Autocatalytic sets extended: Dynamics, inhibition, and a generalization

Journal of Systems Chemistry

Volumn 3, Issue 1, 2012, Pages

  Hordijk, Wim ^a   Steel, Mike ^b  

^a SmartAnalytiXcom   (Switzerland)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873376896     PISSN: None     EISSN: 17592208     Source Type: Journal    
DOI: 10.1186/1759-2208-3-5     Document Type: Article

References (31)

1. Kauffman SA: Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. J Cybernetics 1971, 1:71-96.
2. Eigen M, Schuster P: The hypercycle: a principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften 1977, 64:541-565.
3. Dyson FJ: Amodel for the origin of life. JMol Evolution 1982, 18:344-350.
4. Ẅachterḧauser G: Evolution of the first metabolic cycles. PNAS 1990, 87:200-204.
5. Ǵanti T: Biogenesis itself. J Theor Biol 1997, 187:583-593.
6. Rosen R: Life Itself. New York: Columbia University Press; 1991.
7. Letelier JC, Soto-Andrade J, Abarźua FG, Cornish-Bowden A, Ćardenas ML: Organizational invariance and metabolic closure: Analysis in terms of (M;R) systems. J Theor Biol 2006, 238:949-961.
8. Sievers D, Von Kiedrowski G: Self-replication of complementary nucleotide-based oligomers. Nature 1994, 369:221-224.
9. Ashkenasy G, Jegasia R, Yadav M, Ghadiri MR: Design of a directed molecular network. PNAS 2004, 101(30):10872-10877.
10. Hayden EJ, Von Kiedrowski, G, Lehman N: Systems chemistry on ribozyme self-construction: Evidence for anabolic autocatalysis in a recombination network. Angew Chem Int Ed 2008, 120:8552-8556.
11. Taran O, Thoennessen O, Achilles K, Von Kiedrowski G: Synthesis of information-carrying polymers of mixed sequences from double stranded short deoxynucleotides. J Syst Chem 2010, 1:9.
12. Braakman R, Smith E: The emergence and early evolution of biological carbon-fixation. PLoS Comput Biol 2012, 8(4):e1002455.
13. Steel M: The emergence of a self-catalysing structure in abstract origin-of-life models. Appl Mathematics Lett 2000, 3:91-95.
14. Hordijk W, Steel M: Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J Theor Biol 2004, 227(4):451-461.
15. Mossel E, Steel M: Random biochemical networks: The probability of self-sustaining autocatalysis. J Theor Biol 2005, 233(3):327-336.
16. Hordijk W, Hein J, Steel M: Autocatalytic sets and the origin of life. Entropy 2010, 12(7):1733-1742.
17. Hordijk W, Kauffman SA, Steel M: Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. Int J Molecular Sciences 2011, 12(5):3085-3101.
18. Hordijk W, Steel M: Predicting template-based catalysis rates in a simple catalytic reactionmodel. J Theor Biol 2012, 295:132-138.
19. Hordijk W, Steel M, Kauffman S: The structure of autocatalytic sets: Evolvability, enablement, and emergence. Acta Biotheoretica 2012, 60(4):379-392.
20. Kauffman SA: Autocatalytic sets of proteins. J Theor Biol 1986, 119:1-24.
21. Kauffman SA: The Origins of Order. New York: Oxford University Press; 1993.
22. Andersen JL, Flamm C, Merkle D, Stadler PF: Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete. J Syst Chem 2012, 3:1.
23. Vasas V, Fernando C, Santos M, Kauffman S, Sathḿary E: Evolution before genes. Biol Direct 2012, 7:1.
24. Filisetti A, Graudenzi A, Serra R, Villani M, De Lucrezia D, Füchslin RM, Kauffman SA, Packard N, Poli I: A stochasticmodel of the emergence of autocatalytic cycles. J Syst Chem 2011, 2:2.
25. Gillespie DT: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 1976, 22:403-434.
26. Gillespie DT: Exact stochastic simulation of coupled chemical reactions. J Physical Chem 1977, 81(25):2340-2361.
27. Segŕe D, Ben-Eli D, Deamer DW, Lancet D: The lipid world. Origin of Life and Evol Biospheres 2001, 31(1-2):119-145.
28. Martin W, Russel MJ: On the origins of cells: A hypothesis for the evolutionary transition from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc B 2003, 358:59-85.
29. Martin W, Russel MJ: On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc B 2007, 362:1887-1925.
30. Papadimitriou CH: Computational complexity. Boston: Addison Wesley; 1994.
31. Adleman LM: Molecular computation of solutions to combinatorial problems. Science 1994, 266(5187):1021-1024.