Related papers: Potential for modulation of the hydrophobic effect…
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…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
Using molecular dynamics simulations we study the dynamics of a water-like TIP5P model of water in hydrophilic and hydrophobic confinement. We find that in case of extreme nanocofinement such that there is only one molecular layer of water…
The phase behavior of hydrocarbon fluids confined in porous media has been reported to deviate significantly from that in the bulk environment due to the existence of sub-10nm pores. Though experiments and simulations have measured the…
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…
We study the effect of spatial confinement on the strength of propulsive diffusiophoretic forces acting on a particle that generates density gradients by exploiting the chemical free energy of its environment. Using a recently proposed…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
Understanding the phase behaviors of nanoconfined water has driven notable research interests recently. In this work, we examine the structures and thermodynamics of water encapsulated under a graphene cover. We find layered water…
We introduce and study the behavior of a tethered membrane of non-zero thickness embedded in three dimensions subject to an effective self-attraction induced by hydrophobicity arising from the tendency to minimize the area exposed to a…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
We study hydrodynamic slowing-down of a particle moving in a temperature gradient perpendicular to a wall. At distances much smaller than the particle radius, $h\ll a$, lubrication approximation leads to the reduced velocity…
Confinement can modify the dynamics, the thermodynamics and the structural properties of liquid water, the prototypical anomalous liquid. By considering a general anomalous liquid, suitable for globular proteins, colloids or liquid metals,…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…
The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
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…
Geometric confinement plays an important role in the dynamics of natural and synthetic microswimmers from bacterial cells to self-propelled particles in high-throughput microfluidic devices. However, little is known about the effects of…
This study investigates the interplay between Strong Coupling (SC) attraction and hydration repulsion in nanoconfined water between like-charged phospholipid layers. It challenges the assumption that SC attraction requires multivalent…
Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…