A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.

@article{Freeman2011ACT,
  title={A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.},
  author={Gordon S. Freeman and Daniel M. Hinckley and Juan J de Pablo},
  journal={The Journal of chemical physics},
  year={2011},
  volume={135 16},
  pages={
          165104
        }
}
The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom… CONTINUE READING

Citations

Publications citing this paper.
SHOWING 1-10 OF 12 CITATIONS