RNA model

From OxDNA
Revision as of 17:09, 6 March 2014 by Sulc (talk | contribs)
Jump to navigation Jump to search

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 V_(b.b.),
  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:

Image duplex combined annotated.png


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 8.518x10Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle ^{-10}} m
1 unit of energy 4.142x10Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle ^{-20}} J
1 unit of temperature 3000 K
1 unit of force 4.863x10Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle ^{-11}} N
1 unit of mass 1.66x10Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle ^{-25}} kg
1 unit of time 1.71x10Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\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)