Sequence-dependent thermodynamics of a coarse-grained DNA model.

@article{ulc2012SequencedependentTO,
  title={Sequence-dependent thermodynamics of a coarse-grained DNA model.},
  author={Petr {\vS}ulc and Flavio Romano and Thomas E. Ouldridge and Lorenzo Rovigatti and Jonathan P. K. Doye and Ard A. Louis},
  journal={The Journal of chemical physics},
  year={2012},
  volume={137 13},
  pages={
          135101
        }
}
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our… 

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