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Sample records for nodal diffusion solver

  1. NESTLE: Few-group neutron diffusion equation solver utilizing the nodal expansion method for eigenvalue, adjoint, fixed-source steady-state and transient problems

    SciTech Connect

    Turinsky, P.J.; Al-Chalabi, R.M.K.; Engrand, P.; Sarsour, H.N.; Faure, F.X.; Guo, W.

    1994-06-01

    NESTLE is a FORTRAN77 code that solves the few-group neutron diffusion equation utilizing the Nodal Expansion Method (NEM). NESTLE can solve the eigenvalue (criticality); eigenvalue adjoint; external fixed-source steady-state; or external fixed-source. or eigenvalue initiated transient problems. The code name NESTLE originates from the multi-problem solution capability, abbreviating Nodal Eigenvalue, Steady-state, Transient, Le core Evaluator. The eigenvalue problem allows criticality searches to be completed, and the external fixed-source steady-state problem can search to achieve a specified power level. Transient problems model delayed neutrons via precursor groups. Several core properties can be input as time dependent. Two or four energy groups can be utilized, with all energy groups being thermal groups (i.e. upscatter exits) if desired. Core geometries modelled include Cartesian and Hexagonal. Three, two and one dimensional models can be utilized with various symmetries. The non-linear iterative strategy associated with the NEM method is employed. An advantage of the non-linear iterative strategy is that NSTLE can be utilized to solve either the nodal or Finite Difference Method representation of the few-group neutron diffusion equation.

  2. Nodal Diffusion & Transport Theory

    1992-02-19

    DIF3D solves multigroup diffusion theory eigenvalue, adjoint, fixed source, and criticality (concentration, buckling, and dimension search) problems in 1, 2, and 3-space dimensions for orthogonal (rectangular or cylindrical), triangular, and hexagonal geometries. Anisotropic diffusion theory coefficients are permitted. Flux and power density maps by mesh cell and regionwise balance integrals are provided. Although primarily designed for fast reactor problems, upscattering and internal black boundary conditions are also treated.

  3. A two dimensional nodal Riemann solver based on one dimensional Riemann solver for a cell-centered Lagrangian scheme

    NASA Astrophysics Data System (ADS)

    Liu, Yan; Shen, Weidong; Tian, Baolin; Mao, De-kang

    2015-03-01

    We develop a new and more general formula for the construction of two dimensional nodal Riemann solver for a cell-centered Lagrangian scheme developed by Maire and his co-workers which allows us to use general one dimensional Riemann solvers that have intermediate velocity and pressure in the construction. The old formula for the scheme used in the papers of Maire et al. is only a special case of our new formula. We present an entropy discussion, which indicates that the schemes with nodal solvers constructed following the old formula, which can only use the 1D Riemann solvers satisfying our strong entropy condition, are usually numerically very dissipative. To develop numerically less dissipative schemes we introduce a so-called weak entropy condition, and present a one dimensional Riemann solver that satisfies the weak entropy condition but not the strong entropy condition. Analysis shows that the scheme using this 1D solver is numerically less dissipative than the schemes using solvers satisfying the strong condition. Finally, several numerical examples are presented to show that our new formula works well and the scheme using the one dimensional solver satisfying the weak entropy condition improves the accuracy in smooth region, resolution around rarefaction waves and two dimensional symmetry; however it sometimes produces small velocity oscillations and mesh distortions.

  4. The AN neutron transport by nodal diffusion

    SciTech Connect

    Barbarino, A.; Tomatis, D.

    2013-07-01

    The two group diffusion model combined to a nodal approach in space is the preferred scheme for the industrial simulation of nuclear water reactors. The main selling point is the speed of computation, allowing a large number of parametric studies. Anyway, the drawbacks of the underlying diffusion equation may arise with highly heterogeneous interfaces, often encountered in modern UO{sub 2} and MO{sub x} fuel loading patterns, and boron less controlled systems. This paper aims at showing how the simplified AN transport model, equivalent to the well known SPN, can be implemented in standard diffusion codes with minor modifications. Some numerical results are illustrated. (authors)

  5. The General-Use Nodal Network Solver (GUNNS) Modeling Package for Space Vehicle Flow System Simulation

    NASA Technical Reports Server (NTRS)

    Harvey, Jason; Moore, Michael

    2013-01-01

    The General-Use Nodal Network Solver (GUNNS) is a modeling software package that combines nodal analysis and the hydraulic-electric analogy to simulate fluid, electrical, and thermal flow systems. GUNNS is developed by L-3 Communications under the TS21 (Training Systems for the 21st Century) project for NASA Johnson Space Center (JSC), primarily for use in space vehicle training simulators at JSC. It has sufficient compactness and fidelity to model the fluid, electrical, and thermal aspects of space vehicles in real-time simulations running on commodity workstations, for vehicle crew and flight controller training. It has a reusable and flexible component and system design, and a Graphical User Interface (GUI), providing capability for rapid GUI-based simulator development, ease of maintenance, and associated cost savings. GUNNS is optimized for NASA's Trick simulation environment, but can be run independently of Trick.

  6. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system.

    PubMed

    Müller, Patrick; Rogers, Katherine W; Jordan, Ben M; Lee, Joon S; Robson, Drew; Ramanathan, Sharad; Schier, Alexander F

    2012-05-11

    Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients revealed that Nodals have a shorter range than Lefty proteins. Pulse-labeling analysis indicated that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays revealed that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning.

  7. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system

    PubMed Central

    Müller, Patrick; Rogers, Katherine W.; Jordan, Ben M.; Lee, Joon S.; Robson, Drew; Ramanathan, Sharad; Schier, Alexander F.

    2012-01-01

    Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients reveals that Nodals have a shorter range than Lefty proteins. Pulse-labelinganalysis indicates that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays reveal that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning. PMID:22499809

  8. An AMR capable finite element diffusion solver for ALE hydrocodes [An AMR capable diffusion solver for ALE-AMR

    SciTech Connect

    Fisher, A. C.; Bailey, D. S.; Kaiser, T. B.; Eder, D. C.; Gunney, B. T. N.; Masters, N. D.; Koniges, A. E.; Anderson, R. W.

    2015-02-01

    Here, we present a novel method for the solution of the diffusion equation on a composite AMR mesh. This approach is suitable for including diffusion based physics modules to hydrocodes that support ALE and AMR capabilities. To illustrate, we proffer our implementations of diffusion based radiation transport and heat conduction in a hydrocode called ALE-AMR. Numerical experiments conducted with the diffusion solver and associated physics packages yield 2nd order convergence in the L2 norm.

  9. Nodal Diffusion Burnable Poison Treatment for Prismatic Reactor Cores

    SciTech Connect

    A. M. Ougouag; R. M. Ferrer

    2010-10-01

    The prismatic block version of the High Temperature Reactor (HTR) considered as a candidate Very High Temperature Reactor (VHTR)design may use burnable poison pins in locations at some corners of the fuel blocks (i.e., assembly equivalent structures). The presence of any highly absorbing materials, such as these burnable poisons, within fuel blocks for hexagonal geometry, graphite-moderated High Temperature Reactors (HTRs) causes a local inter-block flux depression that most nodal diffusion-based method have failed to properly model or otherwise represent. The location of these burnable poisons near vertices results in an asymmetry in the morphology of the assemblies (or blocks). Hence the resulting inadequacy of traditional homogenization methods, as these “spread” the actually local effect of the burnable poisons throughout the assembly. Furthermore, the actual effect of the burnable poison is primarily local with influence in its immediate vicinity, which happens to include a small region within the same assembly as well as similar regions in the adjacent assemblies. Traditional homogenization methods miss this artifact entirely. This paper presents a novel method for treating the local effect of the burnable poison explicitly in the context of a modern nodal method.

  10. Status of the Development of an Embedded Transport Treatment of Control Rods and of Radial Flux Expansion in Cylindrical Nodal Diffusion Codes

    SciTech Connect

    Frederick N. Gleicher II; Abderrafi M. Ougouag

    2009-09-01

    A new diffusion-transport hybrid nodal method in R-Z is presented that can effectively treat non-multiplying zones in pebble bed reactors. The new method seamlessly combines the analytic coarse mesh finite difference (CMFD) diffusion formulation and a transport theory based response matrix formulation while retaining the properties and structure of the CMFD diffusion solver. The resulting combined formulation is utilized in selected non-multiplying nodes to capture angular effects on the flux. Test results indicate that the method has been implemented correctly into the CYNOD reactor kinetics code. This document also presents a status report on the development of a better source approximation for the Green’s function nodal solution in the radial direction of cylindrical geometry. The basic theory has been developed, including obtaining polynomials that are orthonormal over the domain of integration and the derivation of approximately half of the required matrix elements (single and double integrals in the source expansions).

  11. ANOVA-HDMR structure of the higher order nodal diffusion solution

    SciTech Connect

    Bokov, P. M.; Prinsloo, R. H.; Tomasevic, D. I.

    2013-07-01

    Nodal diffusion methods still represent a standard in global reactor calculations, but employ some ad-hoc approximations (such as the quadratic leakage approximation) which limit their accuracy in cases where reference quality solutions are sought. In this work we solve the nodal diffusion equations utilizing the so-called higher-order nodal methods to generate reference quality solutions and to decompose the obtained solutions via a technique known as High Dimensional Model Representation (HDMR). This representation and associated decomposition of the solution provides a new formulation of the transverse leakage term. The HDMR structure is investigated via the technique of Analysis of Variance (ANOVA), which indicates why the existing class of transversely-integrated nodal methods prove to be so successful. Furthermore, the analysis leads to a potential solution method for generating reference quality solutions at a much reduced calculational cost, by applying the ANOVA technique to the full higher order solution. (authors)

  12. Advanced Nodal P3/SP3 Axial Transport Solvers for the MPACT 2D/1D Scheme

    SciTech Connect

    Stimpson, Shane G; Collins, Benjamin S

    2015-01-01

    As part of its initiative to provide multiphysics simulations of nuclear reactor cores, the Consortium for Advanced Simulation of Light Water Reactors (CASL) is developing the Virtual Environment for Reactor Applications Core Simulator (VERA-CS). The MPACT code, which is the primary neutron transport solver of VERA-CS, employs the two-dimensional/one-dimensional (2D/1D) method to solve 3-dimensional neutron transport problems and provide sub-pin-level resolution of the power distribution. While 2D method of characteristics is used to solve for the transport effects within each plane, 1D-nodal methods are used axially. There have been extensive studies of the 2D/1D method with a variety nodal methods, and the P3/SP3 solver has proved to be an effective method of providing higher-fidelity solutions while maintaining a low computational burden.The current implementation in MPACT wraps a one-node nodal expansion method (NEM) kernel for each moment, iterating between them and performing multiple sweeps to resolve flux distributions. However, it has been observed that this approach is more sensitive to convergence problems. This paper documents the theory and application two new nodal P3/SP3 approaches to be used within the 2D/1D method in MPACT. These two approaches aim to provide enhanced stability compared with the pre-existing one-node approach. Results from the HY-NEM-SP3 solver show that the accuracy is consistent with the one-node formulations and provides improved convergence for some problems; but the solver has issues with cases in thin planes. Although the 2N-SENM-SP3 solver is still under development, it is intended to resolve the issues with HY-NEM-SP3 but it will incur some additional computational burden by necessitating an additional 1D-CMFD-P3 solver to generate the second moment cell-averaged scalar flux.

