Evolutionary self-organization in complex fluids

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 362, Issue 1486, 2007, Pages 1763-1779

  McCaskill, John S ^a,c,f,g   Packard, Norman H ^b,c,f   Rasmussen, Steen ^c,d,f   Bedau, Mark A ^b,e,f  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b ProtoLife Srl   (Italy)

^c SANTA FE INSTITUTE   (United States)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

^e REED COLLEGE   (United States)

^f EUROPEAN CENTRE FOR LIVING TECHNOLOGY   (Italy)

^g FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Amphiphile; Ising; Molecular evolution; Protocell; Self assembly; Self organization

Indexed keywords

FLUID; HYDROCARBON; MONTE CARLO ANALYSIS; SELF ORGANIZATION;

EID: 35148817466     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2007.2069     Document Type: Article

References (52)

1. Altmeyer, S., Füchslin, R. M. & McCaskill, J. S. 2004 Folding stabilizes the evolution of catalysts. Artif. Life 10, 23-38. (doi:10.1162/106454604322875896)
2. Anderson, P. W. 1958 Absence of diffusion in certain random lattices. Phys. Rev. 109, 1492-1505. (doi:10.1103/PhysRev.109.1492)
3. Anderson, P. W. 1983 Suggested model for prebiotic evolution: the use of chaos. Proc. Natl Acad. Sci. USA 80, 3386-3390. (doi:10.1073/pnas.80.11.3386)
4. Bedau, M. A. & Brown, C. T. 1999 Visualizing evolutionary activity of genotypes. Artif. Life 5, 17-35. (doi:10.1162/106454699568665)
5. Bedau, M. A. & Packard, N. H. 1991 Measurement of evolutionary activity, teleology, and life. In Artificial life II, vol. X (eds C. Langton, C. Taylor, D. Farmer & S. Rasmussen), pp. 431-461. Santa Fe Institute Studies in the Sciences of Complexity. Redwood City, CA: Addison-Wesley.
6. Bedau, M. A., Snyder, E., Brown, C. T. & Packard, N. H. 1997 A comparison of evolutionary activity in artificial evolving systems and the biosphere. In Proc. Fourth Eur. Conf. on Artificial Life, ECAL97 (eds P. Husbands & I. Harvey), pp. 125-134. Cambridge, MA: MIT Press.
7. Biebricher, C. K., Eigen, M. & Gardiner Jr, W. C. 1984 Kinetics of RNA replication: plus-minus asymetry and double strand formation. Biochemistry 23, 3186-3194. (doi:10.1021/bi00309a012)
8. Blum, H. F. 1962 On the origin and evolution of living machines. Am. Sci. 49, 474-501.
9. Böddeker, B. 1995 Physical model for coevolution and simulation on a hardware programmable processor. Dipl. thesis in physics, University Göttingen, Germany.
10. Boerlijst, M. & Hogeweg, P. 1991 Spiral wave structure in prebiotic evolution: hypercycles stable against parasites. Physica D 48, 17-28. (doi:10.1016/0167-2789(91)90049-F)
11. Buchanan, A., Gazzola, G. & Bedau, M. A. 2006 Evolutionary design of a model of self-assembling chemical structures. In Systems self-assembly: multidisciplinary snapshots (eds N. Krasnogor, S. Gustafson, D. Pelta & J. L. Verdegay). Amsterdam, The Netherlands: Elsevier.
12. Colgate, S. A., Rasmussen, S., Solem, J. C. & Lackner, K. 2003 An astrophysical basis for a universal origin of life. Adv. Complex Syst. . (doi10.1142/S0219525903001079)
13. Coveney, P., Emerton, A. & Boghosian, B. 1996 Simulation of self-reproducing micelles using lattice-gas automation. J. Am. Chem. Soc. 118, 10 719-10 724. (doi:10.1021/ja961236z)
14. Cronhjort, M. B. & Blomberg, C. 1997 Cluster compartmentalization may provide resistance to parasites for catalytic networks. Physica D 101, 289-298. (doi:10.1016/S0167-2789(97)87469-6)
15. Dawson, K. A. & Kurtovic, Z. 1990 Lattice model of self-assembly. J. Chem. Phys. 92, 5473-5485. (doi:10.1063/1.458526)
16. Eigen, M. 1971 Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465-523. (doi:10.1007/BF00623322)
17. Eigen, M. & Schuster, P. 1979 The hypercycle - a principle of natural self-organization. Berlin, Germany: Springer.
18. A combined reprint of Naturwissenschaften 64: 541-565 (1977);
19. 65:7-41, 341-369 (1978).
20. Eigen, M., McCaskill, J. S. & Schuster, P. 1989 The molecular quasispecies. Adv. Chem. Phys. 75, 149-263. (doi:full_text)
21. Elliott, R., Szleifer, I. & Schick, M. 2006 Phase diagram of a ternary mixture of cholesterol and saturated and unsaturated lipids calculated from a microscopic model. Phys. Rev. Lett. 96, 098 101. (doi:10.1103/PhysRevLett.96.098101)
22. Fontana, W., Schnabl, W. & Schuster, P. 1989 Physical aspects of evolutionary adaptation and optimization. Phys. Rev. A 40, 3301-3321. (doi:10.1103/PhysRevA.40.3301)
23. Gompper, M. & Schick, M. 1991 Lattice model of microemulsions. Phys. Rev. B 41, 9148-9162. (doi:10.1103/PhysRevB.41.9148)
24. Hansen, A., Schick, M. & Stauffer, D. 1991 Generalized Widom model of amphiphilic systems. Phys. Rev. A 44, 3686-3691. (doi:10.1103/PhysRevA.44.3686)
