Simulations and Models of Lipid Bilayers

Soft Matter

Volumn 4, Issue , 2009, Pages 1-82

  Pandit, Sagar A ^a   Scott, H Larry ^b  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b Illinois Institute of Technology   (United States)

Author keywords

Atomistic models; Coarse grain models; Lipid bilayers; Soft matter

Indexed keywords

EID: 84889375828     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527623372.ch1     Document Type: Chapter

References (136)

1. Allen, M. P. and Tildesley, D. J., 1989, Computer Simulation of Liquids. Oxford University Press. Oxford.
2. Ayton, G., Bardenhagen, S., Sulsky, D., and Voth, G. A., 2001, J. Chem. Phys. 114, 6913.
3. Ayton, G., Smondyrev, A. M., Bardenhagen, S., McMurtry, P., and Voth, G. A., 2002, Biophys. J. 82, 1026.
4. Ayton, G. and Voth, G. A., 2002, Biophys. J. 83, 3357.
5. Ayton, G. S.,MacWhirter, J. L., and Voth, G. A., 2004, Biophys. J. 87(50), 3242.
6. Ayton, G. S., MacWhirter, J. L., and Voth, G. A., 2006, J. Chem. Phys. 124(50), 64906.
7. Ayton, G. S., Noid,W. G., and Voth, G. A., 2007, Curr. Op. Struct. Biol. 17(50), 192.
8. Balazs, A., Ginsburg, V. V., Qiu, F., Peng, G., and Jasnow, D., 2000, J. Phys. Chem. B 104, 3411.
9. Baxter, R. J., 1982, Exactly Solved Models in Statistical Mechanics. Academic Press.
10. Berendsen, H. J. C., van der Spoel, D., and van Drunen, R., 1995, Comp. Phys. Comm. 91, 43.
11. Berger, O., Edholm, O., and Jähnig, F., 1997, Biophys. J. 72, 2002.
12. Bhide, S. Y., Zhang, Z., and Berkowitz, M. L., 2007, Biophys. J. 92, 1284.
13. Binder, K., 1986, Monte Carlo Methods in Statistical Physics. Springer-Verlag.
14. Bodin, S., Soulet, C., Tronchere, H., Sie, P., Gachet, C., Plantavid, M. P., and Payrastre, B., 2005, J. Cell Sci. 118, 749.
15. Bukowski, R., Krzysztof, S., Groenenboom, G., and van der Avoird, A., 2007, Science 315(14), 1249.
16. Carlson, J. M. and Sethna, J. P., 1987, Phys. Rev. A 36, 3359.
17. Cascales, J. J. L., Smith, B. D., Gonzales, C., and Marquez, M., 2006, J. Phys. Chem. B 110, 2358.
18. Cevc, G., 1990, Biochim. Biophys. Acta 1031(3), 311.
19. Chiu, S.-W., Clark, M., Subramaniam, S., Scott, H. L., and Jakobsson, E., 1995, Biophys. J. 69, 1230.
20. Chiu, S.-W., Clark, M. M., Jakobsson, E., Subramaniam, S., and Scott, H. L., 1999a, J. Comp. Chem 20, 1153.
21. Chiu, S.-W., Clark, M. M., Jakobsson, E., Subramaniam, S., and Scott, H. L., 1999b, J. Phys. Chem. B 103, 6323.
22. Chiu, S.-W., Jakobsson, E., Mashl, R. J., and Scott, H. L., 2002, Biophys. J. 83(4), 1842.
23. Chiu, S.-W., Jakobsson, E., and Scott, H. L., 2001a, J. Chem. Phys 114, 5435.
24. Chiu, S.-W., Jakobsson, E., and Scott, H. L., 2001b, Biophys. J. 80(3), 1104.
25. Chiu, S.-W., Vasudevan, S., Jakobsson, E.,Mashl, R. J., and Scott, H. L., 2003, Biophys. J. 85(6), 3624.
26. Christy, W. W., 2003, Lipid Analysis 3rd Edition. Oily Press, Bridgewater UK.
27. Coe, T. J. and Scott, H. L., 1992, Biophys. J. 42, 219.
28. Cramer, C. J., 2006, Essentials of Computational Chemistry: Theories and Models. John Wiley & Sons, West Sussex, England.
29. Damodoran, K. V. and Merz, K., 1994, Biophys. J. 66, 1076.
