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\iteman{io-port 06102523}
\itemau{Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen}
\itemti{DNA self-assembly and computation studied with a coarse-grained dynamic bonded model.}
\itemso{Stefanovic, Darko (ed.) et al., DNA computing and molecular programming. 18th international conference, DNA 18, Aarhus, Denmark, August 14--17, 2012. Proceedings. Berlin: Springer (ISBN 978-3-642-32207-5/pbk). Lecture Notes in Computer Science 7433, 123-134 (2012).}
\itemab
Summary: 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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\itemli{doi:10.1007/978-3-642-32208-2\_10}
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