Related papers: Electrostatic interactions in concentrated protein…
We develop analytic approximations of thermodynamic functions of fully ionized nonideal electron-ion plasma mixtures. In the regime of strong Coulomb coupling, we use our previously developed analytic approximations for the free energy of…
Monoclonal antibodies are among the most promising therapeutic agents in modern medicine, yet their formulation into high-concentration solutions for subcutaneous self-administration poses a major challenge. A key obstacle is the marked…
A simple extension of existing models for protein crystallisation is described, in which salt ions and charge neutrality are explicitly incorporated. This provides a straightforward explanation for the shape of protein crystallisation…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent…
We study the geometric particle-in-cell methods for an electrostatic hybrid plasma model. In this model, ions are described by the fully kinetic equations, electron density is determined by the Boltzmann relation, and space-charge effects…
The analysis of correlation energy of the simplest first approximation of a variational method for the intrashell states of two-electron atoms is the purpose of the present work. This method allows to divide energy of atom on Coulomb and…
The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
The coagulation enhancement factor due to electrostatic (Coulomb and polarization-induced) interaction between silicon nanoparticles was numerically computed for different nanoparticle sizes and charges in typical low-emperature…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant…
A new computational method is presented for study suspensions of charged soft particles undergoing fluctuating hydrodynamic and electrostatic interactions. The proposed model is appropriate for polymers, proteins and porous particles…
Equation of state for partially ionized carbon at temperatures T > ~ 10^5 K is calculated in a wide range of densities, using the method of free energy minimization in the framework of the chemical picture of plasmas. The free energy model…
Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition…
Liquid-liquid phase separation (LLPS) of protein solutions is governed by highly complex protein-protein interactions. Nevertheless, it has been suggested that based on the extended law of corresponding states (ELCS), as proposed for…
Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…
A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a BGK collision operator using the lattice Boltzmann method to simulate binary fluid…