Related papers: More than one dynamic crossover in protein hydrati…
Ionic liquids (ILs) gain much interest as possible electrolytes in the next generation of mixed-solid Li-ion batteries. However, such properties of ionic liquids as melting transition, diffusion, strength and structure of hydrogen bond…
When the hydration shell of a protein is filled with at least 0.6 gram of water per gram of protein, a significant anti-correlation between the vibrational free energy and the potential energy of energy-minimized conformers is observed.…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
Understanding how soft matter systems, including biological ones, can develop collective electromagnetic phenomena under external fields at ambient conditions remains a central challenge, as thermal fluctuations are generally expected to…
The study of protein functions attributed to the conformation and fluctuation that are ruled by both the amino acid sequence and thermodynamics, requires thermodynamic quantities given by calorimetry using thermometric techniques. The…
When water molecules are confined to nanoscale spacings, such as in the nanometer size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures ($\sim$ 150 K), leading to a metastable liquid…
The dynamics of the structured water molecules in the hydration shell of the DNA double helix is of paramount importance for the understanding of many biological mechanisms. In particular, the vibrational dynamics of a water spine that is…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant…
The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the…
The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin…
The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\,\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\,\,The conventional model of H-bonds as…
Water freezing is ubiquitous on Earth, affecting many areas from biology to climate science and aviation technology. Probing the atomic structure in the homogeneous ice nucleation process from scratch is of great value but still…
The thermodynamics of hydration changes gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as…
In this work a series of analyses are performed on ab initio molecular dynamics (AIMD) simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and <span>rattling</span> events, and…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
We performed molecular dynamics simulations to investigate the viscoelastic properties of aqueous protein solutions containing an antifreeze protein, a toxin protein, and bovine serum albumin. These simulations covered a temperature range…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to…
Understanding the pressure-dependent dielectric properties of water is crucial for a wide range of scientific and practical applications. In this study, we employ a deep neural network trained on density functional theory data to…