Skip to main content

Catalysis by Self-Assembled Structures in Emergent Reaction Networks

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4648))

Abstract

We study a new variant of the dissipative particle dynamics (DPD) model that includes the possibility of dynamically forming and breaking strong bonds. The emergent reaction kinetics may then interact with self-assembly processes. We observe that self-assembled amphiphilic aggregations such as micelles have a catalytic effect on chemical reaction networks, changing both equilibrium concentrations and reaction frequencies. These simulation results are in accordance with experimental results on the so-called “concentration effect”.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bedau, M.A., Buchanan, A., Gazzola, G., Hanczyc, M., Maeke, T., McCaskill, J.S., Poli, I., Packard, N.H.: Evolutionary design of a DDPD model of ligation. In: Talbi, E.-G., Liardet, P., Collet, P., Lutton, E., Schoenauer, M. (eds.) EA 2005. LNCS, vol. 3871, pp. 201–212. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  2. Benkö, G., Flamm, C., Stadler, P.F.: A Graph-Based Toy Model of Chemistry. Journal of Chemical Information and Computational Science 43, 1085–1093 (2003)

    Article  Google Scholar 

  3. Benkö, G., Flamm, C., Stadler, P.F.: Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. In: Banzhaf, W., Ziegler, J., Christaller, T., Dittrich, P., Kim, J.T. (eds.) ECAL 2003. LNCS (LNAI), vol. 2801, pp. 10–19. Springer, Heidelberg (2003)

    Google Scholar 

  4. Benkö, G., Flamm, C., Stadler, P.F.: Multi-Phase Artificial Chemistry. In: Schaub, H., Detje, F., Brüggemann, U. (eds.) The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, pp. 16–22. IOS Press, Amsterdam (2004)

    Google Scholar 

  5. Besold, G., Vattulaien, I., Karttunen, M., Polson, J.M.: Towards Better Integrators for Dissipative Partycle Dynamics Simulations. Physical Review E 62, 7611–7614 (2000)

    Article  Google Scholar 

  6. Buchanan, A., Gazzola, G., Bedau, M.A.: Evolutionary Design of a Model of Self-Assembling Chemical Structures. In: Krasnogor, N., Gustafson, S., Pelta, D., Verdegay, J.L. (eds.), Elsevier Science, Amsterdam (2007)

    Google Scholar 

  7. Delort, E., Darbre, T., Reymond, J.-L.: A Strong Positive Dendritic Effect in a Peptide Dendrimer-Catalyzed Ester Hydrolysis Reaction. Journal of the American Chemical Society 126, 15642–15643 (2004)

    Article  Google Scholar 

  8. Farmer, J.D., Kauffman, S.A., Packard, N.H.: Autocatalytic Replication of Polymers. Physica D 22, 50 (1986)

    Article  MathSciNet  Google Scholar 

  9. Farmer, J.D., Packard, N.H., Perelson, A.: The Immune System, Adaptation, and Machine Learning. Physica D 22, 187 (1986)

    Article  MathSciNet  Google Scholar 

  10. Fellerman, H., Rasmussen, S., Ziock, H., Solé, R.: Life cycle of a minimal procell: a dissipative particle (DPD) study. Artificial Life (in press, 2007)

    Google Scholar 

  11. Fendler, J.H., Fendler, E.J.: Catalysis in micellar and macromolecular systems. Academic Press, New York (1975)

    Google Scholar 

  12. Fung, S.Y., Keyes, C., Duhamel, J., Chen, P.: Concentration Effect on the Aggregation of a Self-Assembling Oligopeptide. Biophysical Journal 85, 537–548 (2003)

    Article  Google Scholar 

  13. Groot, R., Warren, P.: Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulations. Journal of Chemical Physics 107, 4423–4435 (1997)

    Article  Google Scholar 

  14. Hoogerbrugge, P., Koelman, J.: Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhysics Letters 19, 155–160 (1992)

    Article  Google Scholar 

  15. Jury, S., Bladon, P., Cates, M., Krishna, S., Hagen, M., Ruddock, N., Warren, P.: Simulation of amphiphilic mesophases using dissipative particle dynamics. Physical Chemistry and Chemical Physics 1, 2051–2056 (1999)

    Google Scholar 

  16. Kauffman, S.A.: Autocatalytic sets of proteins. Journal of Theoretical Biology 119, 1–24 (1986)

    Article  Google Scholar 

  17. Kranenburg, M., Venturoli, M., Smit, B.: Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. Journal of Physical Chemistry 107, 11491–11501 (2003)

