  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.

Soft Condensed Matter;Statistical Mechanics;Biological Physics;Biomolecules