Related papers: The role of water in host-guest interaction

As the most important solvent, water has been at the center of interest since the advent of computer simulations. While early molecular dynamics and Monte Carlo simulations had to make use of simple model potentials to describe the atomic…

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…

The long timescale associated with ligand residence times renders their computation challenging. Therefore, the influence of factors like solvation and steric hindrance on residence times are not fully understood. Here, we demonstrate in a…

Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…

The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…

Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…

Four scenarios have been proposed for the low--temperature phase behavior of liquid water, each predicting different thermodynamics. The physical mechanism which leads to each is debated. Moreover, it is still unclear which of the scenarios…

The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a…

Ab initio molecular dynamics simulations of liquid water under equilibrium ambient conditions, together with a novel energy decomposition analysis, have recently shown that a substantial fraction of water molecules exhibit a significant…

Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…

The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…

At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on…

While the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of…

The use of computer simulations to study the properties of aqueous systems is, today more than ever, an active area of research. In this context, during the last decade there has been a tremendous growth in the use of data-driven approaches…

Oxide-water interfaces govern a wide range of physical and chemical processes fundamental to many fields like catalysis, geochemistry, corrosion, electrochemistry, and sensor technology. Near solid oxide surfaces, water behaves differently…

A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly…

Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…

It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Classical molecular simulation and statistical mechanics methods typically assume pairwise…

Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…