Showing papers by "Steven J. Plimpton published in 2014"
22 May 2014
TL;DR: In this article, the authors present a review and critique of several methods for the simulation of the dynamics of colloidal suspensions at the mesoscale, focusing particularly on simulation techniques for hydrodynamic interactions, including implicit solvents (Fast Lubrication Dynamics, an approximation to Stokesian Dynamics) and explicit/particle-based (Multi Particle Collision Dynamics and Dissipative Particle Dynamics).
Abstract: We present a review and critique of several methods for the simulation of the dynamics of colloidal suspensions at the mesoscale. We focus particularly on simulation techniques for hydrodynamic interactions, including implicit solvents (Fast Lubrication Dynamics, an approximation to Stokesian Dynamics) and explicit/particle-based solvents (Multi-Particle Collision Dynamics and Dissipative Particle Dynamics). Several variants of each method are compared quantitatively for the canonical system of monodisperse hard spheres, with a particular focus on diffusion characteristics, as well as shear rheology and microstructure. In all cases, we attempt to match the relevant properties of a well-characterized solvent, which turns out to be challenging for the explicit solvent models. Reasonable quantitative agreement is observed among all methods, but overall the Fast Lubrication Dynamics technique shows the best accuracy and performance. We also devote significant discussion to the extension of these methods to more complex situations of interest in industrial applications, including models for non-Newtonian solvent rheology, non-spherical particles, drying and curing of solvent and flows in complex geometries. This work identifies research challenges and motivates future efforts to develop techniques for quantitative, predictive simulations of industrially relevant colloidal suspension processes.
138 citations
01 Jul 2014
TL;DR: In the 50 years since its invention, the acceptance and applicability of the DSMC method have increased significantly, whereas the increase in computer speed has been the main factor behind its greater applicability.
Abstract: In the 50 years since its invention, the acceptance and applicability of the DSMC method have increased significantly. Extensive verification and validation efforts have led to its greater acceptance, whereas the increase in computer speed has been the main factor behind its greater applicability. As the performance of a single processor reaches its limit, massively parallel computing is expected to play an even stronger role in its future development.
124 citations
TL;DR: This work describes a lightweight, portable framework named PHISH which provides a communication model enabling a set of independent processes to compute on a stream of data in a distributed-memory parallel manner, and illustrates how streaming MapReduce operations can be implemented using the PHISH communication model.
19 citations
06 Nov 2014
TL;DR: The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step.
Abstract: This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.
2 citations