Related papers: Solvent fluctuations induce non-Markovian kinetics…
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…
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
Using explicit-water molecular dynamics (MD) simulations of a generic pocket-ligand model we investigate how chemical and shape anisotropy of small ligands influences the affinities, kinetic rates and pathways for their association to…
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…
Hypothesis: The collective dynamics and self-assembly of colloids floating at a fluid/fluid interface is a balance between deterministic lateral interaction forces, viscous resistance to colloid motion along the surface and thermal…
The dynamics of adhesion of a spherical micro-particle to a ligand-coated wall, in shear flow, is studied using a Langevin equation that accounts for thermal fluctuations, hydrodynamic interactions and adhesive interactions. Contrary to the…
As a common view the hydrophobic association between molecular-scale binding partners is supposed to be dominantly driven by entropy. Recent calorimetric experiments and computer simulations heavily challenge this established paradigm by…
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Electrolyte solutions play an important role in energy storage devices, whose performance highly relies on the electrokinetic processes at sub-micron scales.\ Although fluctuations and stochastic features become more critical at small…
The fluctuation-dissipation theory is grounded on the Langevin condition expressing the local independence between the thermal force and the particle velocity history. Upon hydrodynamic grounds, it is reasonable to relax this condition in…
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…
The aversion of hydrophobic solutes for water drives diverse interactions and assemblies across materials science, biology and beyond. % Here, we review the theoretical, computational and experimental developments which underpin a…
In microscopic mechanical systems interactions between elastic structures are often mediated by the hydrodynamics of a solvent fluid. At microscopic scales the elastic structures are also subject to thermal fluctuations. Stochastic…
Contact between fluctuating, fluid-lubricated soft surfaces is prevalent in engineering and biological systems, a process starting with adhesive contact, which can give rise to complex coarsening dynamics. One representation of such a…
We investigate the dynamics of elastic microstructures within a fluid that are subjected to thermal fluctuations. We perform analysis to obtain systematically simplified descriptions of the mechanics in the limiting regimes when (i) the…
Liquid crystalline media mediate interactions between suspended particles and confining geometries, which not only has potential to guide patterning and bottom-up colloidal assembly, but can also control colloidal migration in microfluidic…
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…
The fluctuations of ions in polar solvents remain poorly understood theoretically due to the complex coupling between ionic motion and solvent polarization. Indeed, while all-atom resolution can be achieved in numerical simulations,…
Fluctuation-response relations must be modified to describe nonequilibrium systems with non-Markovian dynamics. Here, we experimentally demonstrate that such relation is quantitatively recovered when the appropriate Markovian embedding of…