  13. Undertreatment of patients with localized extranodal compared with nodal diffuse large B-cell lymphoma.

    PubMed

    Kuper-Hommel, Marion J J; van de Schans, Saskia A M; Vreugdenhil, Gerard; van Krieken, J Han; Coebergh, Jan-Willem W

    2013-08-01

    Population-based studies analyzing clinical implications of nodal versus extranodal (EN) presentation of diffuse large B-cell lymphoma (DLBCL) are scarce. We studied clinical differences and trends in incidence, treatment and survival of nodal and EN DLBCL in a population-based cohort. All patients newly diagnosed with localized (Ann Arbor stage [AAS] I and II) nodal (n = 5124) and EN (n = 4776) DLBCL, and primary mediastinal B-cell lymphoma (PMBL; n = 88), diagnosed between 1989 and 2010, were selected from the Netherlands Cancer Registry. Primary EN disease was correlated with older age and more favorable clinical stage (AAS I). The age standardized incidence rates for men with localized EN DLBCL, and for men and women with localized PMBL, increased significantly, whereas the age standardized incidence rates of all other subgroups remained stable. The stomach was the most common EN localization. Patients with EN disease received less chemotherapy and targeted therapy than their nodal counterparts, irrespective of age and period of diagnosis. Their 5-year overall survival (OS) was 48% vs. 54% in the nodal group, but in multivariate analysis primary extranodal presentation was not independently associated with inferior survival. This population-based study shows clinically relevant differences between localized nodal and EN DLBCL and PMBL. Since patients with EN were significantly less often optimally treated, we advocate better interaction between medical disciplines. PMID:23190406

  14. Green's Function Nodal Algorithm for the Diffusion Equation.

    1989-12-04

    Version 00 GRENADE is a coarse-mesh program designed for neutronic flux and power calculations in nuclear reactors. It solves the static diffusion equation for neutrons in multidimensional problems, assuming Cartesian Geometry. The program yields flux and power distributions and the effective neutron multiplication factor .

  15. High-Speed Three-Dimensional Nodal Diffusion Code System.

    2001-03-21

    Version 00 MOSRA-Light is a three-dimensional diffusion calculation code for X-Y-Z geometry. It can be used in: validation of discontinuity factor for adjoint problem; benchmark on discontinuity factor (forward & adjoint cal.); DVP BWR Benchmark (2D,2G calculation); and void reactivity effect benchmark; etc. A utility code called More-MOSRA provides many useful functions with the file produced by MOSRA-Light.

  16. Advanced computational methods for nodal diffusion, Monte Carlo, and S(sub N) problems

    NASA Astrophysics Data System (ADS)

    Martin, W. R.

    1993-01-01

    This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. An alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.

  17. Advanced computational methods for nodal diffusion, Monte Carlo, and S[sub N] problems

    SciTech Connect

    Martin, W.R.

    1993-01-01

    This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. A alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.

  18. A coarse-mesh nodal method-diffusive-mesh finite difference method

    SciTech Connect

    Joo, H.; Nichols, W.R.

    1994-05-01

    Modern nodal methods have been successfully used for conventional light water reactor core analyses where the homogenized, node average cross sections (XSs) and the flux discontinuity factors (DFs) based on equivalence theory can reliably predict core behavior. For other types of cores and other geometries characterized by tightly-coupled, heterogeneous core configurations, the intranodal flux shapes obtained from a homogenized nodal problem may not accurately portray steep flux gradients near fuel assembly interfaces or various reactivity control elements. This may require extreme values of DFs (either very large, very small, or even negative) to achieve a desired solution accuracy. Extreme values of DFs, however, can disrupt the convergence of the iterative methods used to solve for the node average fluxes, and can lead to a difficulty in interpolating adjacent DF values. Several attempts to remedy the problem have been made, but nothing has been satisfactory. A new coarse-mesh nodal scheme called the Diffusive-Mesh Finite Difference (DMFD) technique, as contrasted with the coarse-mesh finite difference (CMFD) technique, has been developed to resolve this problem. This new technique and the development of a few-group, multidimensional kinetics computer program are described in this paper.

  19. A coarse-mesh nodal method, the diffusive-mesh finite difference method

    SciTech Connect

    Joo, H.; Nichols, W.R.

    1994-12-31

    Modern nodal methods have been successfully used for conventional light water reactor core analyses where the homogenized, node average cross section (XSs) and the flux discontinuity factors (DFs) based on equivalence theory can reliably predict core behavior. For other types of cores and other geometries characterized by tightly coupled, heterogeneous core configurations, the intranodal flux shapes obtained from a homogenized nodal problem may not accurately portray steep flux gradients near fuel assembly interfaces or various reactivity control elements. This may require extreme values of DFs (either very large, very small, or even negative) to achieve a desired solution accuracy. Extreme values of DFs, however, can disrupt the convergence of the iterative methods used to solve for the node average fluxes and can lead to difficulty in interpolating adjacent DF values. Several attempts to remedy the problem have been made, but nothing has been satisfactory. A new coarse-mesh nodal scheme called the diffusive-mesh finite difference (DMFD) technique, as contrasted with the coarse-mesh finite difference (CMFD) technique, has been developed to resolve this problem. This new technique and the development of a few-group, multidimensional kinetics computer program are described in this paper.

  20. Nodal predictive error model and Bayesian approach for thermal diffusivity and heat source mapping

    NASA Astrophysics Data System (ADS)

    Massard, H.; Fudym, Olivier; Orlande, H. R. B.; Batsale, J. C.

    2010-07-01

    This article aims at solving a two-dimensional inverse heat conduction problem in order to retrieve both the thermal diffusivity and heat source field in a thin plate. A spatial random heat pulse is applied to the plate and the thermal response is analysed. The inverse approach is based on the minimisation of a nodal predictive error model, which yields a linear estimation problem. As a result of this approach, the sensitivity matrix is directly filled with experimental data, and thus is partially noisy. Bayesian estimators, such as the Maximum A Posteriori and a Markov Chain Monte Carlo approach (Metropolis-Hastings), are implemented and compared with the Ordinary Least Squares solution. Simulated temperature measurements are used in the inverse analysis. The nodal strategy relies on the availability of temperature measurements with fine spatial resolution and high frequency, typical of nowadays infrared cameras. The effects of both the measurement errors and of the model errors on the inverse problem solution are also analysed.

  1. Fast linear solver for radiative transport equation with multiple right hand sides in diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Jia, Jingfei; Kim, Hyun K.; Hielscher, Andreas H.

    2015-12-01

    It is well known that radiative transfer equation (RTE) provides more accurate tomographic results than its diffusion approximation (DA). However, RTE-based tomographic reconstruction codes have limited applicability in practice due to their high computational cost. In this article, we propose a new efficient method for solving the RTE forward problem with multiple light sources in an all-at-once manner instead of solving it for each source separately. To this end, we introduce here a novel linear solver called block biconjugate gradient stabilized method (block BiCGStab) that makes full use of the shared information between different right hand sides to accelerate solution convergence. Two parallelized block BiCGStab methods are proposed for additional acceleration under limited threads situation. We evaluate the performance of this algorithm with numerical simulation studies involving the Delta-Eddington approximation to the scattering phase function. The results show that the single threading block RTE solver proposed here reduces computation time by a factor of 1.5-3 as compared to the traditional sequential solution method and the parallel block solver by a factor of 1.5 as compared to the traditional parallel sequential method. This block linear solver is, moreover, independent of discretization schemes and preconditioners used; thus further acceleration and higher accuracy can be expected when combined with other existing discretization schemes or preconditioners.

  2. DIF3D nodal neutronics option for two- and three-dimensional diffusion theory calculations in hexagonal geometry. [LMFBR

    SciTech Connect

    Lawrence, R.D.

    1983-03-01

    A nodal method is developed for the solution of the neutron-diffusion equation in two- and three-dimensional hexagonal geometries. The nodal scheme has been incorporated as an option in the finite-difference diffusion-theory code DIF3D, and is intended for use in the analysis of current LMFBR designs. The nodal equations are derived using higher-order polynomial approximations to the spatial dependence of the flux within the hexagonal-z node. The final equations, which are cast in the form of inhomogeneous response-matrix equations for each energy group, involved spatial moments of the node-interior flux distribution plus surface-averaged partial currents across the faces of the node. These equations are solved using a conventional fission-source iteration accelerated by coarse-mesh rebalance and asymptotic source extrapolation. This report describes the mathematical development and numerical solution of the nodal equations, as well as the use of the nodal option and details concerning its programming structure. This latter information is intended to supplement the information provided in the separate documentation of the DIF3D code.

  3. Low-diffusion approximate Riemann solvers for Reynolds-stress transport

    NASA Astrophysics Data System (ADS)

    Ben Nasr, N.; Gerolymos, G. A.; Vallet, I.

    2014-07-01

    The paper investigates the use of low-diffusion (contact-discontinuity-resolving) approximate Riemann solvers for the convective part of the Reynolds-averaged Navier-Stokes (RANS) equations with Reynolds-stress model (RSM) for turbulence. Different equivalent forms of the RSM-RANS system are discussed and classification of the complex terms introduced by advanced turbulence closures is attempted. Computational examples are presented, which indicate that the use of contact-discontinuity-resolving convective numerical fluxes, along with a passive-scalar approach for the Reynolds-stresses, may lead to unphysical oscillations of the solution. To determine the source of these instabilities, theoretical analysis of the Riemann problem for a simplified Reynolds-stress transport model-system, which incorporates the divergence of the Reynolds-stress tensor in the convective part of the mean-flow equations, and includes only those nonconservative products which are computable (do not require modelling), was undertaken, highlighting the differences in wave-structure compared to the passive-scalar case. A hybrid solution, allowing the combination of any low-diffusion approximate Riemann solver with the complex tensorial representations used in advanced models, is proposed, combining low-diffusion fluxes for the mean-flow equations with a more dissipative massflux for Reynolds-stress-transport. Several computational examples are presented to assess the performance of this approach, demonstrating enhanced accuracy and satisfactory convergence.

  4. Convergence properties of iterative algorithms for solving the nodal diffusion equations

    SciTech Connect

    Azmy, Y Y; Kirk, B L

    1990-01-01

    We drive the five point form of the nodal diffusion equations in two-dimensional Cartesian geometry and develop three iterative schemes to solve the discrete-variable equations: the unaccelerated, partial Successive Over Relaxation (SOR), and the full SOR methods. By decomposing the iteration error into its Fourier modes, we determine the spectral radius of each method for infinite medium, uniform model problems, and for the unaccelerated and partial SOR methods for finite medium, uniform model problems. Also for the two variants of the SOR method we determine the optimal relaxation factor that results in the smallest number of iterations required for convergence. Our results indicate that the number of iterations for the unaccelerated and partial SOR methods is second order in the number of nodes per dimension, while, for the full SOR this behavior is first order, resulting in much faster convergence for very large problems. We successfully verify the results of the spectral analysis against those of numerical experiments, and we show that for the full SOR method the linear dependence of the number of iterations on the number of nodes per dimension is relatively insensitive to the value of the relaxation parameter, and that it remains linear even for heterogenous problems. 14 refs., 1 fig.

  5. Diffusion-Weighted MRI for Nodal Staging of Head and Neck Squamous Cell Carcinoma: Impact on Radiotherapy Planning

    SciTech Connect

    Dirix, Piet; Vandecaveye, Vincent; De Keyzer, Frederik; Op de beeck, Katya; Poorten, Vincent Vander; Delaere, Pierre; Verbeken, Eric; Hermans, Robert; Nuyts, Sandra

    2010-03-01

    Purpose: To evaluate the use of diffusion-weighted magnetic resonance imaging (DW-MRI) for nodal staging and its impact on radiotherapy (RT) planning. Methods and Materials: Twenty-two patients with locally advanced head and neck squamous cell carcinoma underwent contrast-enhanced computed tomography (CT), as well as MRI (with routine and DW sequences) prior to neck dissection. After topographic correlation, lymph nodes were evaluated microscopically with prekeratin immunostaining. Pathology results were correlated with imaging findings and an RT planning study was performed for these surgically treated patients. One set of target volumes was based on conventional imaging only, and another set was based on the corresponding DW-MRI images. A third reference set was contoured based solely on pathology results. Results: A sensitivity of 89% and a specificity of 97% per lymph node were found for DW-MRI. Nodal staging agreement between imaging and pathology was significantly stronger for DW-MRI (kappa = 0.97; 95% confidence interval [CI], 0.84-1.00) than for conventional imaging (kappa = 0.56; 95% CI, 0.16-0.96; p = 0.019, by McNemar's test). For both imaging modalities, the absolute differences between RT volumes and those obtained by pathology were calculated. Using an exact paired Wilcoxon test, the observed difference was significantly larger for conventional imaging than for DW-MRI for nodal gross tumor volume (p = 0.0013), as well as for nodal clinical target volume (p = 0.0415) delineation. Conclusions: These results suggest that DW-MRI is superior to conventional imaging for preradiotherapy nodal staging of head and neck squamous cell carcinoma, and provides a potential impact on organsparing and tumor control.

