Showing papers by "Steven J. Plimpton published in 2009"

General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions.

Abstract: Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interacting under periodic boundary conditions. All three forms are written in terms of forces acting on atoms, and so are valid for arbitrary many-body interatomic potentials. All three forms are mathematically equivalent. In the special case of atoms interacting with pair potentials, they reduce to previously published forms. (i) The atom-cell form is similar to the standard expression for the virial for a finite nonperiodic system, but with an explicit correction for interactions with periodic images. (ii) The atom form is particularly suited to implementation in modern molecular dynamics simulation codes using spatial decomposition parallel algorithms. (iii) The group form of the virial allows the contributions to the virial to be assigned to individual atoms.

Crossing the Mesoscale No-Man's Land via Parallel Kinetic Monte Carlo

Abstract: The kinetic Monte Carlo method and its variants are powerful tools for modeling materials at the mesoscale, meaning at length and time scales in between the atomic and continuum. We have completed a 3 year LDRD project with the goal of developing a parallel kinetic Monte Carlo capability and applying it to materials modeling problems of interest to Sandia. In this report we give an overview of the methods and algorithms developed, and describe our new open-source code called SPPARKS, for Stochastic Parallel PARticle Kinetic Simulator. We also highlight the development of several Monte Carlo models in SPPARKS for specific materials modeling applications, including grain growth, bubble formation, diffusion in nanoporous materials, defect formation in erbium hydrides, and surface growth and evolution.

Liquid crystal nanodroplets in solution

Abstract: The aggregation of liquid crystal nanodroplets from a homogeneous solution is studied by molecular dynamics simulations. The liquid crystal particles are modeled as elongated ellipsoidal Gay-Berne particles while the solvent is modeled as spherical Lennard-Jones particles. Extending previous studies of Berardi et al. [J. Chem. Phys. 126, 044905 (2007)], we find that liquid crystal nanodroplets are not stable and that after sufficiently long times the nanodroplets always aggregate into a single large droplet. Results describing the droplet shape and orientation for different temperatures and shear rates are presented. The implementation of the Gay-Berne potential for biaxial ellipsoidal particles in a parallel molecular dynamics code is also briefly discussed.

Microscale Immune Studies Laboratory.

Abstract: The overarching goal is to develop novel technologies to elucidate molecular mechanisms of the innate immune response in host cells to pathogens such as bacteria and viruses including the mechanisms used by pathogens to subvert/suppress/obfuscate the immune response to cause their harmful effects. Innate immunity is our first line of defense against a pathogenic bacteria or virus. A comprehensive 'system-level' understanding of innate immunity pathways such as toll-like receptor (TLR) pathways is the key to deciphering mechanisms of pathogenesis and can lead to improvements in early diagnosis or developing improved therapeutics. Current methods for studying signaling focus on measurements of a limited number of components in a pathway and hence, fail to provide a systems-level understanding. We have developed a systems biology approach to decipher TLR4 pathways in macrophage cell lines in response to exposure to pathogenic bacteria and their lipopolysaccharide (LPS). Our approach integrates biological reagents, a microfluidic cell handling and analysis platform, high-resolution imaging and computational modeling to provide spatially- and temporally-resolved measurement of TLR-network components. The Integrated microfluidic platform is capable of imaging single cells to obtain dynamic translocation data as well as high-throughput acquisition of quantitative protein expression and phosphorylation information of selected cell populations. The more » platform consists of multiple modules such as single-cell array, cell sorter, and phosphoflow chip to provide confocal imaging, cell sorting, flow cytomtery and phosphorylation assays. The single-cell array module contains fluidic constrictions designed to trap and hold single host cells. Up to 100 single cells can be trapped and monitored for hours, enabling detailed statistically-significant measurements. The module was used to analyze translocation behavior of transcription factor NF-kB in macrophages upon activation by E. coli and Y. pestis LPS. The chip revealed an oscillation pattern in translocation of NF-kB indicating the presence of a negative feedback loop involving IKK. Activation of NF-kB is preceded by phosphorylation of many kinases and to correlate the kinase activity with translocation, we performed flow cytometric assays in the PhosphoChip module. Phopshorylated forms of p38. ERK and RelA were measured in macrophage cells challenged with LPS and showed a dynamic response where phosphorylation increases with time reaching a maximum at {approx}30-60min. To allow further downstream analysis on selected cells, we also implemented an optical-trapping based sorting of cells. This has allowed us to sort macrophages infected with bacteria from uninfected cells with the goal of obtaining data only on the infected (the desired) population. The various microfluidic chip modules and the accessories required to operate them such as pumps, heaters, electronic control and optical detectors are being assembled in a bench-top, semi-automated device. The data generated is being utilized to refine existing TLR pathway model by adding kinetic rate constants and concentration information. The microfluidic platform allows high-resolution imaging as well as quantitative proteomic measurements with high sensitivity (

miniMD v. 1.0

Abstract: Simple parallel MD code that serves as a microapplication in the Mantevo suite. Study of computer system design and implementation, benchmarking of new and existing computer systems.