Evolving reaction-diffusion ecosystems with self-assembling structures in thin films

Artificial Life

Volumn 4, Issue 1, 1998, Pages 25-40

  Breyer, Jens ^a   Ackermann, Jörg ^a   McCaskill, John ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

3SR; Autopoiesis; DNA; Ecosystem; Evolution; Reaction diffusion; RNA

Indexed keywords

DNA; RNA;

ARTICLE; AUDIOVISUAL EQUIPMENT; BIOREACTOR; COMPUTER PROGRAM; COMPUTER SIMULATION; DIFFUSION; ECOSYSTEM; MOLECULAR EVOLUTION; SYNTHESIS;

BIOREACTORS; COMPUTER SIMULATION; DIFFUSION; DNA; ECOSYSTEM; EVOLUTION, MOLECULAR; MOTION PICTURES; RNA; SOFTWARE;

EID: 0032325062     PISSN: 10645462     EISSN: None     Source Type: Journal    
DOI: 10.1162/106454698568422     Document Type: Article

References (28)

1. Ackermann, J., Wlotzka, B., & McCaskill, J. S. (1998). In-vitro DNA-based predator-prey system with oscillatory kinetics. Bulletin of Mathematical Biology, 60, 329-354.
2. Boerlijst, M. C., & Hogeweg, P. (1991). Spiral wave structures in prebiotic evolution: Hypercycles stable against parasites. Physica D, 48, 17-28.
3. Compton, J. (1991). Nucleic acid sequence-based amplification. Nature, 350, 91-92.
4. Cronhorst, M. B., & Blomberg, C. (1997). Cluster compurtmentalization may provide resistance to parasites for catalytic networks. Physica D, 101, 289-298.
5. Ehricht, R., Kllinger, T., & McCaskill, J. S. (1997). Cooperative amplification of templates by cross-hybridization (CATCH). European Journal of Biochemistry, 243, 358-364.
6. Ehricht, R., Kirner, T., Ellinger, T., Foerster, P., & McCaskill, J. S. (1997). Monitoring the amplification of CATCH, a 3SR based cooperatively coupled isothermal amplification system, by fluorimetric methods. Nucleic Acid Research, 25, 4697-4699.
7. Eigen, M. (1971). The quasispecies model. Naturwissenschaften, 58, 465-523.
8. Eigen, M., McCaskill, J. S., & Schuster, P. (1989). The molecular quasispecies. Advances in Chemical Physics, 75, 149-263.
9. Ganti, T. (1975). Organisation of chemical reactions into dividing and metabilizing units: The chemotons. Biosystems, 7, 189-195.
10. Guatelli, J. C., Whitefield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D., & Gingeras, T. R. (1990). Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proceedings of the National Academy of Sciences, 87, 1874-1878.
11. Hong, J. I., Feng, Q., Rotello, V., & Rebek, J., Jr. (1992). Competition, cooperation and mutation: Improving a synthetic replicator by light irradiation. Science, 255, 848-850.
12. Kapral, R., Lawniczak, A., & Masiar, P. (1991). Oscillations and waves in a reactive Lattice-Gas Automaton. Physical Review Letters, 66, 2539-2543.
13. Lee, D. H., Severin, K., Yokobayashi, Y., & Ghadiri, M. R. (1997). Emergence of symbiosis in peptide self-replicating through a hypercycle network. Nature, 390, 591-594.
14. Luisi, P. L. (1994). The chemical implementation of autopoiesis. In G. R. Fleischaker, S. Colonna, & P. L. Luisi (Eds.), Self-production of supramolecular structures (pp. 179-197). Dordrecht, Holland: Kluwer Academic Publishers.
15. Margolus, N. (1984). Physics-like models of computation. Physica D, 10, 81-95.
16. Maturana, H. R., & Varela, F. J. (1980). Autopoieses and cognition: The realization of the living (Vol. 42, p. 80). Dordrecht, Holland: Reidel.
17. McCaskill, J. S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
18. McCaskill, J. S. (1994). Ursprünge der Molekularen Kooperation: Theorie und Experiment. Antrittsvorlesung an der Schiller Universität Jena, 27-40.
19. McCaskill, J. S. (1997). Spatially resolved in vitro molecular ecology. Biophysical Chemistry, 66, 145-158.
20. McMullin, B., & Varela, F. R. (1997). Rediscovering computational autopoieses. In P. Husband & I. Harvey (Eds.), Proceedings of the Fourth European Conference on Artificial Life (ECAL) (pp. 38-47). Cambridge, MA: MIT Press/Bradford Books.
21. Pearson, J. E. (1993). Complex patterns in simple systems. Science, 261, 189-192.
22. Rasmussen, S., & Smith, J. R. (1994). Lattice polymer automaton. Berichte der Bunsengesellschaft für Physikalische Chemie, 89, 1185-1193.
23. Tangen, U., Schulte, L., & McCaskill, J. S. (1997). A parallel hardware evolvable computer POLYP. In K. L. Pocek & J. Arnold (Eds.), Proceedings of the IEEE Symposium on FBGAs for Custom Computing Machines (p. 238). Los Alamitos, CA: IEEE Computer Society.
24. Toffoli, T. (1984). Cellular automata as an alternative to (rather than an approximation of) differential equations in modeling physics. Physica D, 10, 117-127.
25. Varela, F. R. (1979). Principles of biological autonomy (pp. 38-47). New York: North-Holland.
26. von Kiedrowski, G. (1993). Minimal replicator theory I: Parabolic versus exponential growth. Bioorganic Chemistry Frontiers, 3, 113-146.
27. Wlotzka, B., & McCaskill, J. S. (1997). A molecular predator and its prey: Coupled isothermal amplification of nucleic acids. Biology & Chemistry, 4, 25-33.
28. Zuker, M., & Steigler, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research, 9, 133-148.