DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model
Soft Condensed Matter
2012-06-13 v2 Statistical Mechanics
Biological Physics
Biomolecules
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.
Cite
@article{arxiv.1204.0733,
title = {DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model},
author = {Carsten Svaneborg and Harold Fellermann and Steen Rasmussen},
journal= {arXiv preprint arXiv:1204.0733},
year = {2012}
}
Comments
Submitted for the DNA18 conference