Erratum: Moving beyond Watson–Crick models of coarse grained DNA dynamics (J. Chem. Phys. (2011) 135(20) (205102) (10.1063/1.3662137))

Abstract

We would like to correct several errors in Sec. II of our paper.1 The following formulas are all written in dimensionless form in terms of the forces acting on bead i, where r is a vector drawn from bead j to bead i and r = |r|. For the backbone-backbone excluded volume interactions,[formula omitted]where δ = 0.24. For the backbone-backbone springs,[formula omitted]For the backbone-base springs,[formula omitted]For the hydrogen bonding, stacking, and cross-stacking interactions,[formula omitted]where γ = 22 for hydrogen bonding and γ = 22.32 for stacking and cross-stacking. The force only acts between base beads and does not conserve angular momentum. Corrected values of the [formula omitted] in Tables II and III of the manuscript are included here as Tables I and II. In the Brownian dynamics simulations, the simulations of single-stranded DNA hairpins used a velocity Verlet algorithm. These corrections only affect the description of the model in our paper. The simulation results and conclusions drawn therefrom are unchanged. We thank Abhiram Muralidhar and Dan Hinckley (University of Wisconsin-Madison) for their assistance. © 2012, American Institute of Physics. All rights reserved.