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.