30. de Vries, A. H., Mark, A. E., and Marrink, S.-J., 2004, J. Am. Chem. Soc. 126(14), 4488.
31. de Vries, A. H., Yefimov, S., Mark, A. E., and Marrink, S.-J., 2005, Proc. Natl. Acad. Sci. USA 102, 5392.
32. Dolan, E., Venable, R., Pastor, R. W., and Brooks, B., 2002, Biophys. J. 73(23), 2317.
33. Doniach, S., 1979, J. Chem. Phys. 70, 4587.
34. Douliez, J.-P., Léonard, A., and Dufourc, E. J., 1995, Biophys. J. 68, 1727.
35. Edholm, O. and Nagle, J. F., 2005, Biophys. J. 89(3), 1827.
36. Eisenberg, M., Gresalfi, T., Riccio, T., and McLaughlin, S., 1979, Biochem. 18(23), 5213.
37. Elliott, R., Katsov, K., Szleifer, I., and Schick, M., 2005, J. Chem. Phys. 122, 044904.
38. Elliott, R., Szleifer, I., and Schick, M., 2006, Phys. Rev. Lett. 96, 098101.
39. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G., 1995, J. Chem. Phys. 103(19), 8577.
40. Falconi, M. and Deem, M., 1999, J. Chem. Phys. 110, 1754.
41. Feller, S. E. and Pastor, R. W., 1996, Biophys. J. 71(23), 1350.
42. Filippov, A., Orädd, G., and Lindblom, G., 2003, Biophys. J. 84(5), 3079.
43. Frenkel, D. and Smit, B., 2002, Understanding Molecular Simulation From Algorithm to Applications, Vol. 1 of Computational Science Series. Academic Press.
44. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, Jr., J. A., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A., 2004, Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
45. Goetz, R., Gompper, G., and Lipowsky, R., 1999, Phys. Rev. Lett. 82, 221.
46. Goetz, R. and Lipowsky, R., 1998, J. Chem. Phys. 108, 7397.
47. Gompper, G. and Schick, M., 2006, SoftMatter, Vol. 1: PolymerMelts and Mixtures. Wiley-VCH.
48. Greenwood, A. I., Tristram-Nagle, S., and Nagle, J. F., 2006, Chemistry and Physics of Lipids 143, 1.
49. Groot, R. D. and Rabone, K. L., 2001, Biophys. J. 81, 725.
50. Hofsäß, C., Lindahl, E., and Edholm, O., 2003, Biophys. J. 84(4), 2192.
51. Huang, T.-H., Less, C. W. B., Das Gupta, S. K., Blume, A., and Gri;n, R. G., 1993, Biochem. 32(48), 13277.
52. Jorgensen,W., Chandrasekhar, J.,Madura, J., Ampey, R., and Klein, M., 1983, J. Chem. Phys. 79(14), 926.
53. Khelashvili, G. A., Pandit, S. A., and Scott, H. L., 2005, J. Chem. Phys. 123, 034910.
54. Klauda, J. B., Kucerka, N., Brooks, B. R., Pastor, R. W., and Nagle, J. F., 2006, Biophys. J. 90(8), 2796.
55. Knecht, V., Müller, M., Bonn, M., Marrink, S.-J., and de Vries, A. H., 2005, J. Chem. Phys. 122, 0224704.
56. Kofke, D. A. and Glandt, E. D., 1988, Mol. Phys. 64, 1105.
57. Kranenburg, M., Ventrouli, M., and Smit, B., 2003a, Phys. Rev. E 67, 60901.
58. Kranenburg, M., Ventrouli, M., and Smit, B., 2003b, J. Phys. Chem. B 107, 11491.
59. Kucerka, N., Tristram-Nagle, S., and Nagle, J. F., 2005, J. Membr. Biol. 208, 193.
60. Kucerka, N., Tristram-Nagle, S., and Nagle, J. F., 2006, Biophys. J. 90, L83.
61. Kuwajima, S., Noma, H., and Akasaka, T. (eds.), 1994, Proc. 4th Symp. Comp. Chem., Tokyo, Japan. Japan Chemistry Program Exchange.
62. Landau, L. D. and Lifshitz, E. M., 1980, Statistical Physics 3rd Edition Part 1; Course of Theoretical Physics, Vol. 5. Pergamon Press, 2nd rev. edn.
