A Fast Parallel Poisson Solver on Irregular Domains Applied to Beam Dynamic Simulations

We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or `mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) based algebraic multigrid (AMG) preconditioning. We investigate variants of the implementation of SA-AMG that lead to considerable improvements in the execution times. We demonstrate good scalability of the solver on distributed memory parallel processor with up to 2048 processors. We also compare our SAAMG-PCG solver with an FFT-based solver that is more commonly used for applications in beam dynamics

Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity

Shroom-mediated remodeling of the actomyosin cytoskeleton is a critical driver of cellular shape and tissue morphology that underlies the development of many tissues including the neural tube, eye, intestines, and vasculature. Shroom uses a conserved SD2 domain to direct the subcellular localization of Rho-associated kinase (Rock), which in turn drives changes in the cytoskeleton and cellular morphology through its ability to phosphorylate and activate non-muscle myosin II. Here, we present the structure of the human Shroom-Rock binding module, revealing an unexpected stoichiometry for Shroom in which two Shroom SD2 domains bind independent surfaces on Rock. Mutation of interfacial residues impaired Shroom-Rock binding in vitro and resulted in altered remodeling of the cytoskeleton and loss of Shroom-mediated changes in cellular morphology. Additionally, we provide the first direct evidence that Shroom can function as a Rock activator. These data provide molecular insight into the Shroom-Rock interface and demonstrate that Shroom directly participates in regulating cytoskeletal dynamics, adding to its known role in Rock localization

Formation of helium spectrum in solar quiescent prominences

We present new non-LTE modelling of the helium spectrum emitted by quiescent solar prominences. The calculations are made in the frame of a one-dimensional plane-parallel slab. The physical parameters of our models are the electron temperature, the gas pressure, the slab width, the microturbulent velocity and the height above the solar surface. In this paper, we present isothermal isobaric models for a large range of temperature and pressure values. This work brings considerable improvements over the calculations of Heasley and co-workers (Heasley et al. 1974, Heasley and Milkey 1976, 1978, 1983) with the inclusion in our calculations of partial redistribution effects in the formation of the HI Lyα, Lyβ, HeI λ 584 Å and HeII λ 304 Å lines. In addition we consider detailed incident profiles for the principal transitions. The statistical equilibrium equations are solved for a 33 bound levels (HeI and HeII) plus continuum atom, and the radiative transfer equations are solved by the Feautrier method with variable Eddington factors. In this way we obtain the helium level populations and the emergent line profiles. We discuss the influence of the physical parameters on the helium level populations and on the main helium spectral lines. The effect of helium abundance in the prominence plasma is also studied. Some relations between singlet and triplet lines are given, as well as between optically thin or thick lines, HeI and HeII lines, and between the HeI λ 5876 Å and HI λ 4863 Å lines. In a future work this numerical code will be used for the diagnostic of the prominence plasma by comparing the results with SUMER observations

Verified lifting of stencil computations

This paper demonstrates a novel combination of program synthesis and verification to lift stencil computations from low-level Fortran code to a high-level summary expressed using a predicate language. The technique is sound and mostly automated, and leverages counter-example guided inductive synthesis (CEGIS) to find provably correct translations. Lifting existing code to a high-performance description language has a number of benefits, including maintainability and performance portability. For example, our experiments show that the lifted summaries can enable domain specific compilers to do a better job of parallelization as compared to an off-the-shelf compiler working on the original code, and can even support fully automatic migration to hardware accelerators such as GPUs. We have implemented verified lifting in a system called STNG and have evaluated it using microbenchmarks, mini-apps, and real-world applications. We demonstrate the benefits of verified lifting by first automatically summarizing Fortran source code into a high-level predicate language, and subsequently translating the lifted summaries into Halide, with the translated code achieving median performance speedups of 4.1X and up to 24X for non-trivial stencils as compared to the original implementation.United States. Department of Energy. Office of Science (Award DE-SC0008923)United States. Department of Energy. Office of Science (Award DE-SC0005288

Relationship between Cardiorespiratory Fitness and Anthropometric Variables among school-going adolescents in Nigeria

The increase in physical activity (PA) levels has been known to be associated with improved cardiorespiratory fitness status which helps in reducing the risk factors of non-communicable disease. However, the interaction between cardiorespiratory fitness and anthropometric variables remains unclear and needs further investigation. This study assessed the relationship between cardiorespiratory fitness and anthropometric variables among school-going adolescents in Nigeria. Two hundred and fifty apparently healthy participants ranging from 12 to 20 years of age, who were randomly selected, participated in this study. Height, body weight, and body mass index (BMI) were measured. Cooper’s 12 minutes run/walk test was conducted to assess cardiorespiratory fitness (estimated by maximal oxygen uptake: VO2max). There was a significant correlation betweenVO2max and BMI. In the regression model, weight, height, gender, and BMI accounted for ninety-five percent of the total variance in the participants’ cardiorespiratory fitness. Body weight, height, gender, and BMI were significant predictors of cardiorespiratory fitness in the school-going Nigerian adolescents.IS

