Theory, modelling and simulation in origins of life studies

Chemical Society Reviews

Volumn 41, Issue 16, 2012, Pages 5430-5446

  Coveney, Peter V ^a   Swadling, Jacob B ^a   Wattis, Jonathan A D ^b   Greenwell, H Christopher ^c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c DURHAM UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84864193023     PISSN: 03060012     EISSN: 14604744     Source Type: Journal    
DOI: 10.1039/c2cs35018a     Document Type: Article

References (125)

1. W. Martin, M. J. Russell, Philos. Trans. R. Soc. London, Ser. B 2007, 362, 1486, 1887-1925
2. L. Orgel, Trends Biochem. Sci. 1998, 23, 491-495
3. R. M. Hazen, D. A. Sverjensky, Cold Spring Harbor Perspect. Biol. 2010, 2, 5, a002162
4. B. M. Rode, A. H. Ederand, Y. Yongyai, Inorg. Chim. Acta 1997, 254, 2, 309-314
5. H. Trinks, W. Schröder, C. K. Biebricher, Origins Life Evol. Biosphere 2005, 35, 5, 429-445
6. P. V. Coveney, P. W. Fowler, J. R. Soc. Interface 2005, 2, 4, 267
7. P. V. Coveney and R. Highfield, The Arrow of Time, WH Allen, London, 1991
8. P. V. Coveney and R. Highfield, Frontiers of Complexity: The Search for Order in a Chaotic World, Faber and Faber, London, 1995
9. S. L. Miller, Science 1953, 117, 528-529
10. J. B. S. Haldane, Rationalist Annual 1929, 3, 3-10
11. J. F. Kasting, Science 1993, 259, 920-926
12. J. A. Baross, S. E. Hoffman, Origins Life Evol. Biosphere 1985, 15, 327-345
13. P. Walde, R. Wick, M. Fresta, A. Mangone, P. L. Luisi, J. Am. Chem. Soc. 1994, 116, 11649-11654
14. D. S. Kelley, J. A. Karson, D. K. Blackman, Nature 2001, 412, 145-149
15. J. I. Drever, The Chemistry of Weathering, Springer, 1985
16. M. J. Russell, R. M. Daniel, A. J. Hall, J. Mol. Evol. 1994, 39, 231-243
17. The RNA World, ed. R. F. Gesteland and J. F. Atkins, Cold Spring Harbour Press, New York, 1993
18. T. R. Cech, Proc. Natl. Acad. Sci. U. S. A. 1986, 83, 4360-4363
19. N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz, Science 2000, 289, 905-920
20. M. W. Powner, B. Gerland, J. D. Sutherland, Nature 2009, 459, 239-242
21. K. Plankensteiner, H. Reiner, B. M. Rode, Curr. Org. Chem. 2005, 9, 12, 1107-1114
22. C. Huber, G. Wächtershaüser, Science 1998, 5377, 281, 670
23. P. W. Atkins and J. De Paula, Physical Chemistry, Oxford University Press, 1998
24. L. Onsager, Phys. Rev. 1931, 37, 4, 405-426
25. G. Nicolis and I. Prigogine, Self-Organization in Nonequilibrium Systems, Wiley, 1977
26. A. M. Turing, Philos. Trans. R. Soc. London, Ser. B 1952, 237, 641, 37-72
27. M. Eigen, P. Schuster, Naturwissenschaften 1977, 64, 541-565
28. M. Eigen, P. Schuster, Naturwissenschaften 1978, 65, 7-41
29. M. Eigen, P. Schuster, Naturwissenschaften 1978, 65, 341-369
30. J. Maynard Smith, Nature 1979, 280, 445-446
31. Self-production of supramolecular structures from synthetic structures: to models of minimal living systems, ed. G. R. Fleischaker and S. Colonna, Kluwer, 1994
32. J. W. Szostak, D. P. Bartel, P. L. Luisi, Nature 2001, 409, 387-390
33. W. Ma, C. Yu, Origins Life Evol. Biosphere 2005, 36, 413-420
34. R. Lathe, Icarus 2004, 168, 18-22
35. U. Wiechert, A. N. Halliday, D. C. Lee, G. A. Snyder, L. A. Taylor, D. Rumble, Science 2001, 294, 345-348
36. C. Fernando, G. von Kiedrowski, E. Szathmáry, J. Mol. Evol. 2007, 64, 572-585
37. C. Fernando and E. Di Paolo, The Chemoton: a model for the origin of long RNA templates, Proc. of the 9th Int. Conf. on Simulations and Synthesis of Artificial Life (ALIFE), Boston, MA, 2004
38. T. Ganti, The Principle of Life (In Hungarian), Budapest, Gondolat, 1971
39. T. Ganti, The Principles of Life, Oxford University Press, 2003