63. Lubensky, T. and Chaikin, P., 1995, Principles of Condensed Matter Physics. Cambridge University Press.
64. Macdonald, P. M. and Seelig, J., 1988, Biochem. 27(18), 6769.
65. MacKerell Jr, A. D., 2004, J. Comp. Chem. 25(12), 1505.
66. Maier, W. and Saupe, A., 1959, Z. Naturforsch. A 14, 882.
67. Makino, K., Yamada, T., Kimura, M., Oka, T., Ohshima, H., and Kondo, T., 1991, Biophys. Chem. 41, 175.
68. Marrink, S.-J., de Vries, A. H., and Mark, A. E., 2004, J. Phys. Chem. B 108, 750.
69. Marrink, S.-J. and Mark, A. E., 2003, J. Am. Chem. Soc. 128, 11144.
70. Marrink, S.-J. and Mark, A. E., 2005, Biophys. J. 87, 3894.
71. Marcelja, S., 1974, Biochim. Biophys. Acta 367, 156.
72. Marx, D. and Hutter, J., 2000, in Modern Methods and Algorithms of Quantum Chemistry, Proceedings, Second Edition, John von Neumann Institute for Computing, NIC Series, Vol. 3, pp. 329-477, Jülich.
73. Matson, M. W., in: Gompper, G. and Schick, M., 2006, Soft Matter, Vol. 1: Polymer Melts and Mixtures. Wiley-VCH.
74. McConnell, H. and Radhakrishnan, A., 2006, Proc. Natl. Acad. Sci. USA 103(5), 1184.
75. McCullough, S. and Scott, H. L., 1990, Phys. Rev. Lett. 65, 931.
76. McLaughlin, S., 1989, Annu. Rev. Biophys. Biophys. Chem. 18, 113.
77. Merz Jr., K. M. and Roux, B. (eds.), 1996, Biological Membranes: A Molecular Perspective from Computation and Experiment. Birkhauser.
78. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. N., and Teller, E., 1953, J. Chem. Phys. 21(12), 1087.
79. Mukhopadhyay, P., Monticelli, L., and Tieleman, D. P., 2004, Biophys. J. 86, 1601.
80. Müller, M., in: Gompper, G. and Schick, M., 2006, Soft Matter, Vol. 1: Polymer Melts and Mixtures. Wiley-VCH.
81. Myrzin, K., Rog, T., and Pasenkiewicz-Gierula, M., 2005, Biophys. J. 88, 1090.
82. Nagle, J. F., 1973, J. Chem. Phys. 58, 236.
83. Nagle, J. F. and Scott, H. L., 1978, Biochim. Biophys. Acta 513, 159.
84. Nagle, J. F. and Tristram-Nagle, S., 2000, Biochim. Biophys. Acta 1469, 159.
85. Niemela, P. S., Ollila, S., Hyvonen, M., Kartunen, M., and Vattulainen, I., 2007, PLoS Computational Biology 3(2), 0304.
86. Pandit, S., Chiu, S.-W., Jakobsson, E., Grama, A., and Scott, H. L., 2007a, Biophys. J 92, 920.
87. Pandit, S., Chiu, S.-W., Jakobsson, E., Grama, A., and Scott, H. L., 2007b, preprint.
88. Pandit, S., Khelashvili, G., Jakobsson, E., Grama, A., and Scott, H. L., 2007c, Biophys. J 92, 440.
89. Pandit, S. A. and Berkowitz, M. L., 2002, Biophys. J. 82(4), 1818.
90. Pandit, S. A., Bostick, D., and Berkowitz, M. L., 2003a, J. Chem. Phys. 119(4), 2199.
91. Pandit, S. A., Bostick, D., and Berkowitz, M. L., 2003b, Biophys. J. 85(5), 3120.
92. Pandit, S. A., Bostick, D., and Berkowitz, M. L., 2003c, Biophys. J 86, 3743.
93. Pandit, S. A., Bostick, D. L., and Berkowitz, M. L., 2004a, Biophys. J. 86(3), 1345.
94. Pandit, S. A., Jakobsson, E., and Scott, H. L., 2004b, Biophys. J. 87(5), 3312.
95. Pandit, S. A., Vasudevan, S., Chiu, S.-W., Mashl, R. J., Jakobsson, E., and Scott, H. L., 2004c, Biophys. J. 87(2), 1092.
96. Patra, M., Karttunen, M., Hyvönen, M., Falck, E., Lindqvist, P., and Vattulainen, I., 2003, Biophys. J. 84, 3636.
