2012/04/03 by Carsten Svaneborg, Svaneborg, Carsten, Harold Fellermann +3
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced biosensing and bioanalysis techniques #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #DNA and Biological Computing #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft) #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.soft #cond-mat.stat-mech #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1204.0733
Submitted for the DNA18 conference
openalex publication_date 2012/04/03 · arxiv created 2012/06/12 · arxiv updated 2012/06/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.