25. Ising, E. 1925 Beitrag zur Theorie des Ferromagnetismus. Zeitschr. f. Physik 31, 253-258.
26. Johns, G. C. & Joyce, G. F. 2005 The promise and peril of continuous in vitro evolution. J. Mol. Evol. 61, 253-263. (doi:10.1007/s00239-004-0307-1)
27. Larson, R. G. 1988 Monte Carlo lattice simulation of amphiphilic systems in two and three dimensions. J. Chem. Phys. 89, 1642-1650. (doi:10.1063/1.455110)
28. Larson, R. G. 1989 Self-assembly of surfactant liquid crystalline phases by Monte Carlo simulation. J. Chem. Phys. 91, 2479-2488. (doi:10.1063/1.457007)
29. Larson, R. G. 1992 Monte Carlo simulation of microstructural transitions in surfactant systems. J. Chem. Phys. 96, 7904-7918. (doi:10.1063/1.462343)
30. Luisi, P. L. & Varela, F. J. 1989 "Self-replicating micelles - a chemical version of minimal autopoeitic systems." Orig. Life Evol. Biosph. 19, 633-644.
31. Madina, D., Ono, N. & Ikegami, T. 2003 Cellular evolution in a 3D lattice artificial chemistry. In Proc. ECAL 03 (eds W. Banzhaf et al.), pp. 59-68. Dortmund, Germany: Springer.
32. Mayer, B. & Rasmussen, S. 2000 Dynamics and simulation of self-reproducing micelles. Int. J. Mod. Phys. C 11, 827-836. (doi:10.1142/S0129183100000705)
33. McCaskill, J. S. 1984 A localization threshold for macromolecular quasispecies from continuously distributed replication rates. J. Chem. Phys. 80, 5194-5202. (doi:10.1063/1.446590)
34. McCaskill, J. S. 1997 Spatially resolved in vitro molecular ecology. Biophys. Chem. 66, 145-158. (doi:10.1016/S0301-4622(97) 00073-2)
35. McCaskill, J. S., Füchslin, R. M. & Altmeyer, S. 2001 The stochastic evolution of catalysts in spatially resolved molecular systems. Biol. Chem. 382, 1343-1363. (doi:10.1515/BC.2001.167)
36. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. 1953 Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092. (doi:10.1063/1.1699114)
37. Morawietz, D., Chowdhury, D., Vollmar, S. & Stauffer, D. 1992 Simulation of the kinetics of the Widom model of microemulsion. Physica A 187, 126-132. (doi:10.1016/0378-4371(92)90413-K)
38. Nielsen, S., Lopez, C. F., Srinivas, G. & Klein, M. L. 2004 Coarse grain models and the computer simulation of soft materials. J. Phys. Condens. Matter 16, R481-R512. (doi:10.1088/0953-8984/16/15/R03)
39. Ono, N. & Ikegami, T. 2000 Selection of catalysts through cellular reproduction. In Proc. Int. Conf. artificial life (ALIFE8) (eds R. Standish et al.), pp. 57-64. Cambridge MA: MIT Press.
40. Pearson, J. E. 1993 Complex patterns in a simple system. Science 261, 189-192. (doi:10.1126/science.261.5118.189)
41. Rasmussen, S., Chen, L., Nilsson, M. & Abe, S. 2003 Bridging nonliving and living matter. Artif. Life 9, 269-316. (doi:10.1162/106454603322392479)
42. Rasmussen, S., Chen, L., Deamer, D., Krakauer, D. C., Packard, N. H., Stadler, P. F. & Bedau, M. A. 2004 Transitions between nonliving and living matter. Science 303, 963-965. (doi:10.1126/science.1093669)
43. Schick, M. & Shih, W. 1986 Spin-1 model of a microemulsion. Phys. Rev. B 34, 1797-1801. (doi:10.1103/PhysRevB.34.1797)
44. Schuster, P. 2006 Prediction of RNA secondary structures: from theory to models and real molecules. Rep. Prog. Phys. 69, 1419-1477. (doi:10.1088/0034-4885/69/5/R04)
45. Serge, D., Ben-Eli, D. & Lancet, D. 2000 Compositional genomes. Proc. Natl Acad. Sci. USA 97, 4112-4117. (doi:10.1073/pnas.97.8. 4112)
46. Szathmary, E. & Demeter, L. 1987 Group selection of early replicators and the origin of life. J. Theor. Biol. 128, 463-486. (doi:10.1016/S0022-5193(87)80191-1)
47. Taylor, T. 2004 Niche construction and the evolution of complexity. In Artificial Life IX. Proc. Ninth Int. Conf. on the Simulation and Synthesis of Living Systems (eds J. Pollack, M. Bedau, P. Husbands, T. Ikegami & R. Watson), pp. 375-380. Cambridge, MA: MIT Press.
48. Thorsen, T., Roberts, R. W., Arnold, F. H. & Quake, S. R. 2001 Dynamic pattern formation in a vesicle-generating microfluidic device. Phys. Rev. Lett. 86, 4163-4166. (doi:10.1103/PhysRevLett.86.4163)
49. Turing, A. M. 1952 The chemical basis of morphogenesis. Phil. Trans. R. Soc. B 237, 37-72. (doi:10.1098/rstb.1952.0012)
50. Vanag, V. K. & Epstein, I. R. 2001 Pattern formation in a tunable reaction-diffusion medium: the BZ reaction in an aerosol OT microemulsion. Phys. Rev. Lett. 87, 228 301-1-228 301-4. (doi:10.1103/ PhysRevLett.87.228301)
51. von Kiedrowski, G. 1986 A self-replicating hexadeoxynucleotide. Angew. Chem. 98, 932-934.
52. Widom, B. 1986 Lattice model of microemulsions. J. Chem. Phys. 84(12), 6943-6954. (doi:10.1063/1.450615)