97. Peng, G., Qiu, F., Ginzburg, V. V., Jasnow, D., and Bakazs, A., 2000, Science 288, 1802.
98. Petrache, H. I., Feller, S. E., and Nagle, J. F., 1997, Biophys. J. 70, 2237.
99. Reiling, S., Schlenkrich, M., and Brickmann, J., 1996, J. Comp. Chem. 17, 450.
100. Rhee, Y. M., Sorin, E., Jayacyandran, G., Lindahl, E., and Pande, V. S., 2004, Proc. Natl. Acad. Sci. USA 101, 6456.
101. Rinia, H. A., Snel, M. M. E., van der Eerden, J. P. J. M., and de Kruijff, B., 2001, FEBS Lett. 501, 92.
102. Rosenbluth, M. N. and Rosenbluth, A. W., 1955, J. Chem. Phys. 23, 356.
103. Ryckaert, J. P. and Bellemans, A., 1978, Faraday Disc. Chem. Soc. 66, 95.
104. Sanbonmatsu, K. Y. and Garcia, A. E., 2002, Proteins 46, 225.
105. Scott, H. L., 1975, J. Chem. Phys. 62(4), 347.
106. Scott, H. L., 1977, Biochim. Biophys. Acta 469(4), 264.
107. Scott, H. L., 1984, Comments in Molecular and Cellular Biophysics 11, 197.
108. Scott, H. L., 1993, in Cholesterol in Model Membranes, edited by L. Finegold, pp. 197-222. CRC Press, Boca Raton.
109. Scott, H. L., 2002, Curr. Op. Struct. Biol. 12(4), 495.
110. Scoville-Simonds, M. and Schick, M., 2003, Phys. Rev. E 67, 098101.
111. Sengupta, K., Raghunanthan, V. A., and Katsaras, J., 2003, Phys. Rev. E 68, 0331710.
112. Singer, J. J. and Nicholson, G., 1972, Science 175, 720.
113. Smith, M. J., 2005, J. Am. Chem. Soc. 127, 15530.
114. Stamatoff, J., Feuer, B., Guggenheim, H. J., Tellez, G., and Yamane, T., 1982, Biophys. J. 38, 217.
115. Stillinger, F. and Rahman, A., 1974, J. Chem. Phys. 60(4), 1545.
116. Stillinger, F. H., 1980, Science 209, 451.
117. Sugita, Y. and Okamoto, Y., 1999, Chem. Phys. Lett. 314, 141.
118. Sun, W.-J., Tristram-Nagle, S., Suter, R. M., and Nagle, J. F., 1996, Proc. Natl. Acad. Sci. USA 93, 7008.
119. Tatulian, S. A., 1987, Eur. J. Biochem. 170, 413.
120. Torbet, J. and Wilkins, M. H., 1976, J. Theor. Biol. 62(12), 447.
121. Tristram-Nagle, S. and Nagle, J. F., 2004, Chem. Phys. Lipids 127, 3.
122. Tu, K., Dobias, D., Blasie, J. K., and Klein, M. L., 1996, Biophys. J. 70, 595.
123. Tu, K., Klein, M. L., and Tobias, D. J., 1998, Biophys. J. 75, 2147.
124. Venable, R. M., Zhang, Y., Hardy, B. J., and Pastor, R. W., 1993, Science 262(12), 223.
125. Venable, R.W., Pastor, R.W., and Brooks, B. R., 2000, J. Chem. Phys. 112(23), 4822.
126. Vist, M. R. and Davis, J. H., 1990, Biochem. 29(2), 451.
127. Wack, D. C. and Webb, W. W., 1988, Phys. Rev. Lett. 61, 1210.
128. Whittington, S. G. and Chapman, D., 1966, Trans. Faraday Soc. 62(12), 3319.
129. Wiener, M. C., King, G. I., and White, S. H., 1992, Biophys. J. 61, 428.
130. Wiener, M. C. and White, S. H., 1991, Biophys. J. 59, 162.
131. Wiener, M. C. and White, S. H., 1992, Biophys. J. 61, 434.
132. Wohlert, J. and Edholm, O., 2004, Biophys. J. 87(4), 2433.
133. Woodward, J. T. and Zasadzinski, J. A., 1997, Biophys. J. 72, 964.
134. Xing, J. and Scott, H. L., 1992, Biochim. Biophys. Acta 1106, 227.
135. Yan, Q. and de Pablo, J., 2000, J. Chem. Phys. 110, 1276.
136. Zhou, F. and Schulten, K., 1995, J. Phys. Chem. 99(7), 2194.