Ahmed E. Ismail

Capillary waves at the liquid-vapor interface and the surface tension of water

Capillary waves occurring at the liquid-vapor interface of water are studied using molecular dynamics simulations. In addition, the surface tension, determined thermodynamically from the difference in the normal and tangential pressure at the liquid-vapor interface, is compared for a number of standard three- and four-point water models. We study four three-point models (SPC/E, TIP3P, TIP3P-CHARMM, and TIP3P-Ew) and two four-point models (TIP4P and TIP4P-Ew). All of the models examined underestimate the surface tension; the TIP4P-Ew model comes closest to reproducing the experimental data. The surface tension can also be determined from the amplitude of capillary waves at the liquid-vapor interface by varying the surface area of the interface. The surface tensions determined from the amplitude of the logarithmic divergence of the capillary interfacial width and from the traditional thermodynamic method agree only if the density profile is fitted to an error function instead of a hyperbolic tangent function.

Observed mechanism for the breakup of small bundles of cellulose Iα and Iβ in ionic liquids from molecular dynamics simulations.

Explicit, all-atom molecular dynamics simulations are used to study the breakup of small bundles of cellulose Iα and Iβ in the ionic liquids [BMIM]Cl, [EMIM]Ac, and [DMIM]DMP. In all cases, significant breakup of the bundles is observed with the initial breakup following a common underlying mechanism. Anions bind strongly to the hydroxyl groups of the exterior strands of the bundle, forming negatively charged complexes. Binding also weakens the intrastrand hydrogen bonds present in the cellulose strands, providing greater strand flexibility. Cations then intercalate between the individual strands, likely due to charge imbalances, providing the bulk to push the individual moieties apart and initiating the separation. The peeling of an individual strand from the main bundle is observed in [EMIM]Ac with an analysis of its hydrogen bonds with other strands showing that the chain detaches glucan by glucan from the main bundle in discrete, rapid events. Further analysis shows that the intrastrand hydrogen bonds of each glucan tend to break for a sustained period of time before the interstrand hydrogen bonds break and strand detachment occurs. Examination of similar nonpeeling strands shows that, without this intrastrand hydrogen bond breakage, the structural rigidity of the individual unit can hinder its peeling despite interstrand hydrogen bond breakage.

Effects of Water Concentration on the Structural and Diffusion Properties of Imidazolium-Based Ionic Liquid–Water Mixtures

We have used molecular dynamics simulations to study the properties of three ionic liquid (IL)-water systems: 1-butyl-3-methylimidazolium chloride ([bmim]Cl), 1-ethyl-3-methylimidazolium acetate ([emim][Ac]), and 1,3-dimethylimidazolium dimethylphosphate ([dmim][DMP]). We observe the transition of those mixtures from pure IL to aqueous solution by analyzing the changes in important bulk properties (density) and structural and bonding properties (radial distribution functions, water clustering, hydrogen bonding, and cationic stacking) as well as dynamical properties (diffusion coefficients) at 12 different concentration samplings of each mixture, ranging from 0.0 to 99.95 mol % water. Our simulations revealed across all of the different structural, bonding, and dynamical properties major structural changes consistent with a transition from IL-water mixture to aqueous solution in all three ILs at water concentrations around 75 mol %. Among the structural changes observed were rapid increase in the frequency of hydrogen bonds, both water-water and water-anion. Similarly, at these critical concentrations, the water clusters formed begin to span the entire simulation box, rather than existing as isolated networks of molecules. At the same time, there is a sudden decrease in cationic stacking at the transition point, followed by a rapid increase near 90 mol % water. Finally, the diffusion coefficients of individual cations and anions show a rapid transition from rates consistent with diffusion in ILs to rates consistent with diffusion in water beginning at 75 mol % water. The location of this transition is consistent, for [bmim]Cl and [dmim][DMP], with the water concentration limit above which the ILs are unable to dissolve cellulose.

Multiresolution analysis in statistical mechanics. I. Using wavelets to calculate thermodynamic properties

The wavelet transform, a family of orthonormal bases, is introduced as a technique for performing multiresolution analysis in statistical mechanics. The wavelet transform is a hierarchical technique designed to separate data sets into sets representing local averages and local differences. Although one-to-one transformations of data sets are possible, the advantage of the wavelet transform is as an approximation scheme for the efficient calculation of thermodynamic and ensemble properties. Even under the most drastic of approximations, the resulting errors in the values obtained for average absolute magnetization, free energy, and heat capacity are on the order of 10%, with a corresponding computational efficiency gain of two orders of magnitude for a system such as a 4×4 Ising lattice. In addition, the errors in the results tend toward zero in the neighborhood of fixed points, as determined by renormalization group theory.

