Final year Doctoral Student at the
1 Keble Road
An RNA nanoring simulated with oxDNA (from the oxDNA homepage)
I completed an 11-week rotation in spring 2014 in the group of Ard Louis on salt effects on the structural and thermodynamical properties of DNA and RNA.
The Louis and Doye research groups have developed a coarse grained model of DNA and RNA ( oxDNA ) that has been widely used to simulate many nanostructures (like the nanoring in figure). oxDNA was originally parametrised to model DNA at a fixed salt concentration of 0.5 M ( 1M for RNA), which is relevant to many experiments in nanotechnology. During my project I modified oxDNA so that it could simulate systems in a salt concentration of 0.1 or higher, and optimised the model parameters so that it could reproduce the thermodynamical and structural behaviour of real nucleic acids. This extends oxDNA to biological salt concentrations, and will be used to study how nucleic acids behave inside living organisms, as well as model experiments with nucleic acids at lower salt concentrations. The same has been done in oxRNA, our coarse-grained model of RNA. See publications 2. and 3. from the list above.
A simulated configuration for a 6-arm star polymer. (animated .gif)