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

We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation.