Paul Stewart Crozier

Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics.

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125-A internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and extended simple point charge water. Channel and bath currents were computed from 10 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration dependent and superlinear at high concentrations.

Molecular dynamics calculations of the electrochemical properties of electrolyte systems between charged electrodes

We investigate the interfacial electrochemical properties of an aqueous electrolyte solution with discrete water molecules in slab geometry between charged atomistic electrodes. Long-range intermolecular Coulombic interactions are calculated using the particle–particle–particle–mesh method with a modification to account for the slab geometry. Density distribution profiles and potential drops across the double layer are given for 0, 0.25, and 1 M aqueous electrolyte solutions each at 0, ±0.1, ±0.2, and ±0.3 C/m2 electrode surface charges. Results are compared qualitatively with experimental x-ray scattering findings, other computer simulation results, and traditional electrochemistry theory. The interfacial fluid structure characteristics are generally in good qualitative agreement with the conclusions obtained in some integral equation theories and in the experimental x-ray study. The potential in the simulations shows an oscillatory behavior near the electrode, which theories that do not include the mole...

Comparison of charged sheets and corrected 3D Ewald calculations of long-range forces in slab geometry electrolyte systems with solvent molecules

Two methods of calculating long-range intermolecular potentials are compared for an approximately 3 M aqueous electrolyte solution confined between two charged surfaces. We investigate the ionic density profiles using the charged-sheets method and the corrected three-dimensional (3D) Ewald method at two different system sizes and also compare the Coulomb forces directly. The corrected 3D Ewald method is recommended for the calculation of long-range potentials in systems of this nature because it is less system size dependent than the charged-sheets method and the resultant forces are more consistent with periodic boundaries. However, the charged-sheets method for estimating long-range potentials in Coulombic systems may be useful for certain applications, and the corrected 3D Ewald method also shows some system size dependence.

Molecular-dynamics simulations of ion size effects on the fluid structure of aqueous electrolyte systems between charged model electrodes

The effect of ion size on the structure of aqueous electrolyte solutions between charged nonpolarizable surfaces or electrodes is investigated using molecular-dynamics simulations of discrete water molecules and ions confined to a slab geometry. Long-range intermolecular Coulombic interactions are calculated using the particle–particle–particle–mesh method with a modification to account for the slab geometry. Density distribution and potential profiles are reported for 1 M aqueous electrolyte solutions with ±0.1 C/m2 electrode surface charge at the electrode surfaces. Five different models for the ions are studied. The models can be characterized as (1) ions of equal size, (2) smaller cations, (3) larger anions, (4) smaller cations and larger anions, and (5) ions representing aqueous NaCl. Compared to the equal-size ion reference case, smaller cation size decreases the contact adsorption at the cathode, but interestingly anion size tends to moderate this effect somewhat. Whereas there is no contact adsorp...

Activity coefficient prediction by osmotic molecular dynamics

Abstract The osmotic molecular dynamics method (OMD) is used to calculate activity coefficients for vapour–liquid equilibria (VLE) and liquid–liquid equilibria (LLE) predictions. The previously reported OMD methodology is refined and applied to mixtures of polar, structured molecular fluids. Other computer simulation approaches to phase equilibria prediction are discussed briefly, and comparison to recent Gibbs Ensemble Monte Carlo (GEMC) results is made. OMD-predicted activity coefficients are compared to experimentally-measured activity coefficients for six industrially-significant binary mixtures (methanol/ n -hexane, n -hexane/ n -pentane, chloroform/acetone, chloroform/methanol, methanol/water, chloroform/ n- hexane). Molecular model inadequacies, especially cross-parameters between unlike molecules, are shown. A single cross-parameter for the acetone/chloroform binary is modified to produce good agreement with experimentally-measured activity coefficients. Also, OMD-derived LLE predictions are produced for the methanol/ n -hexane system and compared with experimentally-measured LLE data.

Permeation of ions through a model biological channel: effect of periodic boundary conditions and cell size

The effect of the simulation cell size and periodic boundary conditions on non-equilibrium molecular dynamics simulations of the structure and dynamics with explicit water molecules and ions in and near a model channel in a biological membrane is considered. The approach seems satisfactory. In particular, the presence of image channels that often contain image ions seems to have little effect on the average structure, channel content, or current for this system.

A corrected 3D Ewald calculation of the low effective temperature properties of the electrochemical interface

Abstract The corrected 3D Ewald method is used to verify charged sheets method results that show increasing double-layer capacitance with increasing temperature in the low effective temperature region. The restricted primitive model is used where ions are represented as charged hard spheres and the solvent is represented by a uniform dielectric constant. It is shown that the capacitance temperature plot for the test system exhibits increasing capacitance with increasing temperature in the low effective temperature region, which contradicts common theories of the electrochemical interface. For this system, the corrected 3D Ewald method results coincide well with the charged sheets method results.

Osmotic molecular dynamics simulation of vapor-liquid equilibria for propylene + dimethyl ether and nitroethane + propylene glycol monomethyl ether mixtures

In response to the First Industrial Fluid Simulation Challenge issued by the Computational Molecular Science and Engineering Forum (CoMSEF) of American Institute of Chemical Engineers (AIChE), we have performed osmotic molecular dynamics (OMD) simulations on model mixtures representing propylene + dimethyl ether and nitroethane + propylene glycol monomethyl ether (PGME) at each of two temperatures. The models are standard force-field models available in the literature for site–site interactions between heavy nuclei. Coulombic and Lennard–Jones (LJ) potentials are defined at each site and cross Lennard–Jones interactions are obtained from the Lorentz–Berthelot combining rules. OMD simulations yield the activity coefficients for each component in the mixture at the specified composition. However, because values of individual activity coefficients are less accurate for smaller mole fractions, when the composition difference across the membrane is large, we have chosen to impose thermodynamic consistency to smooth the data over the whole composition range. This is done by fitting simulated values of both activity coefficients simultaneously to the Wilson activity coefficient correlation. Pxy diagrams and data are then reported at the desired compositions for both systems at two different temperatures using the smoothed activity coefficients.

Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations

Several extensions and improvements have been made to the multilevel summation method (MSM) of computing long-range electrostatic interactions. These include pressure calculation, an improved error estimator, faster direct part calculation, extension to non-orthogonal (triclinic) systems, and parallelization using the domain decomposition method. MSM also allows fully non-periodic long-range electrostatics calculations which are not possible using traditional Ewald-based methods. In spite of these significant improvements to the MSM algorithm, the particle-particle particle-mesh (PPPM) method was still found to be faster for the periodic systems we tested on a single processor. However, the fast Fourier transforms (FFTs) that PPPM relies on represent a major scaling bottleneck for the method when running on many cores (because the many-to-many communication pattern of the FFT becomes expensive) and MSM scales better than PPPM when using a large core count for two test problems on Sandias Redsky machine. This FFT bottleneck can be reduced by running PPPM on only a subset of the total processors. MSM is most competitive for relatively low accuracy calculations. On Sandias Chama machine, however, PPPM is found to scale better than MSM for all core counts that we tested. These results suggest that PPPM is usually more efficient than MSM for typical problems running on current high performance computers. However, further improvements to MSM algorithm could increase its competitiveness for calculation of long-range electrostatic interactions.

Substructured multibody molecular dynamics.

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.