Plasma Turbulence in the Local Bubble

Turbulence in the Local Bubble could play an important role in the thermodynamics of the gas that is there. The best astronomical technique for measuring turbulence in astrophysical plasmas is radio scintillation. Measurements of the level of scattering to the nearby pulsar B0950+08 by Philips and Clegg in 1992 showed a markedly lower value for the line-of-sight averaged turbulent intensity parameter $$than is observed for other pulsars, consistent with radio wave propagation through a highly rarefied plasma. In this paper, we discuss the observational progress that has been made since that time. At present, there are four pulsars (B0950+08, B1133+16, J0437-4715, and B0809+74) whose lines of sight seem to lie mainly within the local bubble. The mean densities and line of sight components of the interstellar magnetic field along these lines of sight are smaller than nominal values for pulsars, but not by as much expected. Three of the four pulsars also have measurements of interstellar scintillation. The value of the parameter$$ is smaller than normal for two of them, but is completely nominal for the third. This inconclusive status of affairs could be improved by measurements and analysis of ``arcs'' in ``secondary spectra'' of pulsars.Comment: Submitted to Space Science Reviews as contribution to Proceedings of ISSI (International Space Science Institute) workshop "From the Heliosphere to the Local Bubble". Refereed version accepted for publicatio

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.Comment: 9 pages, 2 figure

On the Strong Scalability of Maritime CFD

Since 2004, supercomputer growth hasbeen constrained by energy efficiency rather than raw hardware speeds. Tomaintain exponential growth of overall computing power, a massive growth inparallelization is under way. To keep up with these changes, computationalfluid dynamics (CFD) must improve its strong scalability – its ability tohandle lower cells-per-core ratios and achieve finer-grain parallelization. Amaritime-focused, unstructured, finite-volume code (ReFRESCO) is used toinvestigate the scalability problems for incompressible, viscous CFD using two classicaltest-cases. Existing research suggests that the linear equation-system solveris the main bottleneck to incompressible codes, due to the stiff Poisson pressure equation. Here, these results are expandedby analysing the reasons for this poor scalability. In particular, a number ofalternative linear solvers and preconditioners are tested to determine if thescalability problem can be circumvented, including GMRES, Pipelined-GMRES,Flexible-GMRES and BCGS. Conventional block-wise preconditioners are tested,along with multi-grid preconditioners and smoothers in various configurations.Memory-bandwidth constraints and global communication patterns are found to bethe main bottleneck, and no state-of-the-art solution techniques which solve thestrong-scalability problem satisfactorily could be found. There is significantincentive for more research and development in this area

Chaotic multigrid methods for the solution of elliptic equations

Supercomputer power has been doubling approximately every 14 months for several decades, increasing the capabilities of scientific modelling at a similar rate. However, to utilize these machines effectively for applications such as computational fluid dynamics, improvements to strong scalability are required. Here, the particular focus is on semi-implicit, viscous-flow CFD, where the largest bottleneck to strong scalability is the parallel solution of the linear pressure-correction equation — an elliptic Poisson equation. State-of-the-art linear solvers, such as Krylov subspace or multigrid methods, provide excellent numerical performance for elliptic equations, but do not scale efficiently due to frequent synchronization between processes. Complete desynchronization is possible for basic, Jacobi-like solvers using the theory of ‘chaotic relaxations’. These non-deterministic, chaotic solvers scale superbly, as demonstrated herein, but lack the numerical performance to converge elliptic equations — even with the relatively lax convergence requirements of the example CFD application. However, these chaotic principles can also be applied to multigrid solvers. In this paper, a ‘chaotic-cycle’ algebraic multigrid method is described and implemented as an open-source library. It is tested on a model Poisson equation, and also within the context of CFD. Two CFD test cases are used: the canonical lid-driven cavity flow and the flow simulation of a ship (KVLCC2). The chaotic-cycle multigrid shows good scalability and numerical performance compared to classical V-, W- and F-cycles. On 2048 cores the chaotic-cycle multigrid solver performs up to faster than Flexible-GMRES and faster than classical V-cycle multigrid. Further improvements to chaotic-cycle multigrid can be made, relating to coarse-grid communications and desynchronized residual computations. It is expected that the chaotic-cycle multigrid could be applied to other scientific fields, wherever a scalable elliptic-equation solver is required

