Related papers: Effects of electrostatic interactions on ligand di…
We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within Density Functional Theory (DFT), with particular emphasis on linear-scaling (LS)…
We studied by X-ray reflectivity the behaviour of fully hydrated solid-supported lipid multilayers under the influence of a transverse electric field, under conditions routinely used in the electroformation process. The kinetics of sample…
The ion populations most frequently adopted for diagnostics in collisional plasmas are derived from the density independent, coronal approximation. In higher density, lower temperature conditions, ionisation rates are enhanced once…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
We have studied the electrostatic screening effect of NaCl solutions on the interactions between anionic lipid bilayers in the fluid lamellar phase using a Poisson-Boltzmann based mean-field approach with constant charge and constant…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
Elastic netwok models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the…
We calculate the ion distributions around an interface in fluid mixtures of highly polar and less polar fluids (water and oil) for two and three ion species. We take into account the solvation and image interactions between ions and…
Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using beta-peptide-inspired nano-rods, we…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
The electrostatic screening length predicted by Debye-H\"uckel theory decreases with increasing ionic strength, but recent experiments have found that the screening length can instead increase in concentrated electrolytes. This phenomenon,…
The influence of the chain degree of ionization on the adsorption of weak polyelectrolytes on neutral and on oppositely and likely charged surfaces is investigated for the first time, by means of Monte Carlo simulations with the mesoscopic…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the…
Ionic solids and melts are compounds in which the interactions are dominated by electrostatic effects. However, the polarization of the ions also plays an important role in many respects as has been clarified in recent years thanks to the…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
We use molecular dynamics simulations of the primitive model of electrolytes to study the ionic structure in aqueous monovalent electrolyte solutions confined by charged planar interfaces over a wide range of electrolyte concentration,…