DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model

  • Carsten Svaneborg
  • Harold Fellermann
  • Steen Rasmussen
Conference paper

DOI: 10.1007/978-3-642-32208-2_10

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7433)
Cite this paper as:
Svaneborg C., Fellermann H., Rasmussen S. (2012) DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model. In: Stefanovic D., Turberfield A. (eds) DNA Computing and Molecular Programming. DNA 2012. Lecture Notes in Computer Science, vol 7433. Springer, Berlin, Heidelberg

Abstract

We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. In our model, a single nucleotide or domain is represented by a single interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the DNA model to perform simulations of the self-assembly kinetics of DNA tetrahedra, an icosahedron, as well as strand displacement operations used in DNA computation.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Carsten Svaneborg
    • 1
  • Harold Fellermann
    • 1
    • 2
  • Steen Rasmussen
    • 1
    • 3
  1. 1.Center for Fundamental Living Technology, Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkOdenseDenmark
  2. 2.Complex Systems Lab., Barcelona Biomedical Research ParkUniversitat Pompeu FabraBarcelonaSpain
  3. 3.Santa Fe InstituteSanta FeUSA

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