Modeling DNA loops using the theory of elasticity.

@article{Balaeff2003ModelingDL,
  title={Modeling DNA loops using the theory of elasticity.},
  author={Alexander Balaeff and Lakshminarayanan Mahadevan and Klaus Schulten},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  year={2003},
  volume={73 3 Pt 1},
  pages={
          031919
        }
}
An elastic rod model of a protein-bound DNA loop is adapted for application in multi-scale simulations of protein-DNA complexes. The classical Kirchhoff system of equations which describes the equilibrium structure of the elastic loop is modified to account for the intrinsic twist and curvature, anisotropic bending properties, and electrostatic charge of DNA. The effects of bending anisotropy and electrostatics are studied for the DNA loop clamped by the lac repressor protein. For two possible… 

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...

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...