# RNA model

The RNA model, oxRNA, treats each RNA nucleotide as a single rigid body with multiple interaction sites, following the coarse-graining apporach adopted for the DNA model. The nucleotides interact with pairwise interaction potentials, which are schematically illustrated below: [[Image::Image_duplex_combined_annotated.png]]

1. Backbone connectivity ${\displaystyle V_{\rm {backbone}}}$,
2. Excluded volume ,
3. Hydrogen bonding,
4. Nearest-neighbour stacking,
5. Cross-stacking between base-pair steps in a duplex,
6. Coaxial stacking.

which are schematically illustrated in the picture:

### Simulation units

The code uses dimensionless energy, mass, length and timescales for convenience. The relationship between simulation units (SU) and SI units is given below.

Simulation unit Physical unit
1 unit of length 8.518x10${\displaystyle ^{-10}}$ m
1 unit of energy 4.142x10${\displaystyle ^{-20}}$ J
1 unit of temperature 3000 K
1 unit of force 4.863x10${\displaystyle ^{-11}}$ N
1 unit of mass 1.66x10${\displaystyle ^{-25}}$ kg
1 unit of time 1.71x10${\displaystyle ^{-12}}$ s

The model and its performance is discussed in detail in the following references (the thesis provides the most complete analysis):

T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011. Coarse-grained modelling of DNA and DNA self-assembly

T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011) Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)

P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012) Sequence-dependent thermodynamics of a coarse-grained DNA model (arxiv)