Michael P. Howard

Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units

Abstract We present an algorithm based on linear bounding volume hierarchies (LBVHs) for computing neighbor (Verlet) lists using graphics processing units (GPUs) for colloidal systems characterized by large size disparities. We compare this to a GPU implementation of the current state-of-the-art CPU algorithm based on stenciled cell lists. We report benchmarks for both neighbor list algorithms in a Lennard-Jones binary mixture with synthetic interaction range disparity and a realistic colloid solution. LBVHs outperformed the stenciled cell lists for systems with moderate or large size disparity and dilute or semidilute fractions of large particles, conditions typical of colloidal systems.

Inertial and viscoelastic forces on rigid colloids in microfluidic channels

We perform hybrid molecular dynamics simulations to study the flow behavior of rigid colloids dispersed in a dilute polymer solution. The underlying Newtonian solvent and the ensuing hydrodynamic interactions are incorporated through multiparticle collision dynamics, while the constituent polymers are modeled as bead-spring chains, maintaining a description consistent with the colloidal nature of our system. We study the cross-stream migration of the solute particles in slit-like channels for various polymer lengths and colloid sizes and find a distinct focusing onto the channel center under specific solvent and flow conditions. To better understand this phenomenon, we systematically measure the effective forces exerted on the colloids. We find that the migration originates from a competition between viscoelastic forces from the polymer solution and hydrodynamically induced inertial forces. Our simulations reveal a significantly stronger fluctuation of the lateral colloid position than expected from thermal motion alone, which originates from the complex interplay between the colloid and polymer chains.

Stratification in Drying Polymer–Polymer and Colloid–Polymer Mixtures

Drying polymer-polymer and colloid-polymer mixtures were studied using Langevin dynamics computer simulations. Polymer-polymer mixtures vertically stratified into layers, with the shorter polymers enriched near the drying interface and the longer polymers pushed down toward the substrate. Colloid-polymer mixtures stratified into a polymer-on-top structure when the polymer radius of gyration was comparable to or smaller than the colloid diameter, and a colloid-on-top structure otherwise. We also developed a theoretical model for the drying mixtures based on dynamical density functional theory, which gave excellent quantitative agreement with the simulations for the polymer-polymer mixtures and qualitatively predicted the observed polymer-on-top or colloid-on-top structures for the colloid-polymer mixtures.

Vapour–liquid phase equilibrium and surface tension of fully flexible Lennard–Jones chains

ABSTRACT We report measurements of the vapour–liquid coexistence densities and surface tension of fully flexible Lennard–Jones chain molecules ranging in length from 4 to 60 beads. We demonstrate that the surface tension for all chain lengths collapses to a single master curve when plotted according to the universal parachor correlation. We find a universal parachor exponent 3.79 ± 0.05 for conditions close to the critical point, with a deviation observed for the longest chains far below the critical point.

Influence of hydrodynamic interactions on stratification in drying mixtures

Nonequilibrium molecular dynamics simulations are used to investigate the influence of hydrodynamic interactions on vertical segregation (stratification) in drying mixtures of long and short polymer chains. In agreement with previous computer simulations and theoretical modeling, the short polymers stratify above the long polymers at the top of the drying film when hydrodynamic interactions between polymers are neglected. However, no stratification occurs under the same drying conditions when hydrodynamic interactions are incorporated through an explicit solvent model. Our analysis demonstrates that models lacking hydrodynamic interactions do not faithfully represent stratification in drying mixtures, in agreement with the recent analysis of an idealized model for diffusiophoresis. Hydrodynamic interactions must be incorporated into such models for drying mixtures in future.

Note: Smooth torsional potentials for degenerate dihedral angles

A general method is proposed for smoothing torsional potentials when the dihedral angle becomes undefined.

Coupling of Nanoparticle Dynamics to Polymer Center-of-Mass Motion in Semidilute Polymer Solutions

We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are subdiffusive on short time scales before transitioning to diffusive motion on long time scales. The long-time diffusivities scale according to theoretical predictions based on full dynamic coupling to the polymer segmental relaxations. In agreement with our recent experiments, however, we observe that the nanoparticle subdiffusive exponents are significantly larger than predicted by the coupling theory over a broad range of polymer concentrations. We attribute this discrepancy in the subdiffusive regime to the presence of an additional coupling mechanism between the nanoparticle dynamics and the polymer center-of-mass motion, which differs from the polymer relaxations that control the long-time diffusion. This coupling is retained even in the absence of many-body hydrodynamic inte...

Evaporation-induced assembly of colloidal crystals

Colloidal crystals are often prepared by evaporation from solution, and there is considerable interest to link the processing conditions to the crystal morphology and quality. Here, we study the evaporation-induced assembly of colloidal crystals using massive-scale nonequilibrium molecular dynamics simulations. We apply a recently developed machine-learning technique to characterize the assembling crystal structures with unprecedented microscopic detail. In agreement with previous experiments and simulations, faster evaporation rates lead to earlier onset of crystallization and more disordered surface structures. Surprisingly, we find that collective rearrangements of the bulk crystal during later stages of drying reduce the influence of the initial surface structure, and the final morphology is essentially independent of the evaporation rate. Our structural analysis reveals that the crystallization process is well-described by two time scales, the film drying time and the crystal growth time, with the latter having an unexpected dependence on the evaporation rate due to equilibrium thermodynamic effects at high colloid concentrations. These two time scales may be leveraged to control the relative influence of equilibrium and nonequilibrium growth mechanisms, suggesting a route to rapidly process colloidal crystals while also removing defects. Our analysis additionally reveals that solvent-mediated interactions play a critical role in the crystallization kinetics and that commonly used implicit-solvent models do not faithfully resolve nonequilibrium processes such as drying.

Efficient mesoscale hydrodynamics: Multiparticle collision dynamics with massively parallel GPU acceleration

Abstract We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU architectures and communication patterns between multiple GPUs. We show that a mixed-precision computing model can improve performance compared to a fully double-precision model while still providing good numerical accuracy. We report weak and strong scaling benchmarks of a reference MPCD solvent and a benchmark of a polymer solution with research-relevant interactions and system size. Our MPCD software enables simulations of mesoscale hydrodynamics at length and time scales that would be otherwise challenging or impossible to access.

Solvent quality influences surface structure of glassy polymer thin films after evaporation

Molecular dynamic simulations are used to investigate the structural effects of treating a glassy polymer thin film with solvents of varying quality and subsequently evaporating the solvent. Both a monodisperse film and a polydisperse film are studied for poor to good solvent conditions, including the limit in which the polymer film is fully dissolved. In agreement with previous studies, the dissolved polymer-solvent mixtures form a polymer-rich skin on top of the forming film during evaporation. In the case of the polydisperse films, a segregation of the lower molecular weight polymer to the film interface is observed. We provide a detailed, systematic analysis of the interface structure and properties during and after evaporation. We find that for non-dissolved films, the surface width of the film after solvent evaporation is enhanced compared to the case without solvent. Our results show that due to the kinetic arrest of the surface structure, the increased surface width is preserved after solvent evaporation for both mono- and polydisperse films. We conclude that it is important to take poor solvent effects into account for the surface morphology of already formed thin glassy films, an effect which is often neglected.