Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Soil Chemical Analysis

1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

Monthly Notices is one of the three largest general primary astronomical research publications. It is an international journal, published by the Royal Astronomical Society. This article 1 describes its publication policy and practice.

Monthly Notices of the Royal Astronomical Society

A comprehensive review of zonal flow phenomena in plasmas is presented. While the emphasis is on zonal flows in laboratory plasmas, planetary zonal flows are discussed as well. The review presents the status of theory, numerical simulation and experiments relevant to zonal flows. The emphasis is on developing an integrated understanding of the dynamics of drift wave–zonal flow turbulence by combining detailed studies of the generation of zonal flows by drift waves, the back-interaction of zonal flows on the drift waves, and the various feedback loops by which the system regulates and organizes itself. The implications of zonal flow phenomena for confinement in, and the phenomena of fusion devices are discussed. Special attention is given to the comparison of experiment with theory and to identifying directions for progress in future research.

/pdf/zonal-flows-in-plasma-a-review-3byloag115.pdf

Zonal flows in plasma—a review

Nonlinear wave excitations by orbiting charged space debris objects

We report the modifications in the propagation characteristics of dust acoustic solitary waves (DASWs) due to the polarization force acting on micron- size dust particles in a non-uniform plasma. In the small amplitude limit, we derive a K-dV-type equation and show that there is an increase in the amplitude and a reduction in the width of a solitary structure as the polarization force is enhanced for a given Mach number. For arbitrary amplitude waves we employ the Sagdeev potential method and find that the range of Mach numbers where solitary structures can exist becomes narrower in the presence of the polarization interaction. In both limits there exists a critical value of grain size beyond which the DASW cannot propagate.

https://iopscience.iop.org/article/10.1088/1367-2630/12/7/073002/pdf

Effect of polarization force on the propagation of dust acoustic solitary waves

A statistical test for extracting and identifying coherent structures in the scrape-off layer turbulence is used to analyze Langmuir probe data from the ADITYA and ASDEX tokamaks. This method, the biorthogonal decomposition, allows one to characterize large-scale coherent structures in plasma turbulence in an unambiguous manner. It is shown that such structures effectively contribute to radial transport and to intermittency. Results from numerical simulations of turbulence driven by the resistive interchange instability in the scrape-off layer are compared to the observed statistical properties.

Characterization of Coherent Structures in Tokamak Edge Turbulence

A novel two-dimensional (2D) fluid model is proposed for investigating flux-driven plasma turbulence in the tokamak edge and scrape-off layer (SOL). Unlike most previous turbulence simulations of this region, the 2D model treats the two regions in a consolidated manner with a smooth transition region in between. The unified 2D model is simpler and less computer intensive than 3D models, but captures most features of the 3D edge and 2D SOL turbulence. It also illustrates the influence of tokamak edge turbulence on the SOL transport, something not captured by earlier 2D SOL simulations. Existence of an equilibrium radial electric field in the edge and SOL regions has been found. Two different plasma conductivity models have been used for the simulations. Turbulence in the edge is characterized by radially elongated streamers and zonal flows. The streamer structures occasionally break mainly in a region where the radial electric field changes sign. A phenomenological condition for the breaking has been obtained. Effective diffusion co-efficient and density front propagation speed from the simulation have been calculated. Statistical properties of the particle transport obtained from this simulation are compared with earlier flux-driven 2D SOL turbulence simulations and also with Aditya tokamak results.

Edge and scrape-off layer tokamak plasma turbulence simulation using two-field fluid model

The excitation of precursor solitons ahead of a rapidly moving object in a fluid, a spectacular phenomenon in hydrodynamics that has often been observed ahead of moving ships, has surprisingly not been investigated in plasmas where the fluid model holds good for low frequency excitations such as ion acoustic waves. In this Rapid Communication we report an experimental observation of precursor solitons in a flowing dusty plasma. The nonlinear solitary dust acoustic waves (DAWs) are excited by a supersonic mass flow of the dust particles over an electrostatic potential hill. In a frame where the fluid is stationary and the hill is moving the solitons propagate in the upstream direction as precursors while wake structures consisting of linear DAWs are seen to propagate in the downstream region. A theoretical explanation of these excitations based on the forced Korteweg--deVries model equation is provided and their practical implications in situations involving a charged object moving in a plasma are discussed.

Abhijit Sen

Papers

Nonlinear wave excitations by orbiting charged space debris objects

Effect of polarization force on the propagation of dust acoustic solitary waves

Characterization of Coherent Structures in Tokamak Edge Turbulence

Edge and scrape-off layer tokamak plasma turbulence simulation using two-field fluid model

Experimental observation of precursor solitons in a flowing complex plasma.