title: Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations.
abstract: Ionic finite size can impose considerable effects to both the equilibrium and non-equilibrium properties of a solvated molecular system, such as the solvation energy, ionic concentration, and transport in a channel. As discussed in our former work [B. Lu and Y. C. Zhou, Biophys. J. 100, 2475 (2011)], a class of size-modified Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) models can be uniformly studied through the general nonuniform size-modified PNP (SMPNP) equations deduced from the extended free energy functional of Borukhov et al. [I. Borukhov, D. Andelman, and H. Orland, Phys. Rev. Lett. 79, 435 (1997)] This work focuses on the nonuniform size effects to molecular solvation energy and to ion current across a channel for real biomolecular systems. The main contributions are: (1) we prove that for solvation energy calculation with nonuniform size effects (through equilibrium SMPNP simulation), there exists a simplified approximation formulation which is the same as the widely used one in PB community. This approximate form avoids integration over the whole domain and makes energy calculations convenient. (2) Numerical calculations show that ionic size effects tend to negate the solvation effects, which indicates that a higher molecular solvation energy (lower absolute value) is to be predicted when ionic size effects are considered. For both calculations on a protein and a DNA fragment systems in a 0.5M 1:1 ionic solution, a difference about 10 kcal/mol in solvation energies is found between the PB and the SMPNP predictions. Moreover, it is observed that the solvation energy decreases as ionic strength increases, which behavior is similar as those predicted by the traditional PB equation (without size effect) and by the uniform size-modified Poisson-Boltzmann equation. (3) Nonequilibrium SMPNP simulations of ion permeation through a gramicidin A channel show that the ionic size effects lead to reduced ion current inside the channel compared with the results without considering size effects. As a component of the current, the drift term is the main contribution to the total current. The ionic size effects to the total current almost come through the drift term, and have little influence on the diffusion terms in SMPNP.
authors.affiliation: State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Tu
authors.affiliation: State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Benzhuo
authors.initials: B
authors.lastname: Lu