Related papers: Temperature-dependent mechanisms for the dynamics …
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
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…
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions…
An open question is whether the liquid and glassy phases of water are thermodynamically distinct or continuous. Here we address this question using molecular dynamics simulations in comparison with neutron scattering experiments to study…
We propose a computational strategy to quantify the temperature evolution of the timescales and lengthscales over which dynamic facilitation affects the relaxation dynamics of glass-forming liquids at low temperatures, that requires no…
The ultraviolet (UV) photodissociation of amorphous water ice at different ice temperatures is investigated using molecular dynamics (MD) simulations and analytical potentials. Previous MD calculations of UV photodissociation of amorphous…
We explored the composition dependence of a rather comprehensive set of properties of liquid water-ethanol mixtures by using the isobaric-isothermal molecular dynamics computer simulations. The united atom non-polarizable model from the…
We use large-scale molecular dynamics simulations to study the kinetics of the liquid-gas phase separation if the temperature is lowered across the glass transition of the dense phase. We observe a gradual change from phase separated…
Using molecular dynamics simulations, we study the slow dynamics of supercooled liquids confined in a random matrix of immobile obstacles. We study the dynamical crossover from glass-like to Lorentz-gas-like behavior in terms of the density…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
While deeply supercooled liquids exhibit divergent viscosity and increasingly heterogeneous dynamics as the temperature drops, their structure shows only seemingly marginal changes. Understanding the nature of relaxation processes in this…
We develop an approach to liquid thermodynamics based on collective modes. We perform extensive molecular dynamics simulations of noble, molecular and metallic liquids and provide the direct evidence that liquid energy and specific heat are…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $\delta t$ for integrating the equations of motion. Thus $\delta t = 2$ fs is often used in…
Molecular dynamics simulations with separate thermostats for rotational and translational motions were used to study the effects of these degrees of freedom on the structure of water at a fixed density. To describe water molecules, we used…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…