Related papers: Hydration Mimicry by Membrane Ion Channels
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…
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…
The finely tuned structures of membrane channels allow selective passage of ions through the available aqueous pores. In order to understand channel function, it is crucial to locate the pore and study its physical and chemical properties.…
We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and…
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…
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
Anion hydration is complicated by H-bond donation between neighboring water molecules in addition to H-bond donation to the anion. This situation can lead to competing structures for chemically simple clusters like (H$_2$O)$_n$Cl$^-$ and to…
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,…
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each…
Hydrophobic solid-water interfaces underpin processes in nanofluidics, electrochemistry, and energy technologies. Microscopic insights into these systems are often inferred from our understanding of the air-water interface, which is assumed…
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the…
Polymer materials with low water uptake exhibit a highly heterogeneous interior, characterized by water clusters in the form of nanodroplets and nanochannels. Here, based on our recent insights from computer simulations, we argue that water…
Partitioning and transport of water and small solutes into and through nanopores is important to a variety of chemical and biological processes and applications. Here we study the partitioning of positive ions of increasing size into the…
The HO$^-$(aq) ion participates in myriad aqueous phase chemical processes of biological and chemical interest. A molecularly valid description of its hydration state, currently poorly understood, is a natural prerequisite to modeling…
The structure of ionic adsorption layers is studied via a proper thermodynamic treatment of the electrostatic and non-electrostatic interactions between the surfactant ions as well as of the effect of thermodynamic non-locality. The…
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as solid-liquid interfaces. Here, we present a machine learning…
The permeation, rejection, and transport of electrolytes in water-filled nanopores are critical to ion current gating and desalinalion processes in synthetic porous membranes and the functions of biological ion channels. Mile the effects of…