Understanding Cu binding with DNA: A molecular dynamics study comparing Cu and Mg binding to the Dickerson DNA.

Cu ions led DNA damage by reactive oxygen species (ROS) is widely known biological phenomena. The ionic radii of Cu and Mg being similar, the binding of Cu ions to DNA is expected to be similar to that of the Mg ions. However, little is known how Cu ions bind in different parts (phosphate, major and minor grooves) of a double-strand (ds) DNA, especially at atomic level.

Three-body interaction of gold nanoparticles: the role of solvent density and ligand shell orientation.

Molecular dynamics simulations are used to study the effective interactions of alkanethiol passivated gold nanoparticles in supercritical ethane at two- and three-particle levels with different solvent densities. Effective interaction is calculated as the potential of mean force (PMF) between two nanoparticles, and the three-body effect is estimated as the difference in PMFs calculated at the two- and three-particle levels. The variation in the three-body effect is examined as a function of solvent density.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study.

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a β-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH, -CH, and -CF. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation.

Hydrophobic association and solvation of neopentane in urea, TMAO and urea-TMAO solutions.

A detailed knowledge of hydrophobic association and solvation is crucial for understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using molecular dynamics simulations, it is found that the hydrophobic association of neopentane molecules is greater in a mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, 4 M TMAO solution and neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water.

Understanding the binary interactions of noble metal and semiconductor nanoparticles.

Molecular dynamics simulations are used to study the solvation and effective pair interactions of Au (1.2 nm) and CdSe (2.2 nm) nanoparticles passivated with alkanethiol and alkylamine ligands, respectively, for two different chain lengths in vacuum and n-hexane at 300 K.

Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study.

A good understanding of the surface hydrophobicity of fluorinated materials is useful for their application as coating materials. The present study investigates the surface hydrophobicity of perfluoroalkyl acrylate (PFA) thin films using molecular dynamics simulations. Surface hydrophobicity is characterized by examining the contact angle of a water droplet on PFA surfaces and the cavity formation free energy in the vicinity of the surface.

Thiolated gold nanoparticle solvation in near-critical fluids: The role of density, temperature, and topology.

We employ molecular dynamics simulations to study the structure and solvation thermodynamics of thiolated gold nanoparticles of size 1.2 and 1.6 nm with ligand of chain length 8-16 carbons in ethane and propane over a wide range of densities close to the critical isotherm.

Effective interactions between nanoparticles: Creating temperature-independent solvation environments for self-assembly.

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I.

Fluctuation-driven anisotropy in effective pair interactions between nanoparticles: thiolated gold nanoparticles in ethane.

Fluctuations within the ligand shell of a nanoparticle give rise to a significant degree of anisotropy in effective pair interactions for low grafting densities [B. Bozorgui, D. Meng, S.

Relating structure, entropy, and energy of solvation of nanoscale solutes: application to gold nanoparticle dispersions.

Structural estimators for the entropy are combined with an analysis of the different contributions to the energy of solvation to understand the molecular basis of the thermodynamics of solvation of passivated nanoparticles. Molecular dynamics simulations of thiolated gold clusters in ethane are performed over a wide range of densities close to the critical isotherm. The entropic changes associated with solvent reorganization around the passivated nanoparticle are estimated from the nanoparticle-solvent pair correlation function, while the entropy of the ligand shell is estimated from the covariance in the positional fluctuations of the ligand atoms.