40. G. F. Joyce, Nature 2002, 418, 214-221
41. B. Obermayer, E. Frey, J. Theor. Biol. 2010, 267, 653-662
42. J. A. D. Wattis, P. V. Coveney, J. Phys. Chem. B 1999, 103, 4231-4250
43. P. V. Coveney, J. A. D. Wattis, Mol. Phys. 2006, 104, 177-185
44. J. A. D. Wattis, Phys. D 2006, 222, 1-20
45. R. Hanel, M. Pochacker, N. S. Thurner, Philos. Trans. R. Soc. London, Ser. A 2010, 368, 5583-5596
46. N. Lehman, Chem. Biodiversity 2008, 5, 1707-1717
47. P. V. Coveney, J. A. D. Wattis, J. Chem. Soc. Faraday Trans. 1998, 102, 233-246
48. C. D. Bolton, J. A. D. Wattis, J. Phys. Chem. B 2003, 107, 7126-7134
49. S. Lonchin, P. L. Luisi, P. Walde, B. H. Robinson, J. Phys. Chem. B 1999, 103, 10910-10916
50. N. Berclaz, E. Blöchliger, M. Müler, P. L. Luisi, J. Phys. Chem. B 2001, 105, 1065-1071
51. N. Berclaz, M. Müler, P. Walde, P. L. Luisi, J. Phys. Chem. B 2001, 105, 1056-1064
52. F. Faglioni, A. Passalacqua, P. Lazzeretti, Origins Life Evol. Biosphere 2005, 35, 461-475
53. H. B. Kagan, Dang Tuan-Phat, J. Am. Chem. Soc. 1972, 94, 6429-6433
54. K. Soai, T. Shibata, H. Morioka, K. Choji, Nature 1995, 378, 767-768
55. F. C. Frank, Biochim. Biophys. Acta 1953, 11, 459-463
56. Y. Saito, H. Hyuga, J. Phys. Soc. Jpn. 2004, 73, 33-35
57. V. I. Goldanskii, V. V. Kuzmin, Nature 1991, 352, 114-114
58. V. I. Goldanskii, J. Phys. Chem. A 1997, 101, 3424-3432
59. Y. A. Berlin, A. L Burin, V. I. Goldanskii, Z. Phys. D, At. Mol. Clusters 1996, 37, 333-339
60. V. I. Goldanskii, V. V. Kuzmin, Usp. Fiz. Nauk 1989, 157, 3-50
61. V. A. Avetisov, V. I. Goldanskii, Usp. Fiz. Nauk 1996, 166, 873-891
62. V. A. Avetisov, V. I. Goldanskii, Phys. Lett. A 1993, 172, 407-410
63. V. A. Avetisov, V. I. Goldanskii, V. V. Kuzmin, Phys. Today 1991, 44, 33-41
64. D. K. Kondepudi, R. J. Kaufman, N. Singh, Science 1990, 250, 975-976
65. D. K. Kondepudi, K. L. Bullock, J. A. Digits, P. D. Yarborough, J. Am. Chem. Soc. 1995, 117, 401-404
66. D. K. Kondepudi, G. W. Nelson, Phys. Lett. A 1984, 106, 203-206
67. D. K. Kondepudi, G. W. Nelson, Nature 1985, 314, 438-441
68. V. A. Avetisov, V. I. Goldanskii, S. N. Grechukha, V. V. Kuzmin, Chem. Phys. Lett. 1991, 184, 526-530
69. C. Viedma, Phys. Rev. Lett. 2005, 94, 065504, 1-4
70. W. L. Noorduin, T. Izumi, A. Millemaggi, M. Leeman, H. Meekes, W. J. P. van Enckevort, R. M. Kellogg, B. Kaptein, E. Vlieg, D. G. Blackmond, J. Am. Chem. Soc. 2008, 130, 1158-1159
71. J. M. McBride, J. C. Tully, Nature 2008, 452, 161-162
72. M. Uwaha, J. Phys. Soc. Jpn. 2004, 73, 2601-2603
73. J. A. D. Wattis, Origins Life Evol. Biosphere 2011, 41, 133-173
74. P. G. H. Sandars, Origins Life Evol. Biospheres 2003, 33, 575-587
75. A. Brandenburg, A. C. Andersen, S. Höfner, M. Nilsson, Origins Life Evol. Biosphere 2005, 35, 3, 225-241
76. J. A. D. Wattis, P. V. Coveney, Origins Life Evol. Biosphere 2005, 35, 243-273
77. A. Brandenburg, A. C. Andersen, M. Nilsson, Origins Life Evol. Biosphere 2005, 35, 507-521
78. C. Blanco, D. Hochberg, Phys. Chem. Chem. Phys. 2011, 13, 839-849
79. M. Gleiser, J. Thorarinson, S. I. Walker, Origins Life Evol. Biosphere 2008, 38, 499-508
80. N. Eldridge and S. J. Gould, Models in Paleobiology, Freeman, San Francisco, 1972, pp. 82–115
81. R. Plasson, H. Bersini, A. Commeyras, Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 16733-16738
82. M. Gleiser, S. I. Walker, Origins Life Evol. Biosphere 2009, 39, 479-493
83. S. J. Mojzsis, T. M. Harrison, R. T. Pidgeon, Nature 2001, 409, 178-181
84. P. Baaske, F. M. Weinert, S. Duhr, K. H. Lemke, M. J. Russell, D. Braun, Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9346-9351
