Modeling of flow and transport in environmental systems often involves formulation of conservation equations at spatial scales involving tens to hundreds of pore diameters in porous media or the depth of flow in a channel. Quantities such as density, temperature, internal energy, and velocity may not be uniform over these macroscopic length scales. The external gravitational potential causes gr...

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations ...

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. ...

The effect of impurities on quantum chemical parameters of single-walled nanotubes (SWNTs) was studied using density functional theory (DFT). The density of states (DOS), Fermi energy and thermodynamic energies of (5,5) carbon nanotubes were calculated in the presence of nitrogen impurity. It was found that this nanotube remains metallic after being doped with one nitrogen atom. The partial den...

Applications of molecular simulations targeted at the estimation of free energies are reviewed, with a glimpse into their promising future. The methodological milestones paving the road of free energy calculations are summarized, in particular free energy perturbation and thermodynamic integration, in the framework of constrained or unconstrained molecular dynamics. The continuing difficulties ...