Related papers: Simultaneous identification of multiple binding si…
In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water…
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
Hydrogen bonding plays a crucial role in biology and technology, yet it remains poorly understood and quantified despite its fundamental importance. Traditional models, which describe hydrogen bonds as electrostatic interactions between…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…
We demonstrate for the first time a tight binding model for water incorporating polarizable anions. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Based on recent studies on hydrophobic interactions, it is devoted to investigate the directional nature of hydrophobic interactions. It means that the hydrophobic interactions are dependent on the relative orientations as the solutes tend…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins. The effective dielectric constant of the solvated protein, representing the average dipole moment induced at the protein by a…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
The behaviour and stability of soft and biological matter depend significantly on electrostatic interactions, as particles such as proteins and colloids acquire a charge when dispersed in an electrolytic solution. A typical simplification…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…