Related papers: Electrostatic interactions in concentrated protein…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
Ion partitioning between different compartments (\emph{e.g.} a porous material and a bulk solution reservoir), known as Donnan equilibrium, plays a fundamental role in various contexts such as energy, environment, or water treatment. The…
The interaction between charged bodies in an ionic solution is a general problem in colloid physics and becomes a central topic in the study of biological systems where the electrostatic interaction between proteins, nucleic acids,…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
We investigate theoretically the fluid-crystal coexistence of solutions of globular charged nanoparticles like proteins and inorganic colloids. The thermodynamic properties of the fluid phase are computed via the optimized Baxter model.…
The dependence of the lower critical solution temperature (LCST) of charged, thermosensitive copolymers on their charge fraction and the salt concentration is investigated by employing systematic cloud-point experiments and analytical…
A variational approach is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing monomer-monomer force constants…
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) or lysozyme with linear…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
In order to find the exact form of the electrostatic interaction between two proteins with dissociable charge groups in aqueous solution, we have studied a model system composed of two macroscopic surfaces with charge dissociation sites…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
The effective Coulomb interaction between globular proteins is calculated as a function of monovalent salt concentration $c_s$, by explicit Molecular Dynamics simulations of pairs of model proteins in the presence of microscopic co and…
In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…
A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
In this thesis we study the lateral electrostatic interaction between a pair of non-identical, moderately charged colloidal particles trapped at an electrolyte interface in the limit of short inter-particle separations. Using a simplified…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
In this paper, we present an analytical solution to nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…