Related papers: Ion specific effects on phase transitions in prote…
We present the self-dynamics of protein amino acids of hydrated lysozyme powder around the physiological temperature by means of molecular dynamics (MD) simulations. The self-intermediate scattering functions (SISF) of the amino acid…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of…
In this study, molecular dynamic simulations are employed to investigate the nucleation of NaCl crystal in solutions. According to the simulations, the dissolved behaviors of NaCl in water are dependent on ion concentrations. With…
The solvation structures and ion dynamics of CaCl$_2$ aqueous electrolytes have been investigated using ab initio molecular dynamics simulations and molecular dynamics simulations with deep learning potentials. We found multiple solvation…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Ion channels orchestrate the communication between cells and their environment. These are special proteins capable of changing their shape to allow ions to pass through membranes in response to stimuli like membrane tension. As the letters…
It is theoretically shown that the excess liquid-liquid interfacial tension between two electrolyte solutions as a function of the ionic strength I behaves asymptotically as O(- I^0.5) for small I and as O(+- I) for large I. The former…
We have studied a model of a complex fluid consisting of particles interacting through a hard core and a short range attractive potential of both Yukawa and square-well form. Using a hybrid method, including a self-consistent and quite…
Hydrodynamic model simulations of Au-Au collisions at RHIC have indicated recently, that with improved simulations in the coming years, it may be feasible to quantify the viscosity of the matter produced in heavy ion collisions. To this…
The morphology and transport properties of thin films of the ionomer Nafion, with thicknesses on the order of the bulk cluster size, have been investigated as a model system to explain the anomalous behaviour of catalyst/electrode-polymer…
Recent discussions of RHIC data emphasized the exciting possibility that the matter produced in nucleus-nucleus collisions shows properties of a near-perfect fluid. Here, we aim at delineating the applicability of fluid dynamics, which is…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
Ions in water are important in biology, from molecules to organs. Classically, ions in water are treated as ideal noninteracting particles in a perfect gas. Excess free energy of ion was zero. Mathematics was not available to deal…
This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement between graphene sheets. By means of molecular dynamics simulations, an adsorption of water molecules…
The presence of a critical point in the QCD phase diagram can deform the trajectories describing the evolution of the expanding fireball in the QCD phase diagram. The deformation of the hydrodynamic trajectories will change the transverse…
At low temperatures proteins exist in a glassy state, a state which has no conformational flexibility and shows no biological functions. In a hydrated protein, at and above 220 K, this flexibility is restored and the protein is able to…
Antagonistic salts are composed of hydrophilic and hydrophobic ions. In a mixture solvent (water-oil) such ion pairs are preferentially attracted to water or oil, giving rise to a coupling between the charge density and the composition.…
Specifically, we examine concentrations from [NaCl]=1m to [NaCl]=6m, where 6.1m represents the solubility threshold of NaCl in H2O. For the water model, we employ the flexible TIP4P/$\epsilon_{Flex}$ model, which offers an enhanced…
In this tutorial we discuss the chemical potential of ions in water (i.e., in a salt solution, in an electrolyte phase) and inside (charged) nanoporous materials such as porous membranes. In water treatment, such membranes are often used to…