Difference between revisions of "RNA model"

From OxDNA
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#Backbone connectivity V_(b.b.),
#Backbone connectivity <math>V_{\rm backbone}</math>,
#Excluded volume ,
#Excluded volume ,
#Hydrogen bonding,
#Hydrogen bonding,
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which are schematically illustrated in the picture:
which are schematically illustrated in the picture:

Revision as of 12:24, 10 March 2014

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 ,
  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 8.518x10 m
1 unit of energy 4.142x10 J
1 unit of temperature 3000 K
1 unit of force 4.863x10 N
1 unit of mass 1.66x10 kg
1 unit of time 1.71x10 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)