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.