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arXiv · 1204.0733

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

Carsten Svaneborg·Harold Fellermann·Steen Rasmussen
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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.

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Carsten Svaneborg, Harold Fellermann, Steen Rasmussen. 2012-04-03. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. https://arxiv.org/abs/1204.0733

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