Related papers: Physical origin underlying the entropy loss upon h…
We apply a hybrid Molecular Dynamics and mesoscopic simulation technique to study the steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.08 to 12. Hydrodynamic back-flow causes a reduction of the…
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total…
The physics of air-water interfaces plays a central role in modern theories of the hydrophobic effect. Implementing these theories, however, has been hampered by the difficulty of addressing fluctuations in the shape of such soft…
Thermodynamics tells us to expect underwater contact between two hydrophobic surfaces to result in stronger adhesion compared to two hydrophilic surfaces. However, presence of water changes not only energetics, but also the dynamic process…
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,…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
We examine correlations of energy density induced by initial state fluctuations, which are localized in both transverse and longitudinal extent. The hotspots are evolved according to hydrodynamics in a background which includes radial flow.…
Effect of ionic solute on a near-critical binary aqueous mixture confined between charged walls with different adsorption preferences is considered within a simple density functional theory. For the near-critical system containing small…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
We show that macroscopic irreversible thermodynamics for viscous fluids can be derived from exact information-theoretic thermodynamic identities valid at the microscale. Entropy production, in particular, is a measure of the loss of…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
We argue that the entropy of a black hole is due to the entanglement of matter fields and gravitons across the horizon. While the entanglement entropy of the vacuum is divergent because of UV correlations, we show that low-energy…
We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and…
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
Two interaction mechanisms of particles in a fluid are proposed on base of forces, mediated by hydrodynamic thermal fluctuations. The first one is similar to the conventional van der Waals interaction, but instead of been mediated by…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
Several hydrodynamic models the atomic Bose-Einstein condensate beyond the mean-field approximation are discussed together from one point of view. All these models are derived from microscopic quantum description. The derivation is made…