README

This is a coarse grained simulation of DNA to study hairpin formation.

The model is based on the three beads per nucleotide model due to Knotts et 
al [1], with extensions by the same group [2] and later by Florescu & 
Joyeux [3]. 

Author:
  Roald Frederickx

Contributors:
  Thomas in't Veld
  Kasper Meerts


[1] T. Knotts IV, N. Rathore, D. Schwartz, and J. De Pablo, "A coarse grain 
    model for dna," p. 084901, 2007.
[2] E. Sambriski, D. Schwartz, and J. De Pablo, "A mesoscale model of dna 
    and its renaturation," Biophysical journal, vol. 96, no. 5, pp. 
    1675–1690, 2009.
[3] A. Florescu and M. Joyeux, "Thermal and mechanical denaturation 
    properties of a dna model with three sites per nucleotide," Journal of 
    Chemical Physics, vol. 135, p. 085105, 2011.