@article {53296, title = {Ab initio determination of coarse-grained interactions in double-stranded DNA}, journal = {Journal of Chemical Physics}, volume = {137}, year = {2012}, pages = {105102}, abstract = {We derive the coarse-grained interactions between\ DNA\ nucleotides from\ ab initio\ total-energy calculations based on\ density functional theory\ (DFT).\ The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that includehydrogen bonding,\ stacking interactions, backbone, and backbone-base interactions. The interaction\ energies\ of each contribution are calculated from\ DFT\ for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA\ structure\ and gives good predictions for the persistence length. It may be used to realistically probe dynamics of\ DNA\ strands in various environments at the μs time scale and the μm length scale.}, author = {Chia Wei Hsu and Maria Fyta and Greg Lakatos and Simone Melchionna and Efthimios Kaxiras} }