Electrokinetic flow of an aqueous electrolyte in amorphous silica nanotubes.

We study the pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models. Different pressures, electrolyte concentrations and pore sizes are examined. Our results indicate a flow that deviates considerably from the predictions of Poiseuille fluid mechanics.

The docking of chiral analytes on proline-based chiral stationary phases: A molecular dynamics study of selectivity.

Molecular dynamics simulations are employed to examine the selectivity of four proline-based chiral stationary phases in two solvent environments, a relatively apolar n-hexane/2-propanol solvent and a polar water/methanol solvent. The four chiral surfaces are based on a BOC-terminated diproline, a TMA-terminated diproline, a TMA-terminated triproline and a TMA-terminated hexaproline. This range of chiral selectors allows an analysis of the impact of oligomer length and terminal group on selectivity while the two solvent environments indicate the impact of solvent hydrogen bonding and polarity.

The photoexcitation of crystalline ice and amorphous solid water: A molecular dynamics study of outcomes at 11 K and 125 K.

Photoexcitation of crystalline ice Ih and amorphous solid water at 7-9 eV is examined using molecular dynamics simulations and a fully flexible water model. The probabilities of photofragment desorption, trapping, and recombination are examined for crystalline ice at 11 K and at 125 K and for amorphous solid water at 11 K. For 11 K crystalline ice, a fully rigid water model is also employed for comparison.

Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals.

A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed.

Poly-proline-based chiral stationary phases: a molecular dynamics study of triproline, tetraproline, pentaproline and hexaproline interfaces.

Poly-proline chains and derivatives have been recently examined as the basis for new chiral stationary phases in high performance liquid chromatography. The selectivity of poly-proline has been measured for peptides with up to ten proline units. In this article, we employ molecular dynamics simulations to examine the interfacial structure and solvation of surface-bound poly-proline chiral selectors.