Related papers: Structural and dynamic properties of SPC/E water
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray…
Systems of Cooee bitumen and water up to 4 mass % are studied by molecular dynamics simula- tions. The cohesive energy density of the system is shown to decrease with an increasing water content. This decrease is due mainly to an increase…
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…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
In the last decades several hydrogen-bond definitions were proposed by classical computer simulations. Aiming at validating their self-consistency on a wide range of conditions, here we present a comparative study of six among the most…
Since the structural transformations observed in water-ethanol binary mixtures are apparently driven by relatively weak intermolecular forces (like hydrophobicity and hydrogen bonding) that often cooperate to form self assembled structures,…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
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…
Various condensed phases of water, spanning from the liquid state to multiple ice phases, have been systematically investigated under extreme conditions of pressure and temperature to delineate their stability boundaries. This study focuses…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
The steady-state homogeneous vapor-to-liquid nucleation and the succeeding liquid droplet growth process are studied for water system by means of the coarse-grained molecular dynamics simulations with the mW-model suggested originally in…
Molecular dynamics simulations have been performed on TIP4P/2005 supercooled water to investigate the molecular diffusion and shear viscosity at various timescales and assess the Stokes-Einstein (SE) and Stokes-Einstein-Debye (SED)…
In this work, we have carried out molecular dynamics (MD) simulation techniques to study the diffusion coefficient of interlayer molecules at different temperature. Within the wider context of water dynamics in soils, and with a particular…
We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk…
In the last decades a large effort has been devoted to the study of water confined in hydrophobic geometries at the nanoscale (tubes, slit pores), because of the multiple technological applications of such systems, ranging from drugs…
By employing first-principles metadynamics simulations, we explore the 300 K structures of solid hydrogen over the pressure range 150-300 GPa. At 200 GPa, we find the ambient-pressure disordered hexagonal close-packed (hcp) phase transited…
The object of this study is the kinetic process of solid-liquid first-order phase transition - melting of carbon dioxide CS-I hydrate with various cavity occupation ratios. The work was done within a framework of study on the local…
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…
We investigate how the transport properties of a united atoms fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the…