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A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014

Sershen, Cheryl L.; Plimpton, Steven J.; May, Elebeoba E.

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.

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TYPE Journal Article YEAR 2014
ScopusOSTIDOI

Stochastic Particle Real Time Analyzer (SPARTA) Validation and Verification Suite

Gallis, Michail A.; Koehler, Timothy P.; Plimpton, Steven J.

This report presents the test cases used to verify, validate and demonstrate the features and capabilities of the first release of the 3D Direct Simulation Monte Carlo (DSMC) code SPARTA (Stochastic Real Time Particle Analyzer). The test cases included in this report exercise the most critical capabilities of the code like the accurate representation of physical phenomena (molecular advection and collisions, energy conservation, etc.) and implementation of numerical methods (grid adaptation, load balancing, etc.). Several test cases of simple flow examples are shown to demonstrate that the code can reproduce phenomena predicted by analytical solutions and theory. A number of additional test cases are presented to illustrate the ability of SPARTA to model flow around complicated shapes. In these cases, the results are compared to other well-established codes or theoretical predictions. This compilation of test cases is not exhaustive, and it is anticipated that more cases will be added in the future.

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TYPE SAND Report YEAR 2014
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Particle dynamics modeling methods for colloid suspensions

Computational Particle Mechanics

Bolintineanu, Dan S.; Grest, Gary S.; Lechman, Jeremy B.; Pierce, Flint P.; Plimpton, Steven J.; Schunk, Randy

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.

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TYPE Journal Article YEAR 2014
ScopusOSTIDOI

Streaming data analytics via message passing with application to graph algorithms

Journal of Parallel and Distributed Computing

Plimpton, Steven J.; Shead, Tim

The need to process streaming data, which arrives continuously at high-volume in real-time, arises in a variety of contexts including data produced by experiments, collections of environmental or network sensors, and running simulations. Streaming data can also be formulated as queries or transactions which operate on a large dynamic data store, e.g. a distributed database. We describe 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. Datums are routed between processes in patterns defined by the application. PHISH provides multiple communication backends including MPI and sockets/ZMQ. The former means streaming computations can be run on any parallel machine which supports MPI; the latter allows them to run on a heterogeneous, geographically dispersed network of machines. We illustrate how streaming MapReduce operations can be implemented using the PHISH communication model, and describe streaming versions of three algorithms for large, sparse graph analytics: triangle enumeration, sub-graph isomorphism matching, and connected component finding. We also provide benchmark timings comparing MPI and socket performance for several kernel operations useful in streaming algorithms. © 2014 Elsevier Inc. All rights reserved.

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TYPE Journal Article YEAR 2014
ScopusOSTIDOI
Results 126–150 of 210
Results 126–150 of 210