Info simulations

Primary investigator: Carsten Svaneborg and Harold Fellermann University of Southern Denmark. (ongoing research)

Template based replication of DNA

This video shows a dynamic bonded DNA model ["LAMMPS Framework for Dynamic Bonding an Application Modeling DNA". C. Svaneborg. Computer Physics Communications 183, 1793 (2012).] The video illustrates how complimentary oligomers docks on a template, subsequently nearby oligomers ligate with each other. The final result is the production of a strand w

ith the complimentary sequence of the template. Periodically the system is heated for brief period to melt of the copy, such that the template based replication can continue.

Self-assembly of DNA nano-structures

Complimentary single strands hybridize forming a double strand. This can be used to program the molecular self-assembly of desired nano-structures. For instance, by crafting 4 different types of 3-armed single strand complexes with the right complementary DNA sequences, these can be made to self-assemble into well-defined structures such as a tetrahedron.

Using instead 12 5-functional DNA constructs, they can be made to self-assemble into an icosahedron as shown below.

 

Publications


”LAMMPS Framework for Dynamic Bonding an Application Modeling DNA”. C. Svaneborg. Computer Physics Communications 183, 1793 (2012).

DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model. C. Svaneborg, H. Fellermann, and S. Rasmussen. Lecture Notes in Computer Science 7433, 123 (2012) Eds. D. Stafanovic and A. Tuberfield.