Urban Heat Island monitoring with Global Navigation Satellite System (GNSS) data

The Urban Heat Island (UHI) effect occurs when the temperature in an urban area is higher than the temperature at a rural area. UHIs are monitored using remote sensing techniques such as satellite imagery or using temperature sensors de-ployed in a metropolitan area. In this chapter we propose a methodology to moni-tor the UHI intensity from Global Navigation Satellite Systems (GNSS) data. As the GNSS signal travels from the satellite to the receiver it propagates through the troposphere. A delay (Tropospheric delay) affects the signal. The delay is propor-tional to environmental variables. Also, the tropospheric delay in zenith direction (ZTD) is estimated as part of the Precise Point Positioning (PPP) technique. Therefore, in this chapter it is shown how to use process GNSS data to obtain ZTD and obtain temperature at an urban and a rural site simultaneously from the ZTD. The advantages of using GNSS data is its availability and many GNSS networks have been deployed in different cities so no need to deploy sensor net-works. Furthermore, GNSS signal is less affected by bad weather conditions than satellite imagery

Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency ☆

Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPI I170V elicits behavioral abnormalities in Drosophila. An examination of hTPI I170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermal stability demonstrated an increase in enzyme stability. The crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. Collectively these data reveal new observations of the structural and kinetic determinants of TPI Deficiency pathology, providing new insights into disease pathogenesis

PetIGA: A framework for high-performance isogeometric analysis

We present PetIGA, a code framework to approximate the solution of partial differential equations using isogeometric analysis. PetIGA can be used to assemble matrices and vectors which come from a Galerkin weak form, discretized with Non-Uniform Rational B-spline basis functions. We base our framework on PETSc, a high-performance library for the scalable solution of partial differential equations, which simplifies the development of large-scale scientific codes, provides a rich environment for prototyping, and separates parallelism from algorithm choice. We describe the implementation of PetIGA, and exemplify its use by solving a model nonlinear problem. To illustrate the robustness and flexibility of PetIGA, we solve some challenging nonlinear partial differential equations that include problems in both solid and fluid mechanics. We show strong scaling results on up to 4096 cores, which confirm the suitability of PetIGA for large scale simulations

Molecular basis of association of receptor activity-modifying protein 3 with the family B G protein-coupled secretin receptor

The three receptor activity-modifying proteins (RAMPs) have been recognized as being important for the trafficking and function of a subset of family B G protein-coupled receptors, although the structural basis for this has not been well established. In the current work, we use morphological fluorescence techniques, bioluminescence resonance energy transfer, and bimolecular fluorescence complementation to demonstrate that the secretin receptor associates specifically with RAMP3, but not with RAMP1 or RAMP2. We use truncation constructs, peptide competition experiments, and chimeric secretin-GLP1 receptor constructs to establish that this association is structurally specific, dependent on the intramembranous region of the RAMP and TM6 and TM7 of this receptor. There were no observed changes in secretin-stimulated cAMP, intracellular calcium, ERK1/2 phosphorylation, or receptor internalization in receptor-bearing COS or CHO-K1 cells in the presence or absence of exogenous RAMP transfection, although the secretin receptor trafficks normally to the cell surface in these cells in a RAMP-independent manner, resulting in both free and RAMP-associated receptor on the cell surface. RAMP3 association with this receptor was shown to be capable of rescuing a receptor mutant (G241C) that is normally trapped intracellularly in the biosynthetic machinery. Similarly, secretin receptor expression had functional effects on adrenomedullin activity, with increasing secretin receptor expression competing for RAMP3 association with the calcitonin receptor-like receptor to yield a functional adrenomedullin receptor. These data provide important new insights into the structural basis for RAMP3 interaction with a family B G protein-coupled receptor, potentially providing a highly selective target for drug action. This may be representative of similar interactions between other members of this receptor family and RAMP proteins

Parallel algebraic multilevel Schwarz preconditioners for a class of elliptic PDE systems

Algebraic multilevel preconditioners for algebraic problems arising from the discretization of a class of systems of coupled elliptic partial differential equations (PDEs) are presented. These preconditioners are based on modifications of Schwarz methods and of the smoothed aggregation technique, where the coarsening strategy and the restriction and prolongation operators are defined using a point-based approach with a primary matrix corresponding to a single PDE. The preconditioners are implemented in a parallel computing framework and are tested on two representative PDE systems. The results of the numerical experiments show the effectiveness and the scalability of the proposed methods. A convergence theory for the twolevel case is presented