Fluctuating hydrodynamics of multicomponent membranes with embedded proteins

Journal of Chemical Physics

Volumn 141, Issue 7, 2014, Pages

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

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDRODYNAMICS; LIPID BILAYERS; STOCHASTIC SYSTEMS;

FLUCTUATING HYDRODYNAMICS; LIPID BILAYER MEMBRANES; LIPID COMPOSITION; MEMBRANE COMPOSITION; MEMBRANE PROTEINS; MULTICOMPONENTS; MULTIPLE APPLICATIONS; PHASE SEPARATION DYNAMICS;

PROTEINS;

MEMBRANE PROTEIN;

CELL MEMBRANE; CHEMICAL STRUCTURE; CHEMISTRY; DIFFUSION; HYDRODYNAMICS; METABOLISM; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; STATISTICS; VISCOSITY;

CELL MEMBRANE; DIFFUSION; HYDRODYNAMICS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; STOCHASTIC PROCESSES; VISCOSITY;

EID: 84906568764     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4892802     Document Type: Article

References (142)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell (Garland Science, New York, 2007).
2. R. B. Gennis, Biomembranes: Molecular Structure and Function (Springer-Verlag, Berlin, 1989).
3. H. C. Berg and E. M. Purcell, Biophys. J. 20, 193 (1977).
4. S. Singer and G. L. Nicholson, Science 175, 720 (1972).
5. D. Lingwood and K. Simons, Science 327, 46 (2010).
6. M. J. Saxton and K. Jacobson, Annu. Rev. Biophys. Biomol. Struct. 26, 373 (1997).
7. R. Lipowsky and E. Sackmann, Structure and Dynamics of Membranes (Elsevier Science, Amsterdam, 1995).
8. S. L. Veatch and S. L. Keller, Biochim. Biophys. Acta. 1746, 172 (2005).
9. K. Simons and W. L. Vaz, Ann. Rev. Biophys. Biomol. Struct. 33, 269 (2004).
10. F. L. Brown, Q. Rev. Biophys. 44, 391 (2011).
11. W. L. Ash, M. R. Zlomislic, E. O. Oloo, and D. P. Tieleman, Biochim. Biophys. Acta, Biomembr. 1666, 158 (2004).
12. P. G. Saffman and M. Delbrück, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 (1975).
13. B. D. Hughes, B. A. Pailthorpe, and L. R. White, J. Fluid Mech. 110, 349 (1981).
14. P. Cicuta, S. L. Keller, and S. L. Veatch, J. Phys. Chem. B 111, 3328 (2007).
15. E. P. Petrov and P. Schwille, Biophys. J. 94, L41 (2008).
16. S. Ramadurai, A. Holt, V. Krasnikov, G. Van Den Bogaart, J. Killian, and B. Poolman, J. Am. Chem. Soc. 131, 12650 (2009).
17. K.Weiß, A. Neef, Q. Van, S. Kramer, I. Gregor, and J. Enderlein, Biophys. J. 105, 455 (2013).
18. B. A. Camley and F. L. Brown, Soft Matter 9, 4767 (2013).
19. H. A. Stone and H. M. McConnell, Proc. R. Soc. London, Ser. A 448, 97 (1995).
20. C. Esposito, A. Tian, S. Melamed, C. Johnson, S. Tee, and T. Baumgart, Biophys. J. 93, 3169 (2007).
21. B. A. Camley, C. Esposito, T. Baumgart, and F. L. H. Brown, Biophys. J. 99, L44 (2010).
22. N. Oppenheimer and H. Diamant, Biophys. J. 96, 3041 (2009).
23. V. Prasad, S. Koehler, and E. Weeks, Phys. Rev. Lett. 97, 176001 (2006).
24. Z. H. Nguyen, M. Atkinson, C. S. Park, J. Maclennan, M. Glaser, and N. Clark, Phys. Rev. Lett. 105, 268304 (2010).
25. A. Eremin, S. Baumgarten, K. Harth, R. Stannarius, Z. Nguyen, A. Goldfain, C. Park, J. Maclennan, M. Glaser, and N. Clark, Phys. Rev. Lett. 107, 268301 (2011).