  6. Three-Dimensional, Nodal, Neutron Diffusion Criticality Code System in Hex-Z Geometry.

    1992-07-27

    Version: 00 SIXTUS-3 is a 3D extention of SIXTUS-2 and is based on a response matrix nodal model. The code offers a fast and accurate analysis of critical systems in the regular hex-z geometry with the multigroup cross section representation including arbitrary upscattering.

  7. Extra-nodal Diffuse Large B-cell Lymphoma (Germinal Center Type) Manifesting as Non-healing Extraction Socket.

    PubMed

    Syamala, Manasa; Basavarajappa, Manjunath Anekonda; Pathan, Sana; Raheem, Ahmed Mujib Bangalore; Godavarthy, Divyasri

    2016-08-01

    Lymphomas occurring in the oral cavity are rare. They account only for about 2% of extra-nodal sites. Most of the lymphomas occur in the lymph nodes and in the oral cavity, the most commonly affected region is the Waldeyer's ring. Its occurrence in the mandibular gingiva is rare. Here, we describe a case of Diffuse Large B-cell Lymphoma manifested as a non-healing extraction socket in the mandibular right posterior region in a 62-year-old male patient. PMID:27656575

  8. Extra-nodal Diffuse Large B-cell Lymphoma (Germinal Center Type) Manifesting as Non-healing Extraction Socket

    PubMed Central

    Basavarajappa, Manjunath Anekonda; Pathan, Sana; Raheem, Ahmed Mujib Bangalore; Godavarthy, Divyasri

    2016-01-01

    Lymphomas occurring in the oral cavity are rare. They account only for about 2% of extra-nodal sites. Most of the lymphomas occur in the lymph nodes and in the oral cavity, the most commonly affected region is the Waldeyer’s ring. Its occurrence in the mandibular gingiva is rare. Here, we describe a case of Diffuse Large B-cell Lymphoma manifested as a non-healing extraction socket in the mandibular right posterior region in a 62-year-old male patient. PMID:27656575

  9. Parareal in time 3D numerical solver for the LWR Benchmark neutron diffusion transient model

    SciTech Connect

    Baudron, Anne-Marie; Riahi, Mohamed Kamel; Salomon, Julien

    2014-12-15

    In this paper we present a time-parallel algorithm for the 3D neutrons calculation of a transient model in a nuclear reactor core. The neutrons calculation consists in numerically solving the time dependent diffusion approximation equation, which is a simplified transport equation. The numerical resolution is done with finite elements method based on a tetrahedral meshing of the computational domain, representing the reactor core, and time discretization is achieved using a θ-scheme. The transient model presents moving control rods during the time of the reaction. Therefore, cross-sections (piecewise constants) are taken into account by interpolations with respect to the velocity of the control rods. The parallelism across the time is achieved by an adequate use of the parareal in time algorithm to the handled problem. This parallel method is a predictor corrector scheme that iteratively combines the use of two kinds of numerical propagators, one coarse and one fine. Our method is made efficient by means of a coarse solver defined with large time step and fixed position control rods model, while the fine propagator is assumed to be a high order numerical approximation of the full model. The parallel implementation of our method provides a good scalability of the algorithm. Numerical results show the efficiency of the parareal method on large light water reactor transient model corresponding to the Langenbuch–Maurer–Werner benchmark.

  10. Nodally exact Ritz discretizations of 1D diffusion-absorption and Helmholtz equations by variational FIC and modified equation methods

    NASA Astrophysics Data System (ADS)

    Felippa, C. A.; Oñate, E.

    2007-01-01

    This article presents the first application of the Finite Calculus (FIC) in a Ritz-FEM variational framework. FIC provides a steplength parametrization of mesh dimensions, which is used to modify the shape functions. This approach is applied to the FEM discretization of the steady-state, one-dimensional, diffusion-absorption and Helmholtz equations. Parametrized linear shape functions are directly inserted into a FIC functional. The resulting Ritz-FIC equations are symmetric and carry a element-level free parameter coming from the function modification process. Both constant- and variable-coefficient cases are studied. It is shown that the parameter can be used to produce nodally exact solutions for the constant coefficient case. The optimal value is found by matching the finite-order modified differential equation (FOMoDE) of the Ritz-FIC equations with the original field equation. The inclusion of the Ritz-FIC models in the context of templates is examined. This inclusion shows that there is an infinite number of nodally exact models for the constant coefficient case. The ingredients of these methods (FIC, Ritz, MoDE and templates) can be extended to multiple dimensions

  11. Clinico-biological characterization and outcome of primary nodal and extranodal diffuse large B-cell lymphoma in the rituximab era.

    PubMed

    Gutiérrez-García, Gonzalo; Colomo, Lluis; Villamor, Neus; Arenillas, Leonor; Martínez, Antonio; Cardesa, Teresa; García-Herrera, Adriana; Setoain, Xavier; Rodríguez, Sonia; Ghita, Gabriela; Abrisqueta, Pau; Giné, Eva; Bosch, Francesc; Campo, Elías; Montserrat, Emilio; López-Guillermo, Armando

    2010-07-01

    To study the main clinico-biological characteristics and the outcome of patients with diffuse large B-cell lymphoma (DLBCL) according to the primary site (nodal vs. extranodal), we included 262 patients consecutively diagnosed with DLBCL in a single institution, 5 years before and after immunochemotherapy was considered as the standard treatment. Altogether 116 patients received CHOP (cyclophosphamide, adriamycin, vincristine, and prednisone) and 146 rituximab plus CHOP (R-CHOP). The primary site was the lymph node in 140 patients (53%), Waldeyer's ring (WR) in 22, gastrointestinal (GI) in 33, and other extranodal in 67. The addition of rituximab significantly improved the CR rate in nodal, but not in extranodal, lymphomas. Patients receiving R-CHOP showed higher OS than those treated with CHOP alone (5-year OS: 71% vs. 48%). This difference was maintained in primary nodal (5-year OS: 69% vs. 37%, p < 0.0001), but was not observed in primary extranodal (75% vs. 65%, p = 0.45) lymphomas. The IPI, treatment, and primary site were the main variables for OS in multivariate analysis. In nodal cases, IPI and treatment maintained value, whereas only IPI predicted OS in extranodal cases. In conclusion, immunochemotherapy treatment dramatically improved the outcome of patients with nodal DLBCL; however, its effect was less in primary extranodal cases, so the prognosis of patients with nodal and extranodal lymphomas has been equalized in the rituximab era. PMID:20497002

  12. A fast accurate approximation method with multigrid solver for two-dimensional fractional sub-diffusion equation

    NASA Astrophysics Data System (ADS)

    Lin, Xue-lei; Lu, Xin; Ng, Micheal K.; Sun, Hai-Wei

    2016-10-01

    A fast accurate approximation method with multigrid solver is proposed to solve a two-dimensional fractional sub-diffusion equation. Using the finite difference discretization of fractional time derivative, a block lower triangular Toeplitz matrix is obtained where each main diagonal block contains a two-dimensional matrix for the Laplacian operator. Our idea is to make use of the block ɛ-circulant approximation via fast Fourier transforms, so that the resulting task is to solve a block diagonal system, where each diagonal block matrix is the sum of a complex scalar times the identity matrix and a Laplacian matrix. We show that the accuracy of the approximation scheme is of O (ɛ). Because of the special diagonal block structure, we employ the multigrid method to solve the resulting linear systems. The convergence of the multigrid method is studied. Numerical examples are presented to illustrate the accuracy of the proposed approximation scheme and the efficiency of the proposed solver.

  13. Multigroup 3-Dimensional Neutron Diffusion Nodal Code System with Thermohydraulic Feedbacks.

    1994-02-07

    Version 01 GNOMER is a program which solves the multigroup neutron diffusion equation on coarse mesh in 1D, 2D, and 3D Cartesian geometry. The program is designed to calculate the global core power distributions (with thermohydraulic feedbacks) as well as power distributions and homogenized cross sections over a fuel assembly.

  14. GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem

    NASA Astrophysics Data System (ADS)

    Mena, Andres; Ferrero, Jose M.; Rodriguez Matas, Jose F.

    2015-11-01

    Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50 × for three-dimensional problems.

  15. GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem

    NASA Astrophysics Data System (ADS)

    Mena, Andres; Ferrero, Jose M.; Rodriguez Matas, Jose F.

    2015-11-01

    Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50 × for three-dimensional problems.

  16. Nodal approximations of varying order by energy group for solving the diffusion equation

    SciTech Connect

    Broda, J.T.

    1992-02-01

    The neutron flux across the nuclear reactor core is of interest to reactor designers and others. The diffusion equation, an integro-differential equation in space and energy, is commonly used to determine the flux level. However, the solution of a simplified version of this equation when automated is very time consuming. Since the flux level changes with time, in general, this calculation must be made repeatedly. Therefore solution techniques that speed the calculation while maintaining accuracy are desirable. One factor that contributes to the solution time is the spatial flux shape approximation used. It is common practice to use the same order flux shape approximation in each energy group even though this method may not be the most efficient. The one-dimensional, two-energy group diffusion equation was solved, for the node average flux and core k-effective, using two sets of spatial shape approximations for each of three reactor types. A fourth-order approximation in both energy groups forms the first set of approximations used. The second set used combines a second-order approximation with a fourth-order approximation in energy group two. Comparison of the results from the two approximation sets show that the use of a different order spatial flux shape approximation results in considerable loss in accuracy for the pressurized water reactor modeled. However, the loss in accuracy is small for the heavy water and graphite reactors modeled. The use of different order approximations in each energy group produces mixed results. Further investigation into the accuracy and computing time is required before any quantitative advantage of the use of the second-order approximation in energy group one and the fourth-order approximation in energy group two can be determined.

  17. A preconditioned numerical solver for stiff nonlinear reaction-diffusion equations with fractional Laplacians that avoids dense matrices

    NASA Astrophysics Data System (ADS)

    Simmons, Alex; Yang, Qianqian; Moroney, Timothy

    2015-04-01

    The numerical solution of fractional partial differential equations poses significant computational challenges in regard to efficiency as a result of the spatial nonlocality of the fractional differential operators. The dense coefficient matrices that arise from spatial discretisation of these operators mean that even one-dimensional problems can be difficult to solve using standard methods on grids comprising thousands of nodes or more. In this work we address this issue of efficiency for one-dimensional, nonlinear space-fractional reaction-diffusion equations with fractional Laplacian operators. We apply variable-order, variable-stepsize backward differentiation formulas in a Jacobian-free Newton-Krylov framework to advance the solution in time. A key advantage of this approach is the elimination of any requirement to form the dense matrix representation of the fractional Laplacian operator. We show how a banded approximation to this matrix, which can be formed and factorised efficiently, can be used as part of an effective preconditioner that accelerates convergence of the Krylov subspace iterative solver. Our approach also captures the full contribution from the nonlinear reaction term in the preconditioner, which is crucial for problems that exhibit stiff reactions. Numerical examples are presented to illustrate the overall effectiveness of the solver.

  18. Applying and validating the RANS-3D flow-solver for evaluating a subsonic serpentine diffuser geometry

    NASA Technical Reports Server (NTRS)

    Fletcher, Michael J.; Won, Mark J.; Cosentino, Gary B.; Te, Alexander

    1993-01-01

    Subsonic inlet ducts for advanced, high-performance aircraft are evolving towards complex three-dimensional shapes for reasons of overall integration and weight. These factors lead to diffuser geometries that may sacrifice inlet performance, unless careful attention to design details and boundary layer management techniques are employed. The ability of viscous computational fluid dynamic (CFD) analysis of such geometries to aid the aircraft configurator in this complex design problem is herein examined. The RANS-3D Reynolds-Averaged Navier-Stokes solver is applied to model the complex flowfield occurring in a representative diffuser geometry and the solutions are compared to experimental results from a static test of the inlet duct. The computational results are shown to compare very favorably with experimental results over a range of mass flow rates, including those involving large amounts of separation in the diffuser. In addition, a novel grid topology is presented, and two turbulence models are evaluated in this study as part of the RANS-3D code.

