Evolutionary dynamics in a simple model of self-assembly

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 83, Issue 6, 2011, Pages

  Johnston, Iain G ^a   Ahnert, Sebastian E ^b   Doye, Jonathan P K ^a   Louis, Ard A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC SYMMETRY; EVOLUTIONARY DYNAMICS; FITNESS LANDSCAPE; GENOME SPACE; IDEALIZED MODELS; MUTATION RATES; POLYOMINOES; POPULATION SIZES; PROTEIN TETRAMERS; RULE SET; SEARCH SPACE SIZE; SELF ASSEMBLED STRUCTURES; SELF ASSEMBLY PROCESS; SHEDDING LIGHT; TARGET STRUCTURE; TWO-DIMENSIONAL STRUCTURES;

OLIGOMERS; POPULATION STATISTICS; SELF ASSEMBLY;

DYNAMICS;

EID: 79961067755     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.83.066105     Document Type: Article

References (65)

1. D. S. Goodsell, Bionanotechnology: Lessons from Nature (Wiley-Liss, Hoboken, NJ, 2004).
2. J. B. Pereira-Leal, E. D. Levy, and S. A. Teichmann, Philos. Trans. R. Soc. London B PTRBAE 0962-8436 10.1098/rstb.2005.1807 361, 507 (2006). (Pubitemid 44870107)
3. A. E. Hirsh and H. B. Fraser, Nature (London) NATUAS 0028-0836 10.1038/35082561 411, 1046 (2001).
4. J. P. K. Doye, A. A. Louis, and M. Vendruscolo, Phys. Biol. NATUAS 1478-3967 10.1088/1478-3967/1/1/P02 1, 9 (2004). (Pubitemid 44362311)
5. E. D. Levy, E. B. Erba, C. V. Robinson, and S. A. Teichmann, Nature (London) NATUAS 0028-0836 10.1038/nature06942 453, 1262 (2008). (Pubitemid 351913589)
6. A. W. Wilber, J. P. K. Doye, A. A. Louis, E. G. Noya, M. A. Miller, and P. Wong, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2759922 127, 085106 (2007). (Pubitemid 47354016)
7. G. Villar, A. W. Wilber, A. J. Williamson, P. Thiara, J. P. K. Doye, A. A. Louis, M. N. Jochum, A. C. F. Lewis, and E. D. Levy, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.102.118106 102, 118106 (2009).
8. J. Andreani, A. W. Wilber, J. P. K. Doye, and A. A. Louis (to be published).
9. S. E. Ahnert, I. G. Johnston, T. M. A. Fink, J. P. K. Doye, and A. A. Louis, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.82.026117 82, 026117 (2010).
10. A. Chworos, I. Severcan, A. Y. Koyfman, P. Weinkam, E. Oroudjev, H. G. Hansma, and L. Jaeger, Science SCIEAS 0036-8075 10.1126/science.1104686 306, 2068 (2004). (Pubitemid 40007653)
11. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, Nature (London) NATUAS 0028-0836 10.1038/28998 394, 539 (1998). (Pubitemid 28366820)
12. M. Cook, P. W. K. Rothemund, and E. Winfree, Lect. Notes Comput. Sci. 2943, 1979 (2004).
13. P. W. K. Rothemund, N. Papadakis, and E. Winfree, PLoS Biol. NATUAS 1544-9173 10.1371/journal.pbio.0020424 2, e424 (2004). (Pubitemid 40280512)
14. C. Lin, Y. Liu, S. Rinker, and H. Yan, Chem. Phys. Chem. 7, 1641 (2006).
15. D. B. Lukatsky, B. M. Mulder, and D. Frenkel, J. Phys. Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/18/18/S05 18, S567 (2006).
16. H. Wang, in Proceedings of the Symposium on Mathematical Theory of Automata, at Polytechnic Institure of Brooklyn (Polytechnic Press of the Polytechnic Institute of Brooklyn, New York, 1963), p. 23.
17. P. W. K. Rothemund and E. Winfree, in Proceedings of the Thirty-second Annual ACM Symposium on Theory of Computing (ACM, New York, 2000), pp. 459-468.
18. R. D. Barish, R. Schulman, P. W. K. Rothemund, and E. Winfree, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0808736106 106, 6054 (2009).
19. E. Winfree and R. Bekbolatov, Lect. Notes Comput. Sci. 2943, 1980 (2004).
20. D. E. Goldberg, Genetic Algorithms in Search and Optimization (Addison-Wesley, Reading, MA, 1989).
21. M. Mitchell, An Introduction to Genetic Algorithms (MIT Press, Cambridge, MA, 1998).
22. K. A. De Jong and W. M. Spears, Parallel Prob. Solv. Nature (London) 1, 38 (1990).
23. T. Bäck, in Proceedings of the 5th International Conference on Genetic Algorithms (Morgan Kaufmann, San Francisco, CA, 1993), p. 2.
24. D. Metzgar and C. Wills, Cell CELLB5 0092-8674 10.1016/S0092-8674(00) 80869-7 101, 581 (2000).
25. J. W. Drake, B. Charlesworth, D. Charlesworth, and J. F. Crow, Genetics 148, 1667 (1998).
26. M. Eigen, Naturwissenschaften NATWAY 0028-1042 10.1007/BF00623322 58, 465 (1971).
27. M. Eigen and P. Schuster, The Hypercycle: A Principle of Natural Self-Organisation (Springer-Verlag, Berlin, 1979).