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation of these contributions, we have implemented a particle-particle particle-mesh Ewald solver for dispersion (r(-6)) interactions into the LAMMPS molecular dynamics package. We demonstrate that the solvers O(N log N) scaling behavior allows its application to large-scale simulations. We carefully determine a set of parameters for the solver that provides accurate results and efficient computation. We perform a series of simulations with Lennard-Jones particles, SPC/E water, and hexane to show that with our choice of parameters the dependence of physical results on the chosen cutoff radius is removed. Physical results and computation time of these simulations are compared to results obtained using either a plain cutoff or a traditional Ewald sum for dispersion.

The role of the cation in the solvation of cellulose by imidazolium-based ionic liquids.

We present a systematic molecular dynamics study examining the roles of the individual ions of different alkylimidazolium-based ionic liquids in the solvation of cellulose. We examine combinations of chloride, acetate, and dimethylphosphate anions paired with cations of increasing tail length to elucidate the precise role of the cation in solvating cellulose. In all cases we find that the cation interacts with the nonpolar domains of cellulose through dispersion interactions, while interacting electrostatically with the anions bound at the polar domains of cellulose. Furthermore, the structure and dimensions of the imidazolium head facilitate the formation of large chains and networks of alternating cations and anions that form a patchwork, satisfying both the polar and nonpolar domains of cellulose. A subtle implication of increasing tail length is the dilution of the anion concentration in the bulk and at the cellulose surface. We show how this decreased concentration of anions in the bulk affects hydrogen bond formation with cellulose and how rearrangements from single hydrogen bonds to multiple shared hydrogen bonds can moderate the loss in overall hydrogen bond numbers. Additionally, for the tail lengths examined in this study we observe only a very minor effect of tail length on the solvation structure and overall interaction energies.

Multiresolution analysis in statistical mechanics. II. The wavelet transform as a basis for Monte Carlo simulations on lattices

In this paper, we extend our analysis of lattice systems using the wavelet transform to systems for which exact enumeration is impractical. For such systems, we illustrate a wavelet-accelerated Monte Carlo (WAMC) algorithm, which hierarchically coarse-grains a lattice model by computing the probability distribution for successively larger block spins. We demonstrate that although the method perturbs the system by changing its Hamiltonian and by allowing block spins to take on values not permitted for individual spins, the results obtained agree with the analytical results in the preceding paper, and “converge” to exact results obtained in the absence of coarse-graining. Additionally, we show that the decorrelation time for the WAMC is no worse than that of Metropolis Monte Carlo (MMC), and that scaling laws can be constructed from data performed in several short simulations to estimate the results that would be obtained from the original simulation. Although the algorithm is not asymptotically faster than traditional MMC, the new algorithm executes several orders of magnitude faster than a full simulation of the original problem because of its hierarchical design. Consequently, the new method allows for rapid analysis of a phase diagram, allowing computational time to be focused on regions near phase transitions.

Forces between functionalized silica nanoparticles in solution.

To prevent the flocculation and phase separation of nanoparticles in solution, nanoparticles are often functionalized with short chain surfactants. Here we present fully atomistic molecular dynamics simulations which characterize how these functional coatings affect the interactions between nanoparticles and with the surrounding solvent. For 5-nm-diameter silica nanoparticles coated with poly(ethylene oxide) (PEO) oligomers in water, we determined the hydrodynamic drag on two approaching nanoparticles moving through solvent and on a single nanoparticle as it approaches a planar surface. In most circumstances, macroscale fluid theory accurately predicts the drag on these nanoscale particles. Good agreement is seen with Brenners analytical solutions for wall separations larger than the soft nanoparticle radius. For two approaching coated nanoparticles, the solvent-mediated (velocity independent) and lubrication (velocity-dependent) forces are purely repulsive and do not exhibit force oscillations that are typical of uncoated rigid spheres.

Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations

We provide a methodology for deducing quantitative reaction models from reactive molecular dynamics simulations by identifying, quantifying, and evaluating elementary reactions of classical trajectories. Simulations of the inception stage of methane oxidation are used to demonstrate our methodology. The agreement of pathways and rates with available literature data reveals the potential of reactive molecular dynamics studies for developing quantitative reaction models.

Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.

Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al., J. Chem. Phys., 2012, 137, 174107] can actually often be faster than truncating dispersion interactions. In addition, because all long-range dispersion interactions are incorporated, physical inaccuracies that arise from truncating the potential can be avoided. Simulations using PPPM or other mesh Ewald solvers for dispersion can provide results more accurately and more efficiently than simulations that truncate dispersion interactions. The use of mesh-based approaches for dispersion is now a viable alternative for all simulations containing dispersion interactions and not merely those where inhomogeneities were motivating factors for their use. We provide a set of parameters for the dispersion PPPM method using either ik or analytic differentiation that we recommend for future use and demonstrate increased simulation efficiency by using the long-range dispersion solver in a series of performance tests on massively parallel computers.