    Google Scholar 

  18. Kuby, J.: Immunology, 3rd edn. W.H. Freeman, New York (1997)

    Google Scholar 

  19. Luisi, P.L., Giomini, M., Pileni, M., Robinson, B.: Reverse micelles as hosts for proteins and small molecules. Biochimica and Biophysica Acta 947, 209–246 (1988)

    Google Scholar 

  20. Luisi, P.L., Walde, P., Oberholzer, T.: Enzymatic synthesis in self-reproducing vesicles: An approach to the construction of a minimal cell. Berichte der Bunsengesellschaft für Physikalische Chemie 98, 1160–1165 (1994)

    Google Scholar 

  21. Mallick, K., Jewrajka, S., Pradhan, N., Pal, T.: Micelle-catalysed redox reaction. Current Science 80, 1408–1412 (2001)

    Google Scholar 

  22. Marsh, C.: Theoretical aspects of dissipative particle dynamics. University of Oxford, Ph.D. Thesis (1998)

    Google Scholar 

  23. Martin, K.I., Twyman, L.J.: Acceleration of an aminolysis reaction using a PAMAM dendrimer with 64 terminal amine groups. Tetrahedron Letters 42, 1123–1126 (2001)

    Article  Google Scholar 

  24. Oehme, G., Grassert, I., Paetzold, E., Fuhrmann, H., Dwars, T., Schmidt, U., Iovel, I.: The Effect of Assembled Amphiphiles on Catalytic Reactions in Aqueous Media. Kinetics and Catalysis 44, 766–777 (2003)

    Article  Google Scholar 

  25. Pollack, G.H.: Cells, Gels and the Engines of Life: A New, Unifying Approach to Cell Function. Ebner & Sons, Seattle (2001)

    Google Scholar 

  26. Rasmussen, S., Chen, L., Stadler, B., Stadler, P.: Proto-organism kinetics: Evolutionary dynamics of lipid aggregates with genes and metabolism, Origins of life and evolution of the biosphere (in press)

    Google Scholar 

  27. Riepe, A., Beier, H., Gross, H.J.: Enhancement of RNA self-cleavage by micellar catalysis. FEBS Letters 457, 193–199 (1999)

    Article  Google Scholar 

  28. Ruasse, M.-F., Blagoevab, I.B., Garcia-Rio, R.C.L.G., Leis, J.R., Marques, A., Mejuto, J., Monnier, E.: Organic reactions in micro-organized media: Why and how? Pure and Applied Chemistry 69, 1923–1932 (1997)

    Google Scholar 

  29. Shilling, C.H., Palsson, B.O.: The underlying pathway structure of biochemical reaction networks. Proceedings of the National Academy of Science 95, 4193–4198 (1998)

    Article  Google Scholar 

  30. Shillcock, J., Lipowsky, R.: Equilibrium structure and lateral stress distribution from dissipative particle dynamics simulations. Journal of Chemical Physics 117, 5048–5061 (2002)

    Article  Google Scholar 

  31. Trofimov, S., Nies, E., Michels, M.: Thermodynamic consistency in dissipative particle dynamics simulations of strongly nonideal liquids and liquid mixtures. Journal of Chemical Physics 117, 9383–9394 (2002)

    Article  Google Scholar 

  32. Vattulainen, I., Karttunen, M., Besold, G., Polson, J.: Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models. Journal of Chemical Physics 116, 3967–3979 (2002)

    Article  Google Scholar 

  33. Yamamoto, S., Maruyama, Y., Hyodo, S.: Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules. Journal of Chemical Physics 116, 5842–5849 (2002)

    Article  Google Scholar 

  34. Yamamoto, S., Hyodo, S.: Budding and fission dynamics of two-component vesicles. Journal of Chemical Physics 118, 7937–7943 (2003)

    Article  Google Scholar 

  35. Zingaretti, L., Boscatto, L., Chiacchiera, S.M., Silber, J.J.: Kinetics and mechanism for the reaction of 1-chloro-2,4-dinitrobenzene with n-butylamine and piperidine in AOT/n-hexane/water reverse micelles. In: Arkivoc X, pp. 189-200 (2003)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Fernando Almeida e Costa Luis Mateus Rocha Ernesto Costa Inman Harvey António Coutinho

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Gazzola, G., Buchanan, A., Packard, N., Bedau, M. (2007). Catalysis by Self-Assembled Structures in Emergent Reaction Networks. In: Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I., Coutinho, A. (eds) Advances in Artificial Life. ECAL 2007. Lecture Notes in Computer Science(), vol 4648. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74913-4_88

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-74913-4_88

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-74912-7

  • Online ISBN: 978-3-540-74913-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics