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. Author manuscript; available in PMC: 2016 Apr 14.

Published in final edited form as: J Chem Theory Comput. 2015 Mar 11;11(4):1792–1808. doi: 10.1021/ct5009558

Illustration of two orientations of polar uncharged side chain (PSC) and DNA base for (a) $θ_{i j}^{(1)} = 90 °, θ_{i j}^{(2)} = 90 °$ , and φ_ij = 0 (side-to-side); (b) $θ_{i j}^{(1)} = 0 °, θ_{i j}^{(2)} = 180 °$ , and φ_ij undefined (head-to-head). The lines represent the long axis of the ellipsoid. The circle at one end of the particle represents the dipole on the ellipsoid.