Topological doping and the stability of stripe phases

We analyze the properties of a general Ginzburg-Landau free energy with competing order parameters, long-range interactions, and global constraints (e.g., a fixed value of a total ``charge'') to address the physics of stripe phases in underdoped high-Tc and related materials. For a local free energy limited to quadratic terms of the gradient expansion, only uniform or phase-separated configurations are thermodynamically stable. ``Stripe'' or other non-uniform phases can be stabilized by long-range forces, but can only have non-topological (in-phase) domain walls where the components of the antiferromagnetic order parameter never change sign, and the periods of charge and spin density waves coincide. The antiphase domain walls observed experimentally require physics on an intermediate lengthscale, and they are absent from a model that involves only long-distance physics. Dense stripe phases can be stable even in the absence of long-range forces, but domain walls always attract at large distances, i.e., there is a ubiquitous tendency to phase separation at small doping. The implications for the phase diagram of underdoped cuprates are discussed.Comment: 18 two-column pages, 2 figures, revtex+eps

Molecular dynamics study of melting of a bcc metal-vanadium II : thermodynamic melting

We present molecular dynamics simulations of the thermodynamic melting transition of a bcc metal, vanadium using the Finnis-Sinclair potential. We studied the structural, transport and energetic properties of slabs made of 27 atomic layers with a free surface. We investigated premelting phenomena at the low-index surfaces of vanadium; V(111), V(001), and V(011), finding that as the temperature increases, the V(111) surface disorders first, then the V(100) surface, while the V(110) surface remains stable up to the melting temperature. Also, as the temperature increases, the disorder spreads from the surface layer into the bulk, establishing a thin quasiliquid film in the surface region. We conclude that the hierarchy of premelting phenomena is inversely proportional to the surface atomic density, being most pronounced for the V(111) surface which has the lowest surface density

HI Clouds Beyond the Galactic Disk

Recent observations in the 21cm line with the Green Bank Telescope have changed our view of the neutral interstellar medium (ISM) in several ways. The new data show that in the inner parts of the Milky Way the disk-halo interface is composed of many discrete HI clouds. The clouds lie in a layer more than one kpc thick and follow Galactic rotation. Their origin and evolution is unknown. In the outer Galaxy, the new data show that the high-velocity cloud Complex H is likely a satellite on a retrograde orbit interacting with some extended component of the Milky Way's ISM. These observations place new constraints on models of the ISM and are directly related to the work of Don Cox and Ron Reynolds.Comment: 8 pages includes 2 figures. To appear in "How Does the Galaxy Work?", eds. E.J. Alfaro, E. Perez, & J. Franco, Kluwer, Proceedings of a Conference held 23-27 June 2003 in Granada, Spai

Dynamic nuclear polarization and spin-diffusion in non-conducting solids

There has been much renewed interest in dynamic nuclear polarization (DNP), particularly in the context of solid state biomolecular NMR and more recently dissolution DNP techniques for liquids. This paper reviews the role of spin diffusion in polarizing nuclear spins and discusses the role of the spin diffusion barrier, before going on to discuss some recent results.Comment: submitted to Applied Magnetic Resonance. The article should appear in a special issue that is being published in connection with the DNP Symposium help in Nottingham in August 200

Horizontal Branch Stars: The Interplay between Observations and Theory, and Insights into the Formation of the Galaxy

We review HB stars in a broad astrophysical context, including both variable and non-variable stars. A reassessment of the Oosterhoff dichotomy is presented, which provides unprecedented detail regarding its origin and systematics. We show that the Oosterhoff dichotomy and the distribution of globular clusters (GCs) in the HB morphology-metallicity plane both exclude, with high statistical significance, the possibility that the Galactic halo may have formed from the accretion of dwarf galaxies resembling present-day Milky Way satellites such as Fornax, Sagittarius, and the LMC. A rediscussion of the second-parameter problem is presented. A technique is proposed to estimate the HB types of extragalactic GCs on the basis of integrated far-UV photometry. The relationship between the absolute V magnitude of the HB at the RR Lyrae level and metallicity, as obtained on the basis of trigonometric parallax measurements for the star RR Lyrae, is also revisited, giving a distance modulus to the LMC of (m-M)_0 = 18.44+/-0.11. RR Lyrae period change rates are studied. Finally, the conductive opacities used in evolutionary calculations of low-mass stars are investigated. [ABRIDGED]Comment: 56 pages, 22 figures. Invited review, to appear in Astrophysics and Space Scienc

Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization