/bip.1967.360050202
36. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Clarendon Press, 1999).
37. J. McCammon and J. Deutch, Biopolymers 15, 1397 (1976). 10.1002/bip.1976.360150712
38. E. Swanson, C. Teller, and C. de Haën, J. Chem. Phys. 68, 5097 (1978). 10.1063/1.435628
39. C. S. Peskin, Acta Numer. 11, 479 (2002). 10.1017/S0962492902000077
40. J. García de la Torre, G. del Rio Echenique, and A. Ortega, J. Phys. Chem. B 111, 955 (2007). 10.1021/jp0647941
41. N. Wang, G. A. Huber, and J. A. McCammon, J. Chem. Phys. 138, 204117 (2013). 10.1063/1.4807590
42. A. J. Levine, T. B. Liverpool, and F. C. MacKintosh, Phys. Rev. E. 69, 021503 (2004). 10.1103/PhysRevE.69.021503
43. A. J. Levine, T. B. Liverpool, and F. C. MacKintosh, Phys. Rev. Lett. 93, 038102 (2004). 10.1103/PhysRevLett.93.038102
44. R. D. Koker, Ph.D. thesis, Stanford University, 1996.
45. K. Seki, S. Mogre, and S. Komura, Phys. Rev. E 89, 022713 (2014). 10.1103/PhysRevE.89.022713
46. R. Zwanzig, J. Kiefer, and G. H. Weiss, Proc. Nat. Acad. Sci. U.S.A. 60, 381 (1968). 10.1073/pnas.60.2.381
47. J. Rotne and S. Prager, J. Chem. Phys. 50, 4831 (1969). 10.1063/1.1670977
48. R. Cortez, SIAM J. Sci. Comput. 23, 1204 (2001). 10.1137/S106482750038146X
49. R. Cortez, L. Fauci, and A. Medovikov, Phys. Fluids 17, 031504 (2005). 10.1063/1.1830486
50. B. A. Camley and F. L. H. Brown, Soft Matter 9, 4767 (2013). 10.1039/c3sm00073g
51. J. John A. Montgomery and B. J. Berne, J. Chem. Phys. 67, 4589 (1977). 10.1063/1.434619
52. J. A. Montgomery, B. J. Berne, P. G. Wolynes, and J. M. Deutch, J. Chem. Phys. 67, 5971 (1977). 10.1063/1.434773
53. G. K. Batchelor, J. Fluid Mech. 74, 1 (1976). 10.1017/S0022112076001663
54. J. L. Aguirre and T. J. Murphy, J. Chem. Phys. 59, 1833 (1973). 10.1063/1.1680268
55. S. Kim and S. J. Karrila, Microhydrodynamics: Principles and Selected Applications (Dover Publications, New York, 2005).
56. R. Schmitz and B. Felderhof, Physica A 113, 103 (1982). 10.1016/0378-4371(82)90008-5
57. B. Felderhof, Physica A 89, 373 (1977). 10.1016/0378-4371(77)90111-X
58. P. Reuland, B. Felderhof, and R. Jones, Physica A 93, 465 (1978). 10.1016/0378-4371(78)90167-X
59. B. Felderhof and R. Jones, Physica A 122, 89 (1983). 10.1016/0378-4371(83)90084-5
60. R. Schmitz and B. Felderhof, Physica A 116, 163 (1982). 10.1016/0378-4371(82)90236-9
61. B. Felderhof, Physica A 151, 1 (1988). 10.1016/0378-4371(88)90036-2
62. D. L. Ermak and J. A. McCammon, J. Chem. Phys. 69, 1352 (1978). 10.1063/1.436761
63. J. F. Brady and G. Bossis, Annu. Rev. Fluid Mech. 20, 111 (1988). 10.1146/annurev.fl.20.010188.000551
64. S. J. Bussell, D. L. Koch, and D. A. Hammer, J. Fluid Mech. 243, 679 (1992). 10.1017/S002211209200288X
65. M. Henle and A. Levine, Phys. Fluids 21, 033106 (2009). 10.1063/1.3086831
66. V. Prasad, S. A. Koehler, and E. R. Weeks, Phys. Rev. Lett. 97, 176001 (2006). 10.1103/PhysRevLett.97.176001
67. E. P. Petrov, R. Petrosyan, and P. Schwille, Soft Matter 8, 7552 (2012). 10.1039/c2sm25796c
68. J. D. Knight, M. G. Lerner, J. G. Marcano-Velázquez, R. W. Pastor, and J. J. Falke, Biophys. J. 99, 2879 (2010). 10.1016/j.bpj.2010.08.046
69. D. W. Condiff and J. S. Dahler, J. Chem. Phys. 44, 3988 (1966). 10.1063/1.1726561
70. J. Happel and H. Brenner, Low Reynolds Number Hydrodynamics (Prentice-Hall, Englewood Cliffs, 1965).
71. Y. Saad and M. Schultz, SIAM J. Sci. Stat. Comput. 7, 856 (1986). 10.1137/0907058
72. H. Lodish, D. Baltimore, A. Berk, S. L. Zipursky, P. Matsudaira, and J. Darnell, Molecular Cell Biology, 3rd ed. (Scientific American Books, New York, 1995).
73. B. A. Camley and F. L. H. Brown, J. Chem. Phys. 141, 075103 (2014). 10.1063/1.4892802