Related papers: Hydrophobic interactions and hydrogen bonds in \be…
Mesoscale water-hydrophobic interfaces are of fundamental importance in multiple disciplines, but their molecular properties have remained elusive for decades due to experimental complications and alternate theoretical explanations.…
A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
We present an analytical calculation of the hydrodynamic interaction between two spherical particles near an elastic interface such as a cell membrane. The theory predicts the frequency dependent self- and pair-mobilities accounting for the…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
We study, by Monte Carlo simulations, a coarse-grained model of a water monolayer between hydrophobic walls at partial hydration, with a wall-to-wall distance of about 0.5 nm. We analyze how the diffusion constant parallel to the walls,…
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and…
By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
The layers of graphene oxide (GO) are found to be good for permeation of water but not for helium (Science 2012 335 (6067): 442-444) suggesting that the GO layers are dynamic in the formation of permeation route depending on the environment…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
We present a model for the joint self-assembly of amphiphilic polymers and small amphiphilic molecules (surfactants) in a dilute aqueous solution. The polymer is assumed to consist of a hydrophilic backbone and a large number of hydrophobic…
Using extensive Molecular Dynamics simulations we study the behavior of polyelectrolytes with hydrophobic side chains, which are known to form cylindrical micelles in aqueous solution. We investigate the stability of such bundles with…
Polymer thin films exhibit pronounced interfacial mobility gradients that modify chain relaxation, yet how these gradients govern chain-scale dynamics across depth remains incompletely understood. Using molecular dynamics simulations of…
Based on our recent study on physical origin of hydrophobic effects, this is applied to investigate the dependence of hydrophobic interactions on the solute size. As two same hydrophobic solutes are dissolved into water, the hydration free…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…