We utilize a coarse-grained  directional dynamic bonding DNA model [ C. URL, 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.
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework [ C. URL, 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.
R
utilize
study DNA self-assembly and DNA computation using
A
DNA model within the
R
DNA model
framework
R
(In Press DOI:10.1016/j.cpc.2012.03.005)
183, 1793 (2012)
D
to study DNA self-assembly and DNA computation
D
DNA
A
or domain
R
, and complementary sites can hybridize reversibly . Along with the dynamic hybridization bonds,
. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the
R
are dynamically introduced and removed to
, that
R
properties of double helix
effects of chemical
R
DNA zippering
hybridization
R
this
the
R
simulate the temperature dependent
perform simulations of the
A
kinetics
R
at several temperatures, a DNA icosahedron, and also
, an icosahedron, as well as