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

Source: [DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model](<https://www.sota2.com/research/paper/68fa2b4c1e209131ce84592e>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-24T14:06:30.281Z

Authors: Carsten Svaneborg, Harold Fellermann, Steen Rasmussen

Published: 2012-04-03T17:08:13.000Z

## 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.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1204.0733>)

[PDF](<https://arxiv.org/pdf/1204.0733.pdf>)