  19. Advanced computational methods for nodal diffusion, Monte Carlo, and S{sub N} problems. Progress report, January 1, 1992--March 31, 1993

    SciTech Connect

    Martin, W.R.

    1993-01-01

    This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. A alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.

  20. Second-order accurate interface- and discontinuity-aware diffusion solvers in two and three dimensions

    SciTech Connect

    Dai, William W. Scannapieco, Anthony J.

    2015-01-15

    A numerical scheme is developed for two- and three-dimensional time-dependent diffusion equations in numerical simulations involving mixed cells. The focus of the development is on the formulations for both transient and steady states, the property for large time steps, second-order accuracy in both space and time, the correct treatment of the discontinuity in material properties, and the handling of mixed cells. For a mixed cell, interfaces between materials are reconstructed within the cell so that each of resulting sub-cells contains only one material and the material properties of each sub-cell are known. Diffusion equations are solved on the resulting polyhedral mesh even if the original mesh is structured. The discontinuity of material properties between different materials is correctly treated based on governing physics principles. The treatment is exact for arbitrarily strong discontinuity. The formulae for effective diffusion coefficients across interfaces between materials are derived for general polyhedral meshes. The scheme is general in two and three dimensions. Since the scheme to be developed in this paper is intended for multi-physics code with adaptive mesh refinement (AMR), we present the scheme on mesh generated from AMR. The correctness and features of the scheme are demonstrated for transient problems and steady states in one-, two-, and three-dimensional simulations for heat conduction and radiation heat transfer. The test problems involve dramatically different materials.

  1. Characterization of a variant of t(14;18) negative nodal diffuse follicular lymphoma with CD23 expression, 1p36/TNFRSF14 abnormalities, and STAT6 mutations.

    PubMed

    Siddiqi, Imran N; Friedman, Julia; Barry-Holson, Keegan Q; Ma, Charles; Thodima, Venkata; Kang, Irene; Padmanabhan, Raghavendra; Dias, Lizalynn M; Kelly, Kevin R; Brynes, Russell K; Kamalakaran, Sitharthan; Houldsworth, Jane

    2016-06-01

    A predominantly diffuse growth pattern and CD23 co-expression are uncommon findings in nodal follicular lymphoma and can create diagnostic challenges. A single case series in 2009 (Katzenberger et al) proposed a unique morphologic variant of nodal follicular lymphoma, characterized by a predominantly diffuse architecture, lack of the t(14;18) IGH/BCL2 translocation, presence of 1p36 deletion, frequent inguinal lymph node involvement, CD23 co-expression, and low clinical stage. Other studies on CD23+ follicular lymphoma, while associating inguinal location, have not specifically described this architecture. In addition, no follow-up studies have correlated the histopathologic and cytogenetic/molecular features of these cases, and they remain a diagnostic problem. We identified 11 cases of diffuse, CD23+ follicular lymphoma with histopathologic features similar to those described by Katzenberger et al. Along with pertinent clinical information, we detail their histopathology, IGH/BCL2 translocation status, lymphoma-associated chromosomal gains/losses, and assessment of mutations in 220 lymphoma-associated genes by massively parallel sequencing. All cases showed a diffuse growth pattern around well- to ill-defined residual germinal centers, uniform CD23 expression, mixed centrocytic/centroblastic cytology, and expression of at least one germinal center marker. Ten of 11 involved inguinal lymph nodes, 5 solely. By fluorescence in situ hybridization analysis, the vast majority lacked IGH/BCL2 translocation (9/11). Deletion of 1p36 was observed in five cases and included TNFRSF14. Of the six cases lacking 1p36 deletion, TNFRSF14 mutations were identified in three, highlighting the strong association of 1p36/TNFRSF14 abnormalities with this follicular lymphoma variant. In addition, 9 of the 11 cases tested (82%) had STAT6 mutations and nuclear P-STAT6 expression was detectable in the mutated cases by immunohistochemistry. The proportion of STAT6 mutations is higher than

  2. Behavior of the Diamond Difference and Low-Order Nodal Numerical Transport Methods in the Thick Diffusion Limit for Slab Geometry

    SciTech Connect

    Gill, Daniel Fury

    2007-05-01

    The objective of this work is to investigate the thick diffusion limit of various spatial discretizations of the one-dimensional, steady-state, monoenergetic, discrete ordinates neutron transport equation. This work specifically addresses the two lowest order nodal methods, AHOT-N0 and AHOT-N1, as well as reconsiders the asymptotic limit of the Diamond Difference method. The asymptotic analyses of the AHOT-N0 and AHOT-N1 nodal methods show that AHOT-N0 does not possess the thick diffusion limit for cell edge or cell average fluxes except under very limiting conditions, which is to be expected considering the AHOT-N0 method limits to the Step method in the thick diffusion limit. The AHOT-N1 method, which uses a linear in-cell representation of the flux, was shown to possess the thick diffusion limit for both cell average and cell edge fluxes. The thick diffusion limit of the DD method, including the boundary conditions, was derived entirely in terms of cell average scalar fluxes. It was shown that, for vacuum boundaries, only when σt, h, and Q are constant and σa = 0 is the asymptotic limit of the DD method close to the finite-differenced diffusion equation in the system interior, and that the boundary conditions between the systems will only agree in the absence of an external source. For a homogeneous medium an effective diffusion coefficient was shown to be present, which was responsible for causing numeric diffusion in certain cases. A technique was presented to correct the numeric diffusion in the interior by altering certain problem parameters. Numerical errors introduced by the boundary conditions and material interfaces were also explored for a two-region problem using the Diamond Difference method. A discrete diffusion solution which exactly solves the one-dimensional diffusion equation in a homogeneous region with constant cross sections and a uniform external source was also developed and shown to be equal to the finite

  3. NODAL DIFFUSE LARGE B-CELL LYMPHOMAS IN CHILDREN AND ADOLESCENTS: IMMUNOHISTOCHEMICAL EXPRESSION PATTERNS AND C-MYC TRANSLOCATION IN RELATION TO CLINICAL OUTCOME

    PubMed Central

    Gualco, Gabriela; Weiss, Lawrence M.; Harrington, William J.; Bacchi, Carlos E.

    2009-01-01

    Diffuse large B-cell lymphoma (DLBCL) is a very infrequent neoplasm in the pediatric age group; therefore there are very few studies on the immunophenotype or genetics of these cases. We studied a series of 16 patients with nodal DLBCL occurring in patients between 10 and 18 years of age. The cases were classified according to the 2008 World Health Organization classification criteria, with application of immunohistochemistry for the detection of CD10, BCL-6 and MUM1 proteins to divide the lymphomas into germinal center and non-germinal center types. In addition, TCL1, BCL-2 expression, and the Ki-67 proliferation index were evaluated by immunohistochemistry, and c-MYC and BCL-2 translocations were evaluated by FISH. All these parameters were correlated with clinical features and outcome. Our study revealed that centroblastic morphology and the germinal center type of DLBCL are more prevalent in these young patients (63%), with 37% containing a c-MYC translocation. Only one case showed a BCL-2 translocation, reflecting a double-hit case with features intermediate between DLBCL and Burkitt lymphoma. We found a higher frequency of BCL-2 expression than previously reported, with no direct influence on the outcome of the disease in univariate or multivariate analysis. The expression of TCL1 has not been specifically studied in nodal pediatric DLBCL before; we found a 31% incidence of TCL1 expression. MUM1 expression was observed in 44% of the cases and these positive cases showed a significant negative impact on clinical outcome. TCL1 is directly and significantly associated with the presence of c-MYC and a high proliferative index. The germinal center and non-germinal center subtypes showed significant differences for both overall survival and disease-free interval. C-MYC translocation was found in 37% of patients, and had a favorable impact on clinical outcome. We conclude that nodal pediatric and adolescent DLBCL are mainly of the germinal center type, with a

  4. Nodal diffuse large B-cell lymphomas in children and adolescents: immunohistochemical expression patterns and c-MYC translocation in relation to clinical outcome.

    PubMed

    Gualco, Gabriela; Weiss, Lawrence M; Harrington, William J; Bacchi, Carlos E

    2009-12-01

    Diffuse large B-cell lymphoma (DLBCL) is a very infrequent neoplasm in the pediatric age group; therefore there are very few studies on the immunophenotype or genetics of these cases. We studied a series of 16 patients with nodal DLBCL occurring in patients between 10 and 18 years of age. The cases were classified according to the 2008 World Health Organization classification criteria, with application of immunohistochemistry for the detection of CD10, BCL-6, and MUM1 proteins to divide the lymphomas into germinal center and nongerminal center types. In addition, TCL1, BCL-2 expression, and the Ki-67 proliferation index were evaluated by immunohistochemistry, and c-MYC and BCL2 translocations were evaluated by fluorescence in situ hybridization. All these parameters were correlated with clinical features and outcome. Our study revealed that centroblastic morphology and the germinal center type of DLBCL are more prevalent in these young patients (63%), with 37% containing a c-MYC translocation. Only 1 case showed a BCL2 translocation, reflecting a double-hit case with features intermediate between DLBCL and Burkitt lymphoma. We found a higher frequency of BCL-2 expression than previously reported, with no direct influence on the outcome of the disease in univariate or multivariate analysis. The expression of TCL1 has not been specifically studied in nodal pediatric DLBCL before; we found a 31% incidence of TCL1 expression. MUM1 expression was observed in 44% of the cases and these positive cases showed a significant negative impact on clinical outcome. TCL1 is directly and significantly associated with the presence of c-MYC and a high proliferative index. The germinal center and nongerminal center subtypes showed significant differences for both overall survival and disease-free interval. c-MYC translocation was found in 37% of patients, and had a favorable impact on clinical outcome. We conclude that nodal pediatric and adolescent DLBCL are mainly of the germinal

  5. The contribution of HGAL/GCET2 in immunohistological algorithms: a comparative study in 424 cases of nodal diffuse large B-cell lymphoma.

    PubMed

    Gualco, Gabriela; Bacchi, Lívia M; Domeny-Duarte, Pollyanna; Natkunam, Yasodha; Bacchi, Carlos E

    2012-11-01

    Diffuse large B-cell lymphoma can be subclassified into at least two molecular subgroups by gene expression profiling: germinal center B-cell like and activated B-cell like diffuse large B-cell lymphoma. Several immunohistological algorithms have been proposed as surrogates to gene expression profiling at the level of protein expression, but their reliability has been an issue of controversy. Furthermore, the proportion of misclassified cases of germinal center B-cell subgroup by immunohistochemistry, in all reported algorithms, is higher compared with germinal center B-cell cases defined by gene expression profiling. We analyzed 424 cases of nodal diffuse large B-cell lymphoma with the panel of markers included in the three previously described algorithms: Hans, Choi, and Tally. To test whether the sensitivity of detecting germinal center B-cell cases could be improved, the germinal center B-cell marker HGAL/GCET2 was also added to all three algorithms. Our results show that the inclusion of HGAL/GCET2 significantly increased the detection of germinal center B-cell cases in all three algorithms (P<0.001). The proportions of germinal center B-cell cases in the original algorithms were 27%, 34%, and 19% for Hans, Choi, and Tally, respectively. In the modified algorithms, with the inclusion of HGAL/GCET2, the frequencies of germinal center B-cell cases were increased to 38%, 48%, and 35%, respectively. Therefore, HGAL/GCET2 protein expression may function as a marker for germinal center B-cell type diffuse large B-cell lymphoma. Consideration should be given to the inclusion of HGAL/GCET2 analysis in algorithms to better predict the cell of origin. These findings bear further validation, from comparison to gene expression profiles and from clinical/therapeutic data.

  6. T-cell leukemia 1 expression in nodal Epstein-Barr virus-negative diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma.

