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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 , with extensions by the same group  and later by Florescu & Joyeux . Author: Roald Frederickx Contributors: Thomas in't Veld Kasper Meerts  T. Knotts IV, N. Rathore, D. Schwartz, and J. De Pablo, "A coarse grain model for dna," p. 084901, 2007.  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.  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.