Related papers: How hydrophobic drying forces impact the kinetics …
We investigate the impact of water fluctuations on the key-lock association kinetics of a hydrophobic ligand (key) binding to a hydrophobic pocket (lock) by means of a minimalistic stochastic model system. It describes the collective…
Solvent plays an important role in the relative motion of nanoscopic bodies, and the study of such phenomena can help elucidate the mechanism of hydrophobic assembly, as well as the influence of solvent-mediated effects on in vivo motion in…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
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…
We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
Solvent often manifests itself as the key determinant of the kinetic aspect of molecular recognition process. While the solvent is often depicted as a source of barrier in the ligand recognition process by polar cavity, the nature of…
Clarifying the factors that control the contact angle of a liquid on a solid substrate is a long-standing scientific problem pertinent across physics, chemistry and materials science. Progress has been hampered by the lack of a…
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…
Ligand unbinding is mediated by the free energy change, which has intertwined contributions from both energy and entropy. It is important but not easy to quantify their individual contributions. We model hydrophobic ligand unbinding for two…
Drops deposited on rough and hydrophobic surfaces can stay suspended with gas pockets underneath the liquid, then showing very low hydrodynamic resistance. When this superhydrophobic state breaks down, the subsequent wetting process can…
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…
Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
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…
Based on recent studies on hydrophobic interactions, it is devoted to investigate the directional nature of hydrophobic interactions. It means that the hydrophobic interactions are dependent on the relative orientations as the solutes tend…
Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…
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 present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…