26. B. A. Camley and F. L. H. Brown, Phys. Rev. Lett. 105, 148102 (2010).
27. B. A. Camley and F. L. Brown, J. Chem. Phys. 135, 225106 (2011).
28. C. Peskin, Acta Numer. 11, 479 (2002).
29. P. J. Atzberger, P. R. Kramer, and C. S. Peskin, J. Comput. Phys. 224, 1255 (2007).
30. D. L. Ermak and J. A. McCammon, J. Chem. Phys. 69, 1352 (1978).
31. D. K. Lubensky and R. E. Goldstein, Phys. Fluids 8, 843 (1996).
32. A. J. Levine and F. C. MacKintosh, Phys. Rev. E 66, 061606 (2002).
33. B. A. Camley and F. L. H. Brown, Phys. Rev. E 84, 021904 (2011).
34. P. Saffman, J. Fluid Mech. 73, 593 (1976).
35. T. Han and M. Haataja, Phys. Rev. E 84, 051903 (2011).
36. A. Serra and J. M. Rubí, Physica A 142, 342 (1987).
37. C. Pozrikidis, Boundary Integral and Singularity Methods for Linearized Viscous Flow (Cambridge University Press, New York, 1992).
38. L. Landau and E. Lifshitz, Fluid Mechanics (Pergamon Press, Massachusetts, 1959).
39. J. Happel and H. Brenner, Low Reynolds Number Hydrodynamics (Kluwer, The Hague, 1983).
40. S. Kim and S. J. Karrila, Microhydrodynamics: Principles and Selected Applications (Dover Publications, 2005).
41. P. J. Atzberger, Physica D 226, 144 (2007).
42. M. Cates, K. Stratford, R. Adhikari, P. Stansell, J. Desplat, I. Pagonabarraga, and A. Wagner, J. Phys.: Condens. Matter 16, S3903 (2004).
43. P. J. Atzberger, Phys. Lett. A 351, 225 (2006).
44. N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, 2007).
45. L. Lin and F. L. Brown, Phys. Rev. Lett. 93, 256001 (2004).
46. L. Lin and F. L. Brown, Phys. Rev. E 72, 011910 (2005).
47. L. C.-L. Lin and F. L. Brown, J. Chem. Theory Comput. 2, 472 (2006).
48. A. J. Ladd, J. Chem. Phys. 88, 5051 (1988).
49. A. Naji, P. Atzberger, and F. L. H. Brown, Phys. Rev. Lett. 102, 138102 (2009).
50. M. Henle and A. Levine, Phys. Fluids 21, 033106 (2009).
51. H. Yamakawa, Modern Theory of Polymer Solutions (Harper & Row, New York, 1971).
52. D. E. Golan, M. R. Alecio, W. R. Veatch, and R. R. Rando, Biochemistry 23, 332 (1984).
53. L. J. Fauci and A. McDonald, Bull. Math. Biol. 57, 679 (1995).
54. B. Vanderlei, J. J. Feng, and L. Edelstein-Keshet, Multiscale Model. Simul. 9, 1420 (2011).
55. H. Qian, M. Sheetz, and E. Elson, Biophys. J. 60, 910 (1991).
56. I.-C. Yeh and G. Hummer, J. Phys. Chem. B 108, 15873 (2004).
57. B. Dünweg and K. Kremer, J. Chem. Phys. 99, 6983 (1993).
58. E. P. Petrov, R. Petrosyan, and P. Schwille, Soft Matter 8, 7552 (2012).
59. R. G. Larson, The Structure and Rheology of Complex Fluids (Oxford University Press, 1999).
60. W. R. Schowalter, Mechanics of Non-Newtonian Fluids (Pergamon Press, Oxford, 1978).
61. R. B. Bird and O. Hassager, Dynamics of Polymeric Liquids (Wiley- Interscience, 1987), Vol. 1.
62. 62S. J. Bussell, D. L. Koch, and D. A. Hammer, Biophys. J. 68, 1836 (1995).
63. S. J. Bussell, D. A. Hammer, and D. L. Koch, J. Fluid Mech. 258, 167 (1994).
64. S. J. Bussell, D. L. Koch, and D. A. Hammer, Biophys. J. 68, 1828 (1995).
65. T. L. Dodd, D. A. Hammer, A. S. Sangani, and D. L. Koch, J. Fluid Mech. 293, 147 (1995).
