Showing papers by "Steven J. Plimpton published in 2002"
TL;DR: In this paper, the boundary effects in gravity-driven, dense granular flows down inclined planes are studied using large-scale molecular dynamics simulations and it is shown that the flow behavior and structure of the flowing pile changes dramatically as the roughness of the supporting base.
Abstract: Boundary effects in gravity-driven, dense granular flows down inclined planes are studied using large-scale molecular dynamics simulations. We find that the flow behavior and structure of the flowing pile changes dramatically as we vary the roughness of the supporting base. For a rough, bumpy base, there are three principal flow regimes that depend on the inclination angle θ: at small angles θ θmax, where θmax is the maximum angle for which stable, steady state flow exists, the flow is unstable; and for θr<θ<θmax, the energy input from gravity is balanced by that dissipated through friction and the system reaches a stable, steady state flow. In the stable regime, we find no slip boundary conditions with a bulk density that is independent of the height above the base. For a chute base that is ordered, the steady state regime splits into a further three distinct flow regimes: at lower angles, the flowing system self-organizes ...
66 citations
TL;DR: In this article, simple shear and torsion of single crystal copper were analyzed by employing experiments, molecular dynamics simulations, and finite element simulations in order to focus on the kinematic responses and the apparent yield strengths at different length scales of the specimens.
Abstract: We analyze simple shear and torsion of single crystal copper by employing experiments, molecular dynamics simulations, and finite element simulations in order to focus on the kinematic responses and the apparent yield strengths at different length scales of the specimens. In order to compare torsion with simple shear, the specimens were designed to be of similar size. To accomplish this, the ratio of the cylinder circumference to the axial gage length in torsion equaled the ratio of the length to height of the simple shear specimens (0.43). With the [110] crystallographic direction parallel to the rotational axis of the specimen, we observed a deformation wave of material that oscillated around the specimen in torsion and through the length of the specimen in simple shear. In torsion, the ratio of the wave amplitude divided by cylinder circumference ranged from 0.02 ‐0.07 for the three different methods of analysis: experiments, molecular dynamics simulations, and finite element simulations. In simple shear, the ratio of the deformation wave amplitude divided by the specimen length and the corresponding values predicted by the molecular dynamics and finite element simulations (simple shear experiments were not performed) ranged from 0.23‐0.26. Although each different analysis method gave similar results for each type boundary condition, the simple shear case gave approximately five times more amplitude than torsion. We attributed this observation to the plastic spin behaving differently as the simple shear case constrained the dislocation activity to planar double slip, but the torsion specimen experienced quadruple slip. The finite element simulations showed a clear relation with the plastic spin and the oscillation of the material wave. As for the yield stress in simple shear, a size scale dependence was found regarding two different size atomistic simulations for copper (332 atoms and 23628 atoms). We extrapolated the atomistic yield stresses to the order of a centimeter, and these comparisons were close to experimental data in the literature and the present study. @DOI: 10.1115/1.1480407#
29 citations
TL;DR: Carbon Sequestration in Synechococcus Sp: From Molecular Machines to Hierarchical Modeling as discussed by the authors ) is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of synechacteria, an abundant marine cyanobacteria known to play an important role in the global carbon cycle.
Abstract: The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO(2) are important terms in the global environmental response to anthropogenic atmospheric inputs of CO(2) and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.
15 citations
15 Apr 2002
TL;DR: Preliminary benchmarks indicate reasonable scalability of the algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees, with parallel efficiencies of 75% or more on up to a few dozen processors.
Abstract: We present a parallel algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees. The algorithm effectively distributes both the computation and memory requirements of the analysis. We discuss an implementation of the algorithm in the Genehunter linkage analysis package (version 2.1), enabling Genehunter to be run on distributed memory platforms for the first time. Our preliminary benchmarks indicate reasonable scalability of the algorithm for even small fixed-size problems, with parallel efficiencies of 75% or more on up to a few dozen processors.
10 citations