Abstract
We present a multi-scale approach aiming at studying DNA immersed in the external field generated by a protein. Our model captures different levels of detail by coupling oxDNA coarse-grained model with a variable representation of a rigid protein -covering the range from coarse grained to full atomistic. The cross-interactions between the nucleic acids and the protein are defined via a Lennard-Jones potential plus Debye interactions that account for the implicit effect of salt on DNA electrostatics.
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