    PubMed

    Gualco, Gabriela; Weiss, Lawrence M; Barber, Glen N; Bacchi, Carlos E

    2010-09-01

    The physiologic expression of the product of the proto-oncogene TCL1 (T-cell leukemia 1) is primarily restricted to early embryonic cells. In nonneoplastic B cells, the expression of TCL1 is determined by the differentiation step with silencing at the germinal center stage. TCL1 protein is overexpressed in a wide variety of human diseases. It has been shown that TCL1 is a powerful B-cell oncogene, which has been implicated in the pathogenesis of various types of mature B-cell lymphomas. There is no comparative information in the literature addressing the expression of TCL1 in pediatric and adult nodal diffuse large B-cell lymphoma or primary mediastinal large B-cell lymphoma. We studied 55 cases of adult and pediatric diffuse large B-cell lymphoma and primary mediastinal large B-cell lymphoma to analyze the phenotypic profile of these lymphomas, including TCL1 expression, and its relationship with clinical outcome in different age groups. The cases were analyzed by immunohistochemistry for the expression of TCL1, CD10, BCL-2, BCL-6, and MUM1. We also evaluated c-MYC translocation by fluorescence in situ hybridization. TCL1 was observed in 11 cases, 5 pediatric and 6 adult cases, all but one diffuse large B-cell lymphoma. Pediatric cases showed a significant association between TCL1 expression, high proliferative index, and presence of c-MYC translocation. TCL1 positivity was predominantly found in germinal center phenotype diffuse large B-cell lymphoma. Overall survival was worse in adult TCL1-positive cases than pediatric ones. Primary mediastinal large B-cell lymphomas infrequently expressed TCL1 in both age groups.

  7. Time-domain Raman analytical forward solvers.

    PubMed

    Martelli, Fabrizio; Binzoni, Tiziano; Sekar, Sanathana Konugolu Venkata; Farina, Andrea; Cavalieri, Stefano; Pifferi, Antonio

    2016-09-01

    A set of time-domain analytical forward solvers for Raman signals detected from homogeneous diffusive media is presented. The time-domain solvers have been developed for two geometries: the parallelepiped and the finite cylinder. The potential presence of a background fluorescence emission, contaminating the Raman signal, has also been taken into account. All the solvers have been obtained as solutions of the time dependent diffusion equation. The validation of the solvers has been performed by means of comparisons with the results of "gold standard" Monte Carlo simulations. These forward solvers provide an accurate tool to explore the information content encoded in the time-resolved Raman measurements. PMID:27607645

  8. Heterogeneous treatment in the variational nodal method

    SciTech Connect

    Fanning, T.H.; Palmiotti, G.

    1995-06-01

    The variational nodal transport method is reduced to its diffusion form and generalized for the treatment of heterogeneous nodes while maintaining nodal balances. Adapting variational methods to heterogeneous nodes requires the ability to integrate over a node with discontinuous cross sections. In this work, integrals are evaluated using composite gaussian quadrature rules, which permit accurate integration while minimizing computing time. Allowing structure within a nodal solution scheme avoids some of the necessity of cross section homogenization, and more accurately defines the intra-nodal flux shape. Ideally, any desired heterogeneity can be constructed within the node; but in reality, the finite set of basis functions limits the practical resolution to which fine detail can be defined within the node. Preliminary comparison tests show that the heterogeneous variational nodal method provides satisfactory results even if some improvements are needed for very difficult, configurations.

  9. KEK NODAL system

    SciTech Connect

    Kurokawa, S.; Abe, K.; Akiyama, A.; Katoh, T.; Kikutani, E.; Koiso, H.; Kurihara, N.; Oide, K.; Shinomoto, M.

    1985-10-01

    The KEK NODAL system, which is based on the NODAL devised at the CERN SPS, works on an optical-fiber token ring network of twenty-four minicomputers (Hitachi HIDIC 80's) to control the TRISTAN accelerator complex, now being constructed at KEK. KEK NODAL retains main features of the original NODAL: the interpreting scheme, the multi-computer programming facility, and the data-module concept. In addition, it has the following characteristics: fast execution due to the compiler-interpreter method, a multicomputer file system, a full-screen editing facility, and a dynamic linkage scheme of data modules and NODAL functions. The structure of the KEK NODAL system under PMS, a real-time multitasking operating system of HIDIC 80, is described; the NODAL file system is also explained.

  10. A multigroup diffusion solver using pseudo transient continuation for a radiation-hydrodynamic code with patch-based AMR

    SciTech Connect

    Shestakov, Aleksei I. Offner, Stella S.R.

    2008-01-10

    We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with Adaptive Mesh Refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate 'level-solve' packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation ({psi}tc). We analyze the magnitude of the {psi}tc parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichlet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the 'partial temperature' scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. We consider a multigroup test problem with a known analytic solution. We demonstrate utility of {psi}tc by running with increasingly larger timesteps. Lastly, we simulate the sudden release of energy Y inside an Al sphere (r = 15 cm) suspended in air at STP. For Y = 11 kT, we find that gray radiation diffusion and MGD produce similar results. However, if Y = 1 MT, the two packages yield different results. Our large Y simulation contradicts a long-standing theory and demonstrates

  11. A Multigroup diffusion Solver Using Pseudo Transient Continuation for a Radiaiton-Hydrodynamic Code with Patch-Based AMR

    SciTech Connect

    Shestakov, A I; Offner, S R

    2007-03-02

    We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with adaptive mesh refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate 'level-solve' packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation ({Psi}tc). We analyze the magnitude of the {Psi}tc parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the 'partial temperature' scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. We consider a multigroup test problem with a known analytic solution. We demonstrate utility of {Psi}tc by running with increasingly larger timesteps. Lastly, we simulate the sudden release of energy Y inside an Al sphere (r = 15 cm) suspended in air at STP. For Y = 11 kT, we find that gray radiation diffusion and MGD produce similar results. However, if Y = 1 MT, the two packages yield different results. Our large Y simulation contradicts a long-standing theory and demonstrates

  12. A Multigroup diffusion solver using pseudo transient continuation for a radiation-hydrodynamic code with patch-based AMR

    SciTech Connect

    Shestakov, A I; Offner, S R

    2006-09-21

    We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with adaptive mesh refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate 'level-solve' packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation ({Psi}tc). We analyze the magnitude of the {Psi}tc parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the 'partial temperature' scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. We consider a multigroup test problem with a known analytic solution. We demonstrate utility of {Psi}tc by running with increasingly larger timesteps. Lastly, we simulate the sudden release of energy Y inside an Al sphere (r = 15 cm) suspended in air at STP. For Y = 11 kT, we find that gray radiation diffusion and MGD produce similar results. However, if Y = 1 MT, the two packages yield different results. Our large Y simulation contradicts a long-standing theory and demonstrates

  13. A multigroup diffusion solver using pseudo transient continuation for a radiation-hydrodynamic code with patch-based AMR

    NASA Astrophysics Data System (ADS)

    Shestakov, Aleksei I.; Offner, Stella S. R.

    2008-01-01

    We present a scheme to solve the nonlinear multigroup radiation diffusion (MGD) equations. The method is incorporated into a massively parallel, multidimensional, Eulerian radiation-hydrodynamic code with Adaptive Mesh Refinement (AMR). The patch-based AMR algorithm refines in both space and time creating a hierarchy of levels, coarsest to finest. The physics modules are time-advanced using operator splitting. On each level, separate "level-solve" packages advance the modules. Our multigroup level-solve adapts an implicit procedure which leads to a two-step iterative scheme that alternates between elliptic solves for each group with intra-cell group coupling. For robustness, we introduce pseudo transient continuation (Ψtc). We analyze the magnitude of the Ψtc parameter to ensure positivity of the resulting linear system, diagonal dominance and convergence of the two-step scheme. For AMR, a level defines a subdomain for refinement. For diffusive processes such as MGD, the refined level uses Dirichlet boundary data at the coarse-fine interface and the data is derived from the coarse level solution. After advancing on the fine level, an additional procedure, the sync-solve (SS), is required in order to enforce conservation. The MGD SS reduces to an elliptic solve on a combined grid for a system of G equations, where G is the number of groups. We adapt the "partial temperature" scheme for the SS; hence, we reuse the infrastructure developed for scalar equations. Results are presented. We consider a multigroup test problem with a known analytic solution. We demonstrate utility of Ψtc by running with increasingly larger timesteps. Lastly, we simulate the sudden release of energy Y inside an Al sphere (r = 15 cm) suspended in air at STP. For Y = 11 kT, we find that gray radiation diffusion and MGD produce similar results. However, if Y = 1 MT, the two packages yield different results. Our large Y simulation contradicts a long-standing theory and demonstrates the

  14. Explicit and implicit ode solvers using Krylov subspace optimization: Application to the diffusion equation and parabolic Maxwell`s system

    SciTech Connect

    Druskin, V.; Knizhnerman, L.

    1994-12-31

    The authors solve the Cauchy problem for an ODE system Au + {partial_derivative}u/{partial_derivative}t = 0, u{vert_bar}{sub t=0} = {var_phi}, where A is a square real nonnegative definite symmetric matrix of the order N, {var_phi} is a vector from R{sup N}. The stiffness matrix A is obtained due to semi-discretization of a parabolic equation or system with time-independent coefficients. The authors are particularly interested in large stiff 3-D problems for the scalar diffusion and vectorial Maxwell`s equations. First they consider an explicit method in which the solution on a whole time interval is projected on a Krylov subspace originated by A. Then they suggest another Krylov subspace with better approximating properties using powers of an implicit transition operator. These Krylov subspace methods generate optimal in a spectral sense polynomial approximations for the solution of the ODE, similar to CG for SLE.

  15. Nodal integral method for transient heat conduction in a cylinder

    SciTech Connect

    Esser, P.D. )

    1993-01-01

    The accuracy and efficiency of nodal solution methods are well established for neutron diffusion in a variety of geometries, as well as for heat transfer and fluid flow in rectangular coordinates. This paper describes the development of a nodal integral method to solve the transient heat conduction equation in cylindrical geometry. Results for a test problem with an analytical solution indicate that the nodal solution provides higher accuracy than a conventional implicit finite difference scheme, while maintaining similar stability characteristics.

  16. Human Cerberus Prevents Nodal-Receptor Binding, Inhibits Nodal Signaling, and Suppresses Nodal-Mediated Phenotypes

    PubMed Central

    Aykul, Senem; Ni, Wendi; Mutatu, Washington; Martinez-Hackert, Erik

    2015-01-01

    The Transforming Growth Factor-ß (TGFß) family ligand Nodal is an essential embryonic morphogen that is associated with progression of breast and other cancers. It has therefore been suggested that Nodal inhibitors could be used to treat breast cancers where Nodal plays a defined role. As secreted antagonists, such as Cerberus, tightly regulate Nodal signaling during embryonic development, we undertook to produce human Cerberus, characterize its biochemical activities, and determine its effect on human breast cancer cells. Using quantitative methods, we investigated the mechanism of Nodal signaling, we evaluated binding of human Cerberus to Nodal and other TGFß family ligands, and we characterized the mechanism of Nodal inhibition by Cerberus. Using cancer cell assays, we examined the ability of Cerberus to suppress aggressive breast cancer cell phenotypes. We found that human Cerberus binds Nodal with high affinity and specificity, blocks binding of Nodal to its signaling partners, and inhibits Nodal signaling. Moreover, we showed that Cerberus profoundly suppresses migration, invasion, and colony forming ability of Nodal expressing and Nodal supplemented breast cancer cells. Taken together, our studies provide mechanistic insights into Nodal signaling and Nodal inhibition with Cerberus and highlight the potential value of Cerberus as anti-Nodal therapeutic. PMID:25603319

  17. Amesos Solver Package

    SciTech Connect

    Stanley, Vendall S.; Heroux, Michael A.; Hoekstra, Robert J.; Sala, Marzio

    2004-03-01

    Amesos is the Direct Sparse Solver Package in Trilinos. The goal of Amesos is to make AX=S as easy as it sounds, at least for direct methods. Amesos provides interfaces to a number of third party sparse direct solvers, including SuperLU, SuperLU MPI, DSCPACK, UMFPACK and KLU. Amesos provides a common object oriented interface to the best sparse direct solvers in the world. A sparse direct solver solves for x in Ax = b. where A is a matrix and x and b are vectors (or multi-vectors). A sparse direct solver flrst factors A into trinagular matrices L and U such that A = LU via gaussian elimination and then solves LU x = b. Switching amongst solvers in Amesos roquires a change to a single parameter. Yet, no solver needs to be linked it, unless it is used. All conversions between the matrices provided by the user and the format required by the underlying solver is performed by Amesos. As new sparse direct solvers are created, they will be incorporated into Amesos, allowing the user to simpty link with the new solver, change a single parameter in the calling sequence, and use the new solver. Amesos allows users to specify whether the matrix has changed. Amesos can be used anywhere that any sparse direct solver is needed.

