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The distributions of different cations around A-RNA are computed by Poisson-Boltzmann (PB) equation and replica exchange molecular dynamics (MD). Both the nonlinear PB and size-modified PB theories are considered. The number of ions bound to A-RNA, which can be measured experimentally, is well reproduced in all methods. On the other hand, the radial ion distribution profiles show differences between...
The predictions of the derivative of the electrostatic binding free energy of a biomolecular complex, ΔG el , with respect to the logarithm of the 1:1 salt concentration, d(ΔG el )/d(ln[NaCl]), SK, by the Poisson–Boltzmann equation, PBE, are very similar to those of the simpler Debye–Hückel equation, DHE, because the terms in the PBE's predictions of SK that depend on the details of...
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