Related papers: Electrostatic interactions in concentrated protein…
The electrostatic interaction between colloidal particles trapped at the interface between two immiscible electrolyte solutions is studied in the limit of small inter-particle distances. Within an appropriate model exact analytic…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
The excess entropy of restricted primitive model electrolytes is calculated using a potential based approach through the symmetric Poisson-Boltzmann and the modified Poisson-Boltzmann theories. The theories are utilized in conjunction with…
Electrochemical desalination devices that use redox-active cation intercalation electrodes show promise for desalination of salt-rich water resources with high water recovery and low energy consumption. While previous modeling and…
The non-equilibrium dynamics of electrons is of a great experimental and theoretical value providing important microscopic parameters of the Coulomb and electron-phonon interactions in metals and other cold plasmas. Because of the…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
The equation of state (EOS) for partially ionized carbon, oxygen, and carbon-oxygen mixtures at temperatures 3\times10^5 K <~ T <~ 3\times10^6 K is calculated over a wide range of densities, using the method of free energy minimization in…
We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of Poisson equation using periodic Green functions. It is shown that the electrostatic energy…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
A methodology for calculating the contribution of charged defects to the configurational free energy of an ionic crystal is introduced. The temperature-independent Wang-Landau Monte Carlo technique is applied to a simple model of a solid…
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is…
We investigate the phenomenon of counterion condensation in a solution of highly charged rigid polyelectrolytes within the cell model. A method is proposed which -- based on the charge distribution function -- identifies both the fraction…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion…
The thermodynamics of nucleic acid processes is heavily affected by the electric double-layer of micro-ions around the polyions. We focus here on the Coulombic contribution to the salt-polyelectrolyte preferential interaction (Donnan)…
We consider a system composed of a monodisperse charge-stabilized colloidal suspension in the presence of monovalent salt, separated from the pure electrolyte by a semipermeable membrane, which allows the crossing of solvent, counterions,…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
We present a nonlocal electrostatic formulation of nonuniform ions and water molecules with interstitial voids that uses a Fermi-like distribution to account for steric and correlation effects in electrolyte solutions. The formulation is…