  18. Amesos Solver Package

    2004-03-01

    Amesos is the Direct Sparse Solver Package in Trilinos. The goal of Amesos is to make AX=S as easy as it sounds, at least for direct methods. Amesos provides interfaces to a number of third party sparse direct solvers, including SuperLU, SuperLU MPI, DSCPACK, UMFPACK and KLU. Amesos provides a common object oriented interface to the best sparse direct solvers in the world. A sparse direct solver solves for x in Ax = b. wheremore » A is a matrix and x and b are vectors (or multi-vectors). A sparse direct solver flrst factors A into trinagular matrices L and U such that A = LU via gaussian elimination and then solves LU x = b. Switching amongst solvers in Amesos roquires a change to a single parameter. Yet, no solver needs to be linked it, unless it is used. All conversions between the matrices provided by the user and the format required by the underlying solver is performed by Amesos. As new sparse direct solvers are created, they will be incorporated into Amesos, allowing the user to simpty link with the new solver, change a single parameter in the calling sequence, and use the new solver. Amesos allows users to specify whether the matrix has changed. Amesos can be used anywhere that any sparse direct solver is needed.« less

  19. Nodal-chain metals

    NASA Astrophysics Data System (ADS)

    Bzdušek, Tomáš; Wu, Quansheng; Rüegg, Andreas; Sigrist, Manfred; Soluyanov, Alexey A.

    2016-10-01

    The band theory of solids is arguably the most successful theory of condensed-matter physics, providing a description of the electronic energy levels in various materials. Electronic wavefunctions obtained from the band theory enable a topological characterization of metals for which the electronic spectrum may host robust, topologically protected, fermionic quasiparticles. Many of these quasiparticles are analogues of the elementary particles of the Standard Model, but others do not have a counterpart in relativistic high-energy theories. A complete list of possible quasiparticles in solids is lacking, even in the non-interacting case. Here we describe the possible existence of a hitherto unrecognized type of fermionic excitation in metals. This excitation forms a nodal chain—a chain of connected loops in momentum space—along which conduction and valence bands touch. We prove that the nodal chain is topologically distinct from previously reported excitations. We discuss the symmetry requirements for the appearance of this excitation and predict that it is realized in an existing material, iridium tetrafluoride (IrF4), as well as in other compounds of this class of materials. Using IrF4 as an example, we provide a discussion of the topological surface states associated with the nodal chain. We argue that the presence of the nodal-chain fermions will result in anomalous magnetotransport properties, distinct from those of materials exhibiting previously known excitations.

  20. Cavitary pulmonary involvement of diffuse large B-cell lymphoma transformed from extra nodal marginal zone B-cell lymphoma MALT type.

    PubMed

    Yamane, Hiromichi; Ohsawa, Masahiro; Shiote, Yasuhiro; Umemura, Shigeki; Suwaki, Toshimitsu; Shirakawa, Atsuko; Kamei, Haruhito; Takigawa, Nagio; Kiura, Katsuyuki

    2011-12-01

    We describe a case of pulmonary diffuse large B-cell lymphoma (DLBCL), which was thought to arise from extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma). A 68-year-old woman presented with a 2-month history of cough and bloody sputum. The chest X-ray and computed tomography revealed a mass with cavitation in the right lower lobe. Transbronchial biopsy specimens revealed a granulomatous infiltration without malignant cells. However, diagnosis of MALT lymphoma was established from gastric biopsy specimen. Subsequently, a right lower lobectomy was performed because of hemoptysis. Examination of the resected specimen revealed a diffuse large B-cell lymphoma, which was considered to have transformed from MALT lymphoma, because both lung and stomach lesions had the chromosomal translocation t(11;18)(q21;q21) in common. In addition, there were no nodules, masses, alveolar or interstitial infiltrates in the lung fields, which are usually observed in the case of marginal zone B-cell lymphoma of bronchial mucosa-associated lymphoid tissue. These findings indicate that involvement of DLBCL have to be considered in patients with MALT lymphoma and cavitary lesion of the lung. PMID:26189744

  1. Wave pinning and spatial patterning in a mathematical model of Antivin/Lefty-Nodal signalling.

    PubMed

    Middleton, A M; King, J R; Loose, M

    2013-12-01

    Nodal signals are key regulators of mesoderm and endoderm development in vertebrate embryos. It has been observed experimentally that in Xenopus embryos the spatial range of Nodal signals is restricted by the signal Antivin (also known as Lefty). Nodal signals can activate both Nodal and Antivin, whereas Antivin is thought to antagonise Nodal by binding either directly to it or to its receptor. In this paper we develop a mathematical model of this signalling network in a line of cells. We consider the heterodimer and receptor-mediated inhibition mechanisms separately and find that, in both cases, the restriction by Antivin to the range of Nodal signals corresponds to wave pinning in the model. Our analysis indicates that, provided Antivin diffuses faster than Nodal, either mechanism can robustly account for the experimental data. We argue that, in the case of Xenopus development, it is wave pinning, rather than Turing-type patterning, that is underlying Nodal-Antivin dynamics. This leads to several experimentally testable predictions, which are discussed. Furthermore, for heterodimer-mediated inhibition to prevent waves of Nodal expression from propagating, the Nodal-Antivin complex must be turned over, and diffusivity of the complex must be negligible. In the absence of molecular mechanisms regulating these, we suggest that Antivin restricts Nodal signals via receptor-mediated, and not heterodimer-mediated, inhibition. PMID:23070212

  2. How to Find a Bug in Ten Thousand Lines Transport Solver? Outline of Experiences from AN Advection-Diffusion Code Verification

    NASA Astrophysics Data System (ADS)

    Zamani, K.; Bombardelli, F.

    2011-12-01

    Almost all natural phenomena on Earth are highly nonlinear. Even simplifications to the equations describing nature usually end up being nonlinear partial differential equations. Transport (ADR) equation is a pivotal equation in atmospheric sciences and water quality. This nonlinear equation needs to be solved numerically for practical purposes so academicians and engineers thoroughly rely on the assistance of numerical codes. Thus, numerical codes require verification before they are utilized for multiple applications in science and engineering. Model verification is a mathematical procedure whereby a numerical code is checked to assure the governing equation is properly solved as it is described in the design document. CFD verification is not a straightforward and well-defined course. Only a complete test suite can uncover all the limitations and bugs. Results are needed to be assessed to make a distinction between bug-induced-defect and innate limitation of a numerical scheme. As Roache (2009) said, numerical verification is a state-of-the-art procedure. Sometimes novel tricks work out. This study conveys the synopsis of the experiences we gained during a comprehensive verification process which was done for a transport solver. A test suite was designed including unit tests and algorithmic tests. Tests were layered in complexity in several dimensions from simple to complex. Acceptance criteria defined for the desirable capabilities of the transport code such as order of accuracy, mass conservation, handling stiff source term, spurious oscillation, and initial shape preservation. At the begining, mesh convergence study which is the main craft of the verification is performed. To that end, analytical solution of ADR equation gathered. Also a new solution was derived. In the more general cases, lack of analytical solution could be overcome through Richardson Extrapolation and Manufactured Solution. Then, two bugs which were concealed during the mesh convergence

  3. An Advanced Integrated Diffusion/Transport Method for the Design, Analysis and Optimization of the Very-High-Temperature Reactors

    SciTech Connect

    Farzad Rahnema; Dingkang Zhang; Abderrafi Ougouag; Frederick Gleicher

    2011-04-04

    The main objective of this research is to develop an integrated diffusion/transport (IDT) method to substantially improve the accuracy of nodal diffusion methods for the design and analysis of Very High Temperature Reactors (VHTR). Because of the presence of control rods in the reflector regions in the Pebble Bed Reactor (PBR-VHTR), traditional nodal diffusion methods do not accurately model these regions, within which diffusion theory breaks down in the vicinity of high neutron absorption and steep flux gradients. The IDT method uses a local transport solver based on a new incident flux response expansion method in the controlled nodes. Diffusion theory is used in the rest of the core. This approach improves the accuracy of the core solution by generating transport solutions of controlled nodes while maintaining computational efficiency by using diffusion solutions in nodes where such a treatment is sufficient. The transport method is initially developed and coupled to the reformulated 3-D nodal diffusion model in the CYNOD code for PBR core design and fuel cycle analysis. This method is also extended to the prismatic VHTR. The new method accurately captures transport effects in highly heterogeneous regions with steep flux gradients. The calculations of these nodes with transport theory avoid errors associated with spatial homogenization commonly used in diffusion methods in reactor core simulators

  4. Code System to Solve the Few-Group Neutron Diffusion Equation Utilizing the Nodal Expansion Method (NEM) for Eigenvalue, Adjoint, and Fixed-Source

    2004-04-21

    Version 04 NESTLE solves the few-group neutron diffusion equation utilizing the NEM. The NESTLE code can solve the eigenvalue (criticality), eigenvalue adjoint, external fixed-source steady-state, and external fixed-source or eigenvalue initiated transient problems. The eigenvalue problem allows criticality searches to be completed, and the external fixed-source steady-state problem can search to achieve a specified power level. Transient problems model delayed neutrons via precursor groups. Several core properties can be input as time dependent. Two- ormore » four-energy groups can be utilized, with all energy groups being thermal groups (i.e., upscatter exits) if desired. Core geometries modeled include Cartesian and hexagonal. Three-, two-, and one-dimensional models can be utilized with various symmetries. The thermal conditions predicted by the thermal-hydraulic model of the core are used to correct cross sections for temperature and density effects. Cross sections are parameterized by color, control rod state (i.e., in or out), and burnup, allowing fuel depletion to be modeled. Either a macroscopic or microscopic model may be employed.« less

  5. An upwind nodal integral method for incompressible fluid flow

    SciTech Connect

    Esser, P.D. ); Witt, R.J. )

    1993-05-01

    An upwind nodal solution method is developed for the steady, two-dimensional flow of an incompressible fluid. The formulation is based on the nodal integral method, which uses transverse integrations, analytical solutions of the one-dimensional averaged equations, and node-averaged uniqueness constraints to derive the discretized nodal equations. The derivation introduces an exponential upwind bias by retaining the streamwise convection term in the homogeneous part of the transverse-integrated convection-diffusion equation. The method is adapted to the stream function-vorticity form of the Navier-Stokes equations, which are solved over a nonstaggered nodal mesh. A special nodal scheme is used for the Poisson stream function equation to properly account for the exponentially varying vorticity source. Rigorous expressions for the velocity components and the no-slip vorticity boundary condition are derived from the stream function formulation. The method is validated with several benchmark problems. An idealized purely convective flow of a scalar step function indicates that the nodal approximation errors are primarily dispersive, not dissipative, in nature. Results for idealized and actual recirculating driven-cavity flows reveal a significant reduction in false diffusion compared with conventional finite difference techniques.

  6. Off-diagonal Jacobian support for Nodal BCs

    SciTech Connect

    Peterson, John W.; Andrs, David; Gaston, Derek R.; Permann, Cody J.; Slaughter, Andrew E.

