Related papers: Hydrophobic interactions and hydrogen bonds in \be…
We investigate the solvation of methane and methane decorated with charges in spherically confined water droplets. Free energy profiles for a single methane molecule in droplets, ranging in diameter D, from 1 to 4 nm, show that the droplet…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
In this paper, we first develop a mathematical model for long-range, hydrophobic attraction between amphiphilic particles. The non-pairwise interactions follow from the first variation of a hydrophobic attraction domain functional. The…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
We perform systematic molecular dynamics simulations of water confined between two nanoscale plates at T=300 K. We investigate the effect of pressure (-0.15 GPa <= P <= 0.2 GPa) and plate separation (0.4 nm <= d <= 1.6 nm) on the phase…
The interaction of interfacial water with graphitic carbon at the atomic scale is studied as a function of the hydrophobicity of epitaxial graphene. High resolution X-ray reflectivity shows that the graphene-water contact angle is…
Using the molecular dynamics method, dynamics of hydrogen bond (HB) networks emerging on the surface of a graphene sheet during its functionalization with hydroxyl groups OH are simulated. It is demonstrated that two OH groups form an…
Heat transfer at the liquid/solid interface, especially at the nanoscale, has enormous importance in nanofluids. This study investigates liquid/solid interfacial thermal resistance and structure of the formed molecular nanolayer around a…
The formation of amyloid fibrils comprising amyloid $\beta$ (A$\beta$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$\beta$ structure at the fibril end using the density…
Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
We directly measured the interactions between a hydrophobic solid and a hydrophobic liquid separated by water using force spectroscopy, where colloidal probes were coated with graphene oxide (GO) to interact with immobilized heptane…
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…
Buckling induced by viscous flow changes the shape of sheet-like nanomaterial particles suspended in liquids. This instability at the particle scale affects collective behavior of suspension flows and has many technological and biological…
The self-assembly of proteins into $\beta$-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte Carlo lattice simulations. The affinity of monomer $i$ for water is characterized by a (scalar) charge $\lambda_{i}$, and the monomer-water interaction is…
Hydrogel consists of a crosslinked polymer matrix imbibed with a solvent such as water at volume fractions that can exceed 90\%. They are important in many scientific and engineering applications due to their tunable physiochemical…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…