28. P. Schuster and K. Sigmund, J. Theor. Biol. JTBIAP 0022-5193 10.1016/0022-5193(83)90445-9 100, 533 (1983).
29. E. Cohen, D. A. Kessler, and H. Levine, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.098102 94, 098102 (2005). (Pubitemid 40620635)
30. S. Wright, Proceedings of the 6th International Congress on Genetics, p. 356 (1932).
31. J. Maynard Smith, Nature (London) NATUAS 0028-0836 10.1038/225563a0 225, 563 (1970).
32. D. Soloveichik and E. Winfree, SIAM J. Comput. SMJCAT 0097-5397 10.1137/S0097539704446712 36, 1544 (2007).
33. H. Wang, AT&T Tech. J. 40, 1 (1961).
34. Necklace, from MathWorld, a Wolfram web resource [http://mathworld. wolfram.com/Necklace.html].
35. R. Schulman and E. Winfree, SIAM J. Comput. SMJCAT 0097-5397 10.1137/070680266 39, 1581 (2009).
36. J. Bitner, G. Ehrlich, and E. Reingold, Commun. ACM CACMA2 0001-0782 10.1145/360336.360343 19, 517 (1976).
37. L. A. Amos, Org. Biomol. Chem. CACMA2 1477-0520 10.1039/b403634d 2, 2153 (2004).
38. E. Reisler and E. H. Egelman, J. Biol. Chem. JBCHA3 0021-9258 10.1074/jbc.R700030200 282, 36133 (2007).
39. W. K. Kegel and P. Van Der Schoot, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.072603 91, 1501 (2006). (Pubitemid 44174267)
40. M. Sára and U. B. Sleytr, J. Bacteriol. JOBAAY 0021-9193 10.1128/JB.182.4.859-868.2000 182, 859 (2000). (Pubitemid 30075004)
41. M. P. Krebs and T. A. Isenbarger, Biochim. Biophys. Acta, Bioenergetics JOBAAY 0005-2728 10.1016/S0005-2728(00)00126-2 1460, 15 (2000).
42. J. P. K. Doye and W. C. K. Poon, Curr. Opin. Colloid In. COCSFL 1359-0294 10.1016/j.cocis.2005.10.002 11, 40 (2006).
43. D. S. Goodsell and A. J. Olson, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.29.1.105 29, 105 (2000). (Pubitemid 30599590)
44. E. Stoger, M. Parker, P. Christou, and R. Casey, Plant Physiol. PLPHAY 0032-0889 10.1104/pp.125.4.1732 125, 1732 (2001). (Pubitemid 32375757)
45. A. Laganowsky, J. L. P. Benesch, M. Landau, L. Ding, M. R. Sawaya, D. Cascio, Q. Huang, C. V. Robinson, J. Horwitz, and D. Eisenberg, Protein Sci. PRCIEI 0961-8368 10.1002/pro.380 19, 1031 (2010).
46. J. L. P. Benesch, Chem. Biol. CBOLE2 1074-5521 10.1016/j.chembiol.2010. 06.016 17, 1008 (2010).
47. D. E. Goldberg and K. Deb, in Foundations of Genetic Algorithms (Morgan Kaufmann, San Mateo, CA, 1991), Vol. 1, p. 69.
48. C. P. Massen and J. P. K. Doye, e-print arXiv: cond-mat/0610077.
49. 2, 8 search space.
50. A. Wagner, Robustness and Evolvability in Living Systems (Princeton University Press, Princeton, NJ, 2005).
51. A. Wagner, Proc. R. Soc. London B PRLBA4 0962-8452 10.1098/rspb.2007.1137 275, 91 (2008). (Pubitemid 350146738)
52. Y. Iwasa, J. Theor. Biol. JTBIAP 0022-5193 10.1016/S0022-5193(88)80243-1 135, 265 (1988).
53. G. Sella and A. E. Hirsh, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0501865102 102, 9541 (2005). (Pubitemid 40981717)
54. C. Wilke, BMC Evol. Biol. PNASA6 1471-2148 10.1186/1471-2148-5-44 5, 44 (2005). (Pubitemid 41316729)
55. M. A. Nowak, Evolutionary Dynamics: Exploring the Equations of Life (Harvard University Press, Cambridge, MA, 2006).
56. C. O. Wilke, J. L. Wang, C. Ofria, R. E. Lenski, and C. Adami, Nature (London) NATUAS 0028-0836 10.1038/35085569 412, 331 (2001). (Pubitemid 32691846)
57. J. March, Organ. Sci. NATUAS 1047-7039 10.1287/orsc.2.1.71 2, 71 (1991).
58. A. Eiben and C. Schippers, Fund. Inform. 35, 35 (1998).
59. J. H. Holland, Adaptation in Natural and Artificial Systems (MIT Press Cambridge, MA, USA, 1992).
60. N. Kashtan, E. Noor, and U. Alon, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0611630104 104, 13711 (2007). (Pubitemid 350003385)
61. P. Oikonomou and P. Cluzel, Nat. Phys. PNASA6 1745-2473 10.1038/nphys359 2, 532 (2006). (Pubitemid 44167277)
62. E. D. Levy, J. B. Pereira-Leal, C. Chothia, and S. A. Teichmann, PLoS Comput. Biol. PNASA6 1553-734X 10.1371/journal.pcbi.0020155 2, e155 (2006). (Pubitemid 44819926)
63. D. B. Lukatsky, K. B. Zeldovich, and E. I. Shakhnovich, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.97.178101 97, 178101 (2006). (Pubitemid 44643610)
64. I. André, C. E. M. Strauss, D. B. Kaplan, P. Bradley, and D. Baker, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0807576105 105, 16148 (2008).
65. G. E. Schulz, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2009.10.044 395, 834 (2010).