    2015-01-01

    In this brief note, we describe the implementation of o-diagonal Jacobian computations for nodal boundary conditions in the Multiphysics Object Oriented Simulation Environment (MOOSE) [1] framework. There are presently a number of applications [2{5] based on the MOOSE framework that solve complicated physical systems of partial dierential equations whose boundary conditions are often highly nonlinear. Accurately computing the on- and o-diagonal Jacobian and preconditioner entries associated to these constraints is crucial for enabling ecient numerical solvers in these applications. Two key ingredients are required for properly specifying the Jacobian contributions of nonlinear nodal boundary conditions in MOOSE and nite element codes in general: 1. The ability to zero out entire Jacobian matrix rows after \

  7. Super-nodal methods for space-time kinetics

    NASA Astrophysics Data System (ADS)

    Mertyurek, Ugur

    The purpose of this research has been to develop an advanced Super-Nodal method to reduce the run time of 3-D core neutronics models, such as in the NESTLE reactor core simulator and FORMOSA nuclear fuel management optimization codes. Computational performance of the neutronics model is increased by reducing the number of spatial nodes used in the core modeling. However, as the number of spatial nodes decreases, the error in the solution increases. The Super-Nodal method reduces the error associated with the use of coarse nodes in the analyses by providing a new set of cross sections and ADFs (Assembly Discontinuity Factors) for the new nodalization. These so called homogenization parameters are obtained by employing consistent collapsing technique. During this research a new type of singularity, namely "fundamental mode singularity", is addressed in the ANM (Analytical Nodal Method) solution. The "Coordinate Shifting" approach is developed as a method to address this singularity. Also, the "Buckling Shifting" approach is developed as an alternative and more accurate method to address the zero buckling singularity, which is a more common and well known singularity problem in the ANM solution. In the course of addressing the treatment of these singularities, an effort was made to provide better and more robust results from the Super-Nodal method by developing several new methods for determining the transverse leakage and collapsed diffusion coefficient, which generally are the two main approximations in the ANM methodology. Unfortunately, the proposed new transverse leakage and diffusion coefficient approximations failed to provide a consistent improvement to the current methodology. However, improvement in the Super-Nodal solution is achieved by updating the homogenization parameters at several time points during a transient. The update is achieved by employing a refinement technique similar to pin-power reconstruction. A simple error analysis based on the relative

  8. Parallel Multigrid Equation Solver

    2001-09-07

    Prometheus is a fully parallel multigrid equation solver for matrices that arise in unstructured grid finite element applications. It includes a geometric and an algebraic multigrid method and has solved problems of up to 76 mullion degrees of feedom, problems in linear elasticity on the ASCI blue pacific and ASCI red machines.

  9. Pliris Solver Package

    2004-03-01

    PLIRIS is an object-oriented solver built on top of a previous matrix solver used in a number of application codes. Puns solves a linear system directly via LU factorization with partial pivoting. The user provides the linear system in terms of Epetra Objects including a matrix and right-hand-sides. The user can then factor the matrix and perform the forward and back solve at a later time or solve for multiple right-hand-sides at once. This packagemore » is used when dense matrices are obtained in the problem formulation. These dense matrices occur whenever boundary element techniques are chosen for the solution procedure. This has been used in electromagnetics for both static and frequency domain problems.« less

  10. Final Report, NERI Project: ''An Innovative Reactor Analysis Methodology Based on a Quasidiffusion Nodal Core Model''

    SciTech Connect

    Dmitriy Y. Anistratov; Marvin L. Adams; Todd S. Palmer; Kord S. Smith; Kevin Clarno; Hikaru Hiruta; Razvan Nes

    2003-08-04

    OAK (B204) Final Report, NERI Project: ''An Innovative Reactor Analysis Methodology Based on a Quasidiffusion Nodal Core Model'' The present generation of reactor analysis methods uses few-group nodal diffusion approximations to calculate full-core eigenvalues and power distributions. The cross sections, diffusion coefficients, and discontinuity factors (collectively called ''group constants'') in the nodal diffusion equations are parameterized as functions of many variables, ranging from the obvious (temperature, boron concentration, etc.) to the more obscure (spectral index, moderator temperature history, etc.). These group constants, and their variations as functions of the many variables, are calculated by assembly-level transport codes. The current methodology has two main weaknesses that this project addressed. The first weakness is the diffusion approximation in the full-core calculation; this can be significantly inaccurate at interfaces between different assemblies. This project used the nodal diffusion framework to implement nodal quasidiffusion equations, which can capture transport effects to an arbitrary degree of accuracy. The second weakness is in the parameterization of the group constants; current models do not always perform well, especially at interfaces between unlike assemblies. The project developed a theoretical foundation for parameterization and homogenization models and used that theory to devise improved models. The new models were extended to tabulate information that the nodal quasidiffusion equations can use to capture transport effects in full-core calculations.

  11. HPCCG Solver Package

    SciTech Connect

    Heroux, Michael A.

    2007-03-01

    HPCCG is a simple PDE application and preconditioned conjugate gradient solver that solves a linear system on a beam-shaped domain. Although it does not address many performance issues present in real engineering applications, such as load imbalance and preconditioner scalability, it can serve as a first "sanity test" of new processor design choices, inter-connect network design choices and the scalability of a new computer system. Because it is self-contained, easy to compile and easily scaled to 100s or 1000s of porcessors, it can be an attractive study code for computer system designers.

  12. Scalable solvers and applications

    SciTech Connect

    Ribbens, C J

    2000-10-27

    The purpose of this report is to summarize research activities carried out under Lawrence Livermore National Laboratory (LLNL) research subcontract B501073. This contract supported the principal investigator (P1), Dr. Calvin Ribbens, during his sabbatical visit to LLNL from August 1999 through June 2000. Results and conclusions from the work are summarized below in two major sections. The first section covers contributions to the Scalable Linear Solvers and hypre projects in the Center for Applied Scientific Computing (CASC). The second section describes results from collaboration with Patrice Turchi of LLNL's Chemistry and Materials Science Directorate (CMS). A list of publications supported by this subcontract appears at the end of the report.

  13. HPCCG Solver Package

    2007-03-01

    HPCCG is a simple PDE application and preconditioned conjugate gradient solver that solves a linear system on a beam-shaped domain. Although it does not address many performance issues present in real engineering applications, such as load imbalance and preconditioner scalability, it can serve as a first "sanity test" of new processor design choices, inter-connect network design choices and the scalability of a new computer system. Because it is self-contained, easy to compile and easily scaledmore » to 100s or 1000s of porcessors, it can be an attractive study code for computer system designers.« less

  14. Progress and applications of the variational nodal method

    SciTech Connect

    Carrico, C.B.; Palmiotti, G.; Lewis, E.E.

    1995-07-01

    This paper summarizes current progress and developments with the variational nodal method(VNM) and its implementaion within the DIF3D code suite. After a brief development of the mathematical basis for the VNM, results from two three-dimensional benchmarks are presented for a variety of computers. Then current applications of the VNM are discussed including diffusion theory calculations, burnup calculations, highly heterogeneous cores, higher-order spherical harmonics approximations, perturbation theory and heterogeneous nodes.

  15. Nodal-mediated epigenesis requires dynamin-mediated endocytosis

    PubMed Central

    Ertl, Robin P.; Robertson, Anthony J.; Saunders, Diane; Coffman, James A.

    2011-01-01

    Nodal proteins are diffusible morphogens that drive pattern formation via short-range feedback activation coupled to long-range Lefty-mediated inhibition. In the sea urchin embryo, specification of the secondary (oral-aboral) axis occurs via zygotic expression of nodal, which is localized to the prospective oral ectoderm at early blastula stage. In mid-blastula stage embryos treated with low micromolar nickel or zinc, nodal expression expands progressively beyond the confines of this localized domain to encompass the entire equatorial circumference of the embryo, producing radialized embryos lacking an oral-aboral axis. RNAseq analysis of embryos treated with nickel, zinc or cadmium (which does not radialize embryos) showed that several genes involved in endocytosis were similarly perturbed by nickel and zinc but not cadmium. Inhibiting dynamin, a GTPase required for receptor-mediated endocytosis, phenocopies the effects of nickel and zinc, suggesting that dynamin-mediated endocytosis is required as a sink to limit the range of Nodal signaling. PMID:21337468

  16. Parallel tridiagonal equation solvers

    NASA Technical Reports Server (NTRS)

    Stone, H. S.

    1974-01-01

    Three parallel algorithms were compared for the direct solution of tridiagonal linear systems of equations. The algorithms are suitable for computers such as ILLIAC 4 and CDC STAR. For array computers similar to ILLIAC 4, cyclic odd-even reduction has the least operation count for highly structured sets of equations, and recursive doubling has the least count for relatively unstructured sets of equations. Since the difference in operation counts for these two algorithms is not substantial, their relative running times may be more related to overhead operations, which are not measured in this paper. The third algorithm, based on Buneman's Poisson solver, has more arithmetic operations than the others, and appears to be the least favorable. For pipeline computers similar to CDC STAR, cyclic odd-even reduction appears to be the most preferable algorithm for all cases.

  17. Amesos2 Templated Direct Sparse Solver Package

    2011-05-24

    Amesos2 is a templated direct sparse solver package. Amesos2 provides interfaces to direct sparse solvers, rather than providing native solver capabilities. Amesos2 is a derivative work of the Trilinos package Amesos.

  18. The embryonic morphogen, Nodal, is associated with channel-like structures in human malignant melanoma xenografts.

    PubMed

    McAllister, Josephine C; Zhan, Qian; Weishaupt, Carsten; Hsu, Mei-Yu; Murphy, George F

    2010-04-01

    Formation of channel-like structures, also termed vasculogenic mimicry (VM), describes the ability of aggressive melanoma cells to form PAS-positive anastomosing structures that correlate with tumor virulence. This phenomenon may indicate differentiation plasticity, a feature melanoma cells may share with stem cells in the developing embryo. Recent studies have indicated that VM and tumorigenicity of human malignant melanoma may depend on the signaling pathways of an embryonic morphogen, Nodal. However, given the secretory nature of Nodal protein and melanoma cell heterogeneity, it remains unclear whether the Nodal-expressing cells participate directly or indirectly in VM that is potentially related to tumorigenic growth. We have developed a humanized murine xenograft model in which developing human melanomas may be sequentially studied during early stages of tumorigenic growth within a physiological human dermal microenvironment. Nodal protein localized diffusely to melanoma cell membranes, with occasional foci of accentuated reactivity in patterns suggestive of channel formation. Similar findings were detected in a limited number of patient-derived tumors. In situ hybridization confirmed Nodal mRNA to be restricted to tumor cells within xenografts that formed arborizing networks in patterns consistent with VM. These data indicate that Nodal gene expression is associated with formation of VM-like structures in a physiologically relevant model of human melanoma tumorigenesis, and further support a key role for Nodal expression in the formation of channel-like structures. The humanized xenograft model should be useful in future studies to define the mechanistic pathways responsible for VM and melanoma progression.

  19. Magnetic Field Solver

    NASA Technical Reports Server (NTRS)

    Ilin, Andrew V.

    2006-01-01

    The Magnetic Field Solver computer program calculates the magnetic field generated by a group of collinear, cylindrical axisymmetric electromagnet coils. Given the current flowing in, and the number of turns, axial position, and axial and radial dimensions of each coil, the program calculates matrix coefficients for a finite-difference system of equations that approximates a two-dimensional partial differential equation for the magnetic potential contributed by the coil. The program iteratively solves these finite-difference equations by use of the modified incomplete Cholesky preconditioned-conjugate-gradient method. The total magnetic potential as a function of axial (z) and radial (r) position is then calculated as a sum of the magnetic potentials of the individual coils, using a high-accuracy interpolation scheme. Then the r and z components of the magnetic field as functions of r and z are calculated from the total magnetic potential by use of a high-accuracy finite-difference scheme. Notably, for the finite-difference calculations, the program generates nonuniform two-dimensional computational meshes from nonuniform one-dimensional meshes. Each mesh is generated in such a way as to minimize the numerical error for a benchmark one-dimensional magnetostatic problem.

  20. Sherlock Holmes, Master Problem Solver.

    ERIC Educational Resources Information Center

    Ballew, Hunter

    1994-01-01

    Shows the connections between Sherlock Holmes's investigative methods and mathematical problem solving, including observations, characteristics of the problem solver, importance of data, questioning the obvious, learning from experience, learning from errors, and indirect proof. (MKR)

  1. MILAMIN 2 - Fast MATLAB FEM solver

    NASA Astrophysics Data System (ADS)

    Dabrowski, Marcin; Krotkiewski, Marcin; Schmid, Daniel W.

