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oxDNA
oxDNA is a simulation code that implements the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. The code implements Monte Carlo and Brownian Dynamics and can be used as a basis to numerically study DNA systems. The developers are F. Romano, P. Šulc and T. E. Ouldridge in the Doye and Louis groups at the University of Oxford and L. Rovigatti in the Sciortino group in Rome.
The model is intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA, as well as the transition between the two. At the same time, the representation of DNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of DNA nanotechnology, as well as many biophysical uses of DNA, allowing the model to be used to understand these fascinating systems.
Acknowledgments
We thank our co-workers C. Matek, B. Snodin and W. Smith for having contributed bits of code and/or material for the examples.