Salting out the polar polymorph: analysis by alchemical solvent transformation.

We computationally examine how adding NaCl to an aqueous solution with α- and γ-glycine nuclei alters the structure and interfacial energy of the nuclei. The polar γ-glycine nucleus in pure aqueous solution develops a melted layer of amorphous glycine around the nucleus. When NaCl is added, a double layer is formed that stabilizes the polar glycine polymorph and eliminates the surface melted layer.

Size-Dependent Surface Free Energy and Tolman-Corrected Droplet Nucleation of TIP4P/2005 Water.

Classical nucleation theory is notoriously inaccurate when using the macroscopic surface free energy for a planar interface. We examine the size dependence of the surface free energy for TIP4P/2005 water nanodroplets (radii ranging from 0.7 to 1.

Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine.

Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge.

Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation.

In the high friction limit of Kramers' theory, the diffusion coefficient for motion along the reaction coordinate is a crucial parameter in determining reaction rates from mean first passage times. The Einstein relation between mean squared displacement, time, and diffusivity is inaccurate at short times because of ballistic motion and inaccurate at long times because trajectories drift away from maxima in the potential of mean force. Starting from the Smoluchowski equation for a downward parabolic barrier, we show how drift induced by the potential of mean force can be included in estimating the diffusivity.

Nucleation in a Potts lattice gas model of crystallization from solution.

Nucleation from solution is important in many pharmaceutical crystallization, biomineralization, material synthesis, and self-assembly processes. Simulation methodology has progressed rapidly for studies of nucleation in pure component and implicit solvent systems; however little progress has been made in the simulation of explicit solvent systems. The impasse stems from the inability of rare events simulation methodology to be combined with simulation techniques which maintain a constant chemical potential driving force (supersaturation) for nucleation.

Nonequilibrium accumulation of surface species and triboelectric charging in single component particulate systems.

Triboelectric charging occurs in granular systems composed of chemically identical particles even though there is no apparent driving force for charge transfer. We show that such charging can result from nonequilibrium dynamics in which collision-induced electron transfer generates electron accumulation on a particle-size-dependent subset of the system. This idea rationalizes experimental results that suggest that smaller particles charge negatively while the large ones charge positively.

Molecular dynamics investigation of the effects of a water surface on the aggregation of bent-core molecules.

Molecular dynamics simulations are used to determine how the presence of a water surface affects the way that bent-core surfactant molecules interact with one another. The simulations are carried out for isolated pairs of bent-core molecules, and for pairs of bent-core molecules on a water surface. The results show that the water surface fundamentally alters the nature of the interaction between the bent-core molecules: a stable complex is formed when the two molecules are on the water surface, but not for an isolated pair of molecules.

Shear-induced crystallization in jammed systems.

Simulations are used to address the effects of oscillating shear strain on jammed systems composed of spherical particles. The simulations show that shear oscillations with amplitudes of more than a few percent lead to substantial crystallization of the system. To ensure that the conclusions are independent of the simulation methodology, a range of simulations are carried out that use both molecular dynamics and athermal dynamics methods, soft and hard potentials, potentials with and without attractive forces, and systems with and without surrounding walls.

Molecular dynamics investigation of bent-core molecules on a water surface.

Molecular dynamics simulations are carried out for bent-core molecules at water surfaces. The water surface is shown to alter the equilibrium molecular structure significantly by causing a different class of torsional states to become more favorable. The equilibrium structure is also altered by the substitution of chlorine atoms for hydrogen atoms on the central phenyl ring in that this substitution forces the bent core to remain in a single torsional state rather than be delocalized among several torsional states.

Stretching the immunoglobulin 27 domain of the titin protein: the dynamic energy landscape.

Molecular simulations are carried out on the Immunoglobulin 27 domain of the titin protein. The energy landscape is mapped out using an implicit solvent model, and molecular dynamics simulations are run with the solvent explicitly modeled. Stretching a protein is shown to produce a dynamic energy landscape in which the energy minima move in configuration space, change in depth, and are created and destroyed.