    2013-04-01

    MILAMIN is a free and efficient MATLAB-based two-dimensional FEM solver utilizing unstructured meshes [Dabrowski et al., G-cubed (2008)]. The code consists of steady-state thermal diffusion and incompressible Stokes flow solvers implemented in approximately 200 lines of native MATLAB code. The brevity makes the code easily customizable. An important quality of MILAMIN is speed - it can handle millions of nodes within minutes on one CPU core of a standard desktop computer, and is faster than many commercial solutions. The new MILAMIN 2 allows three-dimensional modeling. It is designed as a set of functional modules that can be used as building blocks for efficient FEM simulations using MATLAB. The utilities are largely implemented as native MATLAB functions. For performance critical parts we use MUTILS - a suite of compiled MEX functions optimized for shared memory multi-core computers. The most important features of MILAMIN 2 are: 1. Modular approach to defining, tracking, and discretizing the geometry of the model 2. Interfaces to external mesh generators (e.g., Triangle, Fade2d, T3D) and mesh utilities (e.g., element type conversion, fast point location, boundary extraction) 3. Efficient computation of the stiffness matrix for a wide range of element types, anisotropic materials and three-dimensional problems 4. Fast global matrix assembly using a dedicated MEX function 5. Automatic integration rules 6. Flexible prescription (spatial, temporal, and field functions) and efficient application of Dirichlet, Neuman, and periodic boundary conditions 7. Treatment of transient and non-linear problems 8. Various iterative and multi-level solution strategies 9. Post-processing tools (e.g., numerical integration) 10. Visualization primitives using MATLAB, and VTK export functions We provide a large number of examples that show how to implement a custom FEM solver using the MILAMIN 2 framework. The examples are MATLAB scripts of increasing complexity that address a given

  2. Occult nodal metastasis in solid carcinomata

    SciTech Connect

    Moloy, P.J.; Nicolson, G.L.

    1987-01-01

    This book contains 23 selections. Some of the titles are: Rationale for radiotherapy in subclinical nodal disease; rationale of chemotherapy for nodal disease: The stabilization of topoisomerase II-DNA complexes as a mechanism of antineoplastic drug action; magnetic resonance imaging of malignant cervical adenopathy; and local and regional immune function in cancer patients.

  3. Nodal equivalence theory for hexagonal geometry, thermal reactor analysis

    SciTech Connect

    Zika, M.; Downar, T. )

    1992-01-01

    An important aspect of advanced nodal methods is the determination of equivalent few-group parameters for the relatively large homogenized regions used in the nodal flux solution. The theoretical foundation for light water reactor (LWR) assembly homogenization methods has been clearly established, and during the last several years, its successes have secured its position in the stable of dependable LWR analysis methods. Groupwise discontinuity factors that correct for assembly homogenization errors are routinely generated along with the group constants during lattice physics analysis. During the last several years, there has been interest in applying equivalence theory to other reactor types and other geometries. A notable effort has been the work at Argonne National Laboratory to incorporate nodal equivalence theory (NET) for hexagonal lattices into the nodal diffusion option of the DIF3D code. This work was originally intended to improve the neutronics methods used for the analysis of the Experimental Breeder Reactor II (EBR-II), and Ref. 4 discusses the success of that application. More recently, however, attempts were made to apply NET to advanced, thermal reactor designs such as the modular high-temperature gas reactor (MHTGR) and the new production heavy water reactor (NPR/HWR). The same methods that were successful for EBR-II have encountered problems for these reactors. Our preliminary analysis indicates that the sharp global flux gradients in these cores requires large discontinuity factors (greater than 4 or 5) to reproduce the reference solution. This disrupts the convergence of the iterative methods used to solve for the node-wise flux moments and partial currents. Several attempts to remedy the problem have been made over the last few years, including bounding the discontinuity factors and providing improved initial guesses for the flux solution, but nothing has been satisfactory.

  4. A quasi-static polynomial nodal method for nuclear reactor analysis

    SciTech Connect

    Gehin, J.C.

    1992-09-01

    Modern nodal methods are currently available which can accurately and efficiently solve the static and transient neutron diffusion equations. Most of the methods, however, are limited to two energy groups for practical application. The objective of this research is the development of a static and transient, multidimensional nodal method which allows more than two energy groups and uses a non-linear iterative method for efficient solution of the nodal equations. For both the static and transient methods, finite-difference equations which are corrected by the use of discontinuity factors are derived. The discontinuity factors are computed from a polynomial nodal method using a non-linear iteration technique. The polynomial nodal method is based upon a quartic approximation and utilizes a quadratic transverse-leakage approximation. The solution of the time-dependent equations is performed by the use of a quasi-static method in which the node-averaged fluxes are factored into shape and amplitude functions. The application of the quasi-static polynomial method to several benchmark problems demonstrates that the accuracy is consistent with that of other nodal methods. The use of the quasi-static method is shown to substantially reduce the computation time over the traditional fully-implicit time-integration method. Problems involving thermal-hydraulic feedback are accurately, and efficiently, solved by performing several reactivity/thermal-hydraulic updates per shape calculation.

  5. Mapping of nodal disease in locally advanced prostate cancer: Rethinking the clinical target volume for pelvic nodal irradiation based on vascular rather than bony anatomy

    SciTech Connect

    Shih, Helen A. . E-mail: hshih@partners.org; Harisinghani, Mukesh; Zietman, Anthony L.; Wolfgang, John A.; Saksena, Mansi; Weissleder, Ralph

    2005-11-15

    Purpose: Toxicity from pelvic irradiation could be reduced if fields were limited to likely areas of nodal involvement rather than using the standard 'four-field box.' We employed a novel magnetic resonance lymphangiographic technique to highlight the likely sites of occult nodal metastasis from prostate cancer. Methods and Materials: Eighteen prostate cancer patients with pathologically confirmed node-positive disease had a total of 69 pathologic nodes identifiable by lymphotropic nanoparticle-enhanced MRI and semiquantitative nodal analysis. Fourteen of these nodes were in the para-aortic region, and 55 were in the pelvis. The position of each of these malignant nodes was mapped to a common template based on its relation to skeletal or vascular anatomy. Results: Relative to skeletal anatomy, nodes covered a diffuse volume from the mid lumbar spine to the superior pubic ramus and along the sacrum and pelvic side walls. In contrast, the nodal metastases mapped much more tightly relative to the large pelvic vessels. A proposed pelvic clinical target volume to encompass the region at greatest risk of containing occult nodal metastases would include a 2.0-cm radial expansion volume around the distal common iliac and proximal external and internal iliac vessels that would encompass 94.5% of the pelvic nodes at risk as defined by our node-positive prostate cancer patient cohort. Conclusions: Nodal metastases from prostate cancer are largely localized along the major pelvic vasculature. Defining nodal radiation treatment portals based on vascular rather than bony anatomy may allow for a significant decrease in normal pelvic tissue irradiation and its associated toxicities.

  6. On code verification of RANS solvers

    NASA Astrophysics Data System (ADS)

    Eça, L.; Klaij, C. M.; Vaz, G.; Hoekstra, M.; Pereira, F. S.

    2016-04-01

    This article discusses Code Verification of Reynolds-Averaged Navier Stokes (RANS) solvers that rely on face based finite volume discretizations for volumes of arbitrary shape. The study includes test cases with known analytical solutions (generated with the method of manufactured solutions) corresponding to laminar and turbulent flow, with the latter using eddy-viscosity turbulence models. The procedure to perform Code Verification based on grid refinement studies is discussed and the requirements for its correct application are illustrated in a simple one-dimensional problem. It is shown that geometrically similar grids are recommended for proper Code Verification and so the data should not have scatter making the use of least square fits unnecessary. Results show that it may be advantageous to determine the extrapolated error to cell size/time step zero instead of assuming that it is zero, especially when it is hard to determine the asymptotic order of grid convergence. In the RANS examples, several of the features of the ReFRESCO solver are checked including the effects of the available turbulence models in the convergence properties of the code. It is shown that it is required to account for non-orthogonality effects in the discretization of the diffusion terms and that the turbulence quantities transport equations can deteriorate the order of grid convergence of mean flow quantities.

  7. Scalable Parallel Algebraic Multigrid Solvers

    SciTech Connect

    Bank, R; Lu, S; Tong, C; Vassilevski, P

    2005-03-23

    The authors propose a parallel algebraic multilevel algorithm (AMG), which has the novel feature that the subproblem residing in each processor is defined over the entire partition domain, although the vast majority of unknowns for each subproblem are associated with the partition owned by the corresponding processor. This feature ensures that a global coarse description of the problem is contained within each of the subproblems. The advantages of this approach are that interprocessor communication is minimized in the solution process while an optimal order of convergence rate is preserved; and the speed of local subproblem solvers can be maximized using the best existing sequential algebraic solvers.

  8. Keeping a lid on nodal: transcriptional and translational repression of nodal signalling

    PubMed Central

    Robertson, Elizabeth J.

    2016-01-01

    Nodal is an evolutionarily conserved member of the transforming growth factor-β (TGF-β) superfamily of secreted signalling factors. Nodal factors are known to play key roles in embryonic development and asymmetry in a variety of organisms ranging from hydra and sea urchins to fish, mice and humans. In addition to embryonic patterning, Nodal signalling is required for maintenance of human embryonic stem cell pluripotency and mis-regulated Nodal signalling has been found associated with tumour metastases. Therefore, precise and timely regulation of this pathway is essential. Here, we discuss recent evidence from sea urchins, frogs, fish, mice and humans that show a role for transcriptional and translational repression of Nodal signalling during early development. PMID:26791244

  9. On unstructured grids and solvers

    NASA Technical Reports Server (NTRS)

    Barth, T. J.

    1990-01-01

    The fundamentals and the state-of-the-art technology for unstructured grids and solvers are highlighted. Algorithms and techniques pertinent to mesh generation are discussed. It is shown that grid generation and grid manipulation schemes rely on fast multidimensional searching. Flow solution techniques for the Euler equations, which can be derived from the integral form of the equations are discussed. Sample calculations are also provided.

  10. Nodal Quasiparticle in Pseudogapped Colossal Magnetoresistive Manganites

    SciTech Connect

    Mannella, N.

    2010-06-02

    A characteristic feature of the copper oxide high-temperature superconductors is the dichotomy between the electronic excitations along the nodal (diagonal) and antinodal (parallel to the Cu-O bonds) directions in momentum space, generally assumed to be linked to the d-wave symmetry of the superconducting state. Angle-resolved photoemission measurements in the superconducting state have revealed a quasiparticle spectrum with a d-wave gap structure that exhibits a maximum along the antinodal direction and vanishes along the nodal direction. Subsequent measurements have shown that, at low doping levels, this gap structure persists even in the high-temperature metallic state, although the nodal points of the superconducting state spread out in finite Fermi arcs. This is the so-called pseudogap phase, and it has been assumed that it is closely linked to the superconducting state, either by assigning it to fluctuating superconductivity or by invoking orders which are natural competitors of d-wave superconductors. Here we report experimental evidence that a very similar pseudogap state with a nodal-antinodal dichotomous character exists in a system that is markedly different from a superconductor: the ferromagnetic metallic groundstate of the colossal magnetoresistive bilayer manganite La{sub 1.2}Sr{sub 1.8}Mn{sub 2}O{sub 7}. Our findings therefore cast doubt on the assumption that the pseudogap state in the copper oxides and the nodal-antinodal dichotomy are hallmarks of the superconductivity state.

  11. Constrained hierarchical least square nonlinear equation solvers. [for indefinite stiffness and large structural deformations

    NASA Technical Reports Server (NTRS)

    Padovan, J.; Lackney, J.

    1986-01-01

    The current paper develops a constrained hierarchical least square nonlinear equation solver. The procedure can handle the response behavior of systems which possess indefinite tangent stiffness characteristics. Due to the generality of the scheme, this can be achieved at various hierarchical application levels. For instance, in the case of finite element simulations, various combinations of either degree of freedom, nodal, elemental, substructural, and global level iterations are possible. Overall, this enables a solution methodology which is highly stable and storage efficient. To demonstrate the capability of the constrained hierarchical least square methodology, benchmarking examples are presented which treat structure exhibiting highly nonlinear pre- and postbuckling behavior wherein several indefinite stiffness transitions occur.

  12. Nodal domains in open microwave systems.

    PubMed

    