In this dissertation, I combine physical modeling, mathematical analysis, and numerical computation to study several problems concerning electrostatic interactions in biological molecular systems. Biomolecules, such as DNAs and proteins, are highly charged. They interact with each other and with the mobile ions and the polarized solvent to generate strong forces that affect crucially many molecular processes, such as molecular conformational changes, recognition, and self-assembly. My goal is to develop rigorous theories and efficient computational tools to understand some of the principles and mechanisms underlying such complicated interactions. Specifically, I study three closely related problems. The first one is the effect of ionic sizes that has been experimentally observed to be significant. Using a size-modified mean- field model and extensive Monte Carlo simulations, I capture details of the competitive adsorption of counterions of multiple species to charged surfaces. The simulations confirm the crucial role of ionic valence-to- volume ratios that had been predicted by the mean-field theory. The second problem is how the ionic concentration dependent dielectric coefficient can affect the equilibrium properties of charged system. I construct a variational model, derive rigorously the first and second variations of the free-energy functional, and prove that the functional is nonconvex. Numerical studies reveal several important features that cannot be modeled with a constant dielectric coefficient. Finally, I study a general problem of the solvation of charged molecules, aiming at understanding how electrostatic interactions contribute to the shape of underlying molecules. I develop a phase-field implicit-solvent approach to minimize a free -energy functional that couples the interfacial energy, van der Waals solute-solvent interaction energy, and electrostatic energy. I also design numerical methods to implement this approach. A common theme of my dissertation work is the variational approach. Many physical effects such as ionic size effects, solvent entropy, concentration dependent dielectric response can be incorporated into a mean-field free-energy functional of ionic concentrations coupled with the Poisson equation for electrostatics. The techniques of analysis developed in this work may help improve the understanding of the underlying physical properties of charged systems and provide new ways of studying analytically and numerically other problems in the calculus of variations

We construct a mean-field variational model to study how the dependence of dielectric coefficient (i.e., relative permittivity) on local ionic concentrations affects the electrostatic interaction in an ionic solution near a charged surface. The electrostatic free-energy functional of ionic concentrations, which is the key object in our model, consists mainly of the electrostatic potential energy and the ionic ideal-gas entropy. The electrostatic potential is determined by Poisson's equation in which the dielectric coefficient depends on the sum of concentrations of individual ionic species. This dependence is assumed to be qualitatively the same as that on the salt concentration for which experimental data are available and analytical forms can be obtained by the data fitting. We derive the first and second variations of the free-energy functional, obtain the generalized Boltzmann distributions, and show that the free-energy functional is in general nonconvex. To validate our mathematical analysis, we numerically minimize our electrostatic free-energy functional for a radially symmetric charged system. Our extensive computations reveal several features that are significantly different from a system modeled with a dielectric coefficient independent of ionic concentration. These include the non-monotonicity of ionic concentrations, the ionic depletion near a charged surface that has been previously predicted by a one-dimensional model, and the enhancement of such depletion due to the increase of surface charges or bulk ionic concentrations.

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.