85. D. Braun, A. Libchaber, Thermal force approach to molecular evolution. Physical Biology 2004, 1, P1
86. C. J. Cramer, Essentials of Computational Chemistry: Theory and Models, John Wiley & Sons Inc, 2004
87. J. Kohanoff, Electronic Structure Calculations for Solids and Molecules: Theory and Computational Methods, Cambridge University Press, 2006
88. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, 1999
89. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Elsevier (formerly published by Academic Press), 1996
90. J. Wang, P. Cieplak, P. A. Kollman, J. Comput. Chem. 2000, 21, 12, 1049-1074
91. R. T. Cygan, J. J. Liang, A. G. Kalinichev, J. Phys. Chem. B 2004, 108, 4, 1255-1266
92. S. Plimpton, J. Comput. Phys. 1995, 117, 1, 1-19
93. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 2005, 26, 16, 1781-1802
94. H. J. C. Berendsen, D. van der Spoel, R. Van Drunen, Comput. Phys. Commun. 1995, 91, 1–3, 43-56
95. G. Sposito, The surface chemistry of soils, Oxford University Press, New York, 1984
96. R. E. Grim, Clay Mineralogy, McGraw Hill, New York, Second edn, 1968
97. J. Wang, A. G. Kalinichev, J. E. Amonette, R. J. Kirkpatrick, American Mineralogist 2003, 88, 2, 398
98. X. Hou, A. G. Kalinichev, R. J. Kirkpatrick, Chem. Mater. 2002, 14, 5, 2078-2085
99. J. O. Titiloye, N. T. Skipper, Chem. Phys. Lett. 2000, 329, 1–2, 23-28
100. J. L. Suter, P. V. Coveney, H. C. Greenwell, M.-A. Thyveetil, J. Phys. Chem. C 2007, 111, 23, 8248-8259
101. E. S. Boek, P. V. Coveney, N. T. Skipper, J. Am. Chem. Soc. 1995, 117, 50, 12608-12617
102. H. C. Greenwell, W. Jones, P. V. Coveney, S. Stackhouse, J. Mater. Chem. 2006, 16, 8, 708-723
103. J. F. Lambert, Origins Life Evol. Biosphere 2008, 38, 3, 211-242
104. M. G. Schwendinger, B. Rode, Phys. Lett. 1989, 155, 6, 527-532
105. N. Lahav, D. White, S. Chang, Science 1978, 201, 4350, 67
106. N. Lahav, D. White, J. Mol. Evol. 1980, 16, 1, 11-21
107. J. R. Collins, G. H. Loew, B. T. Luke, D. H. White, Origins Life Evol. Biosphere 1988, 18, 1–2, 107-119
108. A. J. A. Aquino, D. Tunega, M. H. Gerzabek, H. Lischka, J. Phys. Chem. B 2004, 108, 28, 10120-10130
109. B. M. Rode, Peptides 1999, 20, 6, 773-786
110. B. M. Rode, Y. Suwannachot, Coord. Chem. Rev. 1999, 190, 1, 1085-1099
111. K. R. Liedl, B. M. Rode, Chem. Phys. Lett. 1992, 197, 1–2, 181-186
112. M. Remko, B. M. Rode, Chem. Phys. Lett. 2000, 316, 5–6, 489-494
113. A. Rimola, L. Rodriguez-Santiago, P. Ugliengo, M. Sodupe, J. Phys. Chem. B 2007, 111, 20, 5740-5747
114. N. N. Nair, E. Schreiner, D. Marx, J. Am. Chem. Soc. 2006, 128, 42, 13815-13826
115. L. Leman, L. Orgel, M. R. Ghadiri, Science 2004, 306, 5694, 283-286
116. C. H. Yu, S. Q. Newton, D. M. Miller, B. J. Teppen, L. Schäfer, Struct. Chem. 2001, 12, 5, 393-398
117. H. C. Greenwell, P. V. Coveney, Origins Life Evol. Biosphere 2006, 36, 1, 13-37
118. D. C. Mathew, Z. Luthey-Schulten, Origins Life Evol. Biosphere 2010, 40, 3, 303-317
119. W. Huang, J. P. Ferris, J. Am. Chem. Soc. 2006, 128, 27, 8914-8919
120. J. B. Swadling, P. V. Coveney, H. C. Greenwell, J. Am. Chem. Soc. 2010, 21, 39, 13750-13764
121. M.-A. Thyveetil, P. V. Coveney, H. C. Greenwell, J. L. Suter, J. Am. Chem. Soc. 2008, 130, 12485-12495
122. G. Arrhenius, Helv. Chim. Acta 2003, 86, 1569-1586
123. J. B. Swadling, P. V. Coveney, H. C. Greenwell, Geochim. Cosmochim. Acta 2012, 83, 360-378
124. M.-A. Thyveetil, P. V. Coveney, H. C. Greenwell, J. L. Suter, J. Am. Chem. Soc. 2008, 130, 4742-4756
125. A. G. Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, Cambridge University Press, New York, 1982