66. N. Oppenheimer and H. Diamant, Phys. Rev. Lett. 107, 258102 (2011).
67. N. Oppenheimer and H. Diamant, Phys. Rev. E. 82, 041912 (2010).
68. J. Abney, B. Scalettar, and J. Owicki, Biophys. J. 55, 817 (1989).
69. S. Veatch, I. Polozov, K. Gawrisch, and S. Keller, Biophys. J. 86, 2910 (2004).
70. S. L. Veatch and S. L. Keller, Biophys. J. 85, 3074 (2003).
71. A. R. Honerkamp-Smith, B. B. Machta, and S. L. Keller, Phys. Rev. Lett. 108, 265702 (2012).
72. A. Honerkamp-Smith, P. Cicuta, M. Collins, S. Veatch, M. Den Nijs, M. Schick, and S. Keller, Biophys. J. 95, 236 (2008).
73. S. Veatch, O. Soubias, S. Keller, and K. Gawrisch, Proc. Natl. Acad. Sci. U.S.A. 104, 17650 (2007).
74. S. Veatch, P. Cicuta, P. Sengupta, A. Honerkamp-Smith, D. Holowka, and B. Baird, ACS Chem. Biol. 3, 287 (2008).
75. S. A. Safran, Statistical Thermodynamics of Surfaces, Interfaces, and Membranes (Westview Press, 2003).
76. P. M. Chaikin and T. C. Lubensky, Principles of Condensed Matter Physics (Cambridge University Press, 2000).
77. P. C. Hohenberg and B. I. Halperin, Rev. Mod. Phys. 49, 435 (1977).
78. A. J. Bray, Adv. Phys. 43, 357 (1994).
79. P. Kloeden and E. Platen, Numerical Solution of Stochastic Differential Equations (Springer, 1999).
80. W. Rümelin, SIAM J. Numer. Ann. 19, 604 (1982).
81. C. Gardiner, Handbook of Stochastic Methods (Springer, 1985).
82. J. Zhu, L.-Q. Chen, J. Shen, and V. Tikare, Phys. Rev. E 60, 3564 (1999).
83. L. N. Trefethen, Spectral Methods in MATLAB (SIAM, 2000), Vol. 10.
84. 84J. K. Sigurdsson, F. L. Brown, and P. J. Atzberger, J. Comput. Phys. 252, 65 (2013).
85. B. Reynwar and M. Deserno, Biointerphases 3, FA117 (2008).
86. B. B. Machta, S. L. Veatch, and J. P. Sethna, Phys. Rev. Lett. 109, 138101 (2012).
87. T. Fischer and R. Vink, J. Chem. Phys. 134, 055106 (2011).
88. A. Yethiraj and J. C. Weisshaar, Biophys. J. 93, 3113 (2007).
89. B. Machta, S. Papanikolaou, J. Sethna, and S. Veatch, Biophys. J. 100, 1668 (2011).
90. J. Ehrig, E. Petrov, and P. Schwille, New J. Phys. 13, 045019 (2011).
91. T. Witkowski, R. Backofen, and A. Voigt, Phys. Chem. Chem. Phys. 14, 14509 (2012).
92. See supplementary material at http://dx.doi.org/10.1063/1.4892802 for movies of simulations.
93. K. Inaura and Y. Fujitani, J. Phys. Soc. Jpn. 77, 114603 (2008).
94. R. R. Netz, Phys. Rev. Lett. 76, 3646 (1996).
95. V. Démery and D. S. Dean, Phys. Rev. Lett. 104, 080601 (2010).
96. V. Démery and D. S. Dean, Europhys. J. E 32, 377 (2010).
97. V. Démery and D. S. Dean, Phys. Rev. E 84, 010103 (2011).
98. D. S. Dean and V. Démery, J. Phys.: Condens. Matter 23, 234114 (2011).
99. V. Démery and D. S. Dean, Phys. Rev. E 84, 011148 (2011).
100. V. Démery, Phys. Rev. E 87, 052105 (2013).
101. A. Naji, A. J. Levine, and P. Pincus, Biophys. J. 93, L49 (2007).
102. B. A. Camley and F. L. Brown, Phys. Rev. E 85, 061921 (2012).
103. P. S. Niemelä, M. S. Miettinen, L. Monticelli, H. Hammaren, P. Bjelkmar, T. Murtola, E. Lindahl, and I. Vattulainen, J. Am. Chem. Soc. 132, 7574 (2010).
104. L. J. Pike, J. Lipid Res. 47, 1597 (2006).
