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Evolutionary Design of a DDPD Model of Ligation

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Artificial Evolution (EA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3871))

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Abstract

Ligation is a form of chemical self-assembly that involves dynamic formation of strong covalent bonds in the presence of weak associative forces. We study an extremely simple form of ligation by means of a dissipative particle dynamics (DPD) model extended to include the dynamic making and breaking of strong bonds, which we term dynamically bonding dissipative particle dynamics (DDPD). Then we use a chemical genetic algorithm (CGA) to optimize the model’s parameters to achieve a limited form of ligation of trimers—a proof of principle for the evolutionary design of self-assembling chemical systems.

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Authors and Affiliations

  1. Protolife S.r.l., Via della Libertà 12, Marghera, Venezia, 30175, Italy

    Mark A. Bedau, Andrew Buchanan, Gianluca Gazzola, Martin Hanczyc & Norman H. Packard

  2. European Center for Living Technology, S. Croce 1681, Venezia, 30135, Italy

    Mark A. Bedau, Andrew Buchanan, Gianluca Gazzola, Martin Hanczyc, Thomas Maeke, John McCaskill, Irene Poli & Norman H. Packard

  3. Reed College, 3203 SE Woodstock Blvd., Portland, OR, 97202, USA

    Mark A. Bedau

  4. Biomolecular Information Processing, Ruhr-Universitat Bochum, c/o IZB Schloss Birlinghoven, D-53754, Sankt Augustin, Germany

    Thomas Maeke & John McCaskill

  5. University of Venice Ca’ Foscari, San Polo 2347, Venezia, 30125, Italy

    Irene Poli

Authors
  1. Mark A. Bedau
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  2. Andrew Buchanan
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  3. Gianluca Gazzola
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  4. Martin Hanczyc
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  5. Thomas Maeke
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  6. John McCaskill
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  7. Irene Poli
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  8. Norman H. Packard
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Editor information

Editors and Affiliations

  1. INRIA Lille - Nord Europe Research Centre, Parc Scientifique de la Haute Borne, 59650, Villeneuve d’Ascq, France

    El-Ghazali Talbi

  2. UMR-CNRS 6632, Université de Provence, 39 rue F. Joliot-Curie, 13453, Marseille cedex 13, France

    Pierre Liardet

  3. Université Louis Pasteur, LSIIT, FDBT, Pôle API, F-67400, Illkirch, France

    Pierre Collet

  4. INRIA Saclay - Ile-de-France, Parc Orsay Université, 4, rue Jacques Monod, 91893, ORSAY Cedex, France

    Evelyne Lutton

  5. TAO, INRIA Saclay & LRI (UMR CNRS 8623), Bât 490, Université Paris-Sud, 91405, Orsay Cedex, France

    Marc Schoenauer

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© 2006 Springer-Verlag Berlin Heidelberg

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Bedau, M.A. et al. (2006). Evolutionary Design of a DDPD Model of Ligation. In: Talbi, EG., Liardet, P., Collet, P., Lutton, E., Schoenauer, M. (eds) Artificial Evolution. EA 2005. Lecture Notes in Computer Science, vol 3871. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11740698_18

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  • DOI: https://doi.org/10.1007/11740698_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33589-4

  • Online ISBN: 978-3-540-33590-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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