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- C R Sovinec, A H Glasser, T A Gianakon, D C Barnes, R A Nebel, S E Kruger +5 others
- 2003

A conforming representation composed of two-dimensional finite elements and finite Fourier series is applied to three-dimensional nonlinear non-ideal magnetohydrodynamics using a semi-implicit time-advance. The self-adjoint semi-implicit operator and variational approach to spatial discretization are synergistic and enable simulation in the extremely stiff… (More)

Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (" strings ") at temperatures well above the glass transition. The mean length of the strings increases upon cooling, and… (More)

The time evolution of species concentrations in biochemical reaction networks is often modeled using the stochastic simulation algorithm (SSA) [Gillespie, J. Phys. Chem. 81, 2340 (1977)]. The computational cost of the original SSA scaled linearly with the number of reactions in the network. Gibson and Bruck developed a logarithmic scaling version of the SSA… (More)

- Steven A Wright, Steven J Plimpton, Thomas P Swiler, Richard M Fye, Michael F Young, Elizabeth A Holm
- 1997

Government nor any agency thereof, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would… (More)

- Steven J Plimpton, Bruce Hendrickson, Shawn P Burns, William Mclendon, Iii, Lawrence Rauchwerger
- 2005

– The method of discrete ordinates is commonly used to solve the Boltzmann transport equation. The solution in each ordinate direction is most efficiently computed by sweeping the radiation flux across the computational grid. For unstructured grids this poses many challenges, particularly when implemented on distributed-memory parallel machines where the… (More)

We describe a particle-based simulator called ChemCell that we are developing with the goal of modeling the protein chemistry of biological cells for phenomena where spatial effects are important. Membranes and organelle structure are represented by triangulated surfaces. Diffusing particles represent proteins, complexes, or other biomolecules of interest.… (More)

The structure and stresses of static granular packs in cylindrical containers are studied by using large-scale discrete element molecular dynamics simulations in three dimensions. We generate packings by both pouring and sedimentation and examine how the final state depends on the method of construction. The vertical stress becomes depth independent for… (More)

We present the results of a molecular dynamics computer simulation study in which we investigate whether a supercooled Lennard-Jones liquid exhibits dynamical heterogeneities. We evaluate the non-Gaussian parameter for the self part of the van Hove correlation function and use it to identify " mobile " particles. We find that these particles form clusters… (More)

Using extensive molecular dynamics simulations of an equilibrium, glass-forming Lennard-Jones mixture, we characterize in detail the local atomic motions. We show that spatial correlations exist among particles undergoing extremely large ("mobile") or extremely small ("immobile") displacements over a suitably chosen time interval. The immobile particles… (More)

- Steven J Plimpton, Bruce A Hendrickson
- 1992

Parallel computing offers new capabilities for using molecular dynamics (MD) to simulate larger numbers of atoms and longer time scales. In this paper we discuss two methods we have used to implement the embedded atom method (EAM) formalism for molecular dynamics on multiple-instruction/multiple-data (MIMD) parallel computers. The first method… (More)