computer modeling in molecular biology.pdf

5 Modelling Nucleic Acids 109ElFigure 5-1. Variations with the distance separating the charges of different dielectric functions(above) and of the corresponding electrostatic energies (below). The curves are, respectively,el = 4r, ~2 = Lavery et al. [20], e3 = Mehler and Eichele [19], 84 = r, e5 = 1. The electrostaticenergies are computed with q, = q2 = 0.3 e and Ei (r) = ~332q1q2 . (From Fritsch [64]).Ei(r)rwhere D = 78, A = 0.36 or A = 0.16. The first value gives the same dependence ondistance than the function developed by Hingerty et al. [21].The second effect, the dampening of ionic interactions due to screening by saltions, is usually handled by a Debye-Hiickel screened potential of the form [22]:e Ka1 + KG--Kr