105. J. Ehrig, E. Petrov, and P. Schwille, Biophys. J. 100, 80 (2011).
106. S. Marrink, H. Risselada, S. Yefimov, D. Tieleman, and A. De Vries, J. Phys. Chem. B 111, 7812 (2007).
107. L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D. Tieleman, and S. Marrink, J. Chem. Theory Comput. 4, 819 (2008).
108. W. den Otter and S. Shkulipa, Biophys. J. 93, 423 (2007).
109. C. Herold, P. Schwille, and E. Petrov, Phys. Rev. Lett. 104, 148102 (2010).
110. J. Knight, M. Lerner, J. Marcano-Velázquez, R. Pastor, and J. Falke, Biophys. J. 99, 2879 (2010).
111. R. Reigada, J. Buceta, J. Gomez, F. Sagues, and K. Lindenberg, J. Chem. Phys. 128, 025102 (2008).
112. R. Elliott, I. Szleifer, and M. Schick, Phys. Rev. Lett. 96, 098101 (2006).
113. T. Yamamoto, R. Brewster, and S. Safran, Europhys. Lett. 91, 28002 (2010).
114. B. Palmieri and S. A. Safran, Phys. Rev. E 88, 032708 (2013).
115. B. Palmieri and S. A. Safran, Langmuir 29, 5246 (2013).
116. S. Chiantia, P. Schwille, A. S. Klymchenko, and E. London, Biophys. J. 100, L1 (2011).
117. T. Han and M. Haataja, Soft Matter 9, 2120 (2013).
118. R. Swaminathan, C. P. Hoang, and A. Verkman, Biophys. J. 72, 1900 (1997).
119. 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).
120. R. Dimova, B. Pouligny, and C. Dietrich, Biophys. J. 79, 340 (2000).
121. R. Dimova, C. Dietrich, A. Hadjiisky, K. Danov, and B. Pouligny, Eur. Phys. J. B 12, 589 (1999).
122. S. Choi, S. Steltenkamp, J. Zasadzinski, and T. Squires, Nat. Commun. 2, 312 (2011).
123. K. Kim, S. Choi, J. Zasadzinski, and T. Squires, Soft Matter 7, 7782 (2011).
124. R. E. Waugh, Biophys. J. 38, 19 (1982).
125. S. Veatch and S. Keller, Phys. Rev. Lett. 94, 148101 (2005).
126. G. Feigenson and J. Buboltz, Biophys. J. 80, 2775 (2001).
127. R. De Almeida, A. Fedorov, and M. Prieto, Biophys. J. 85, 2406 (2003).
128. R. Baxter, Exactly Solved Models in Statistical Mechanics (Academic Press, 1982).
129. J. Gómez, F. Sagués, and R. Reigada, Phys. Rev. E 80, 011920 (2009).
130. H. McConnell, Biophys. J. 88, L23 (2005).
131. S. Veatch, K. Gawrisch, and S. Keller, Biophys. J. 90, 4428 (2006).
132. M. Kardar, Statistical Physics of Fields (Cambridge University Press, 2007).
133. M. Gross and F. Varnik, Phys. Rev. E 85, 056707 (2012).
134. A. J. Levine, T. B. Liverpool, and F. C. MacKintosh, Phys. Rev. E 69, 021503 (2004).
135. A. J. Levine, T. B. Liverpool, and F. C. MacKintosh, Phys. Rev. Lett. 93, 038102 (2004).
136. R. Cortez, SIAM J. Sci. Comput. 23, 1204 (2001).
137. R. Cortez, L. Fauci, and A. Medovikov, Phys. Fluids 17, 031504 (2005).
138. J. G. de la Torre, G. del Rio Echenique, and A. Ortega, J. Phys. Chem. B 111, 955 (2007).
139. P. J. Atzberger, J. Comput. Phys. 230, 2821 (2011).
140. M. Makino and M. Doi, J. Phys. Soc. Jpn. 73, 2739 (2004).
141. Y. Han, A. Alsayed, M. Nobili, J. Zhang, T. Lubensky, and A. Yodh, Science 314, 626 (2006).
142. In order to convert between results with the δk,-k' correlation and the δij correlation, it is often convenient to define Rk = ΣpGkpQp with Qp (t)Qp (t') = δp,p-'(t-t') and thusΣ p GkpGk'p = δk,-k'.