DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model
- 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
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.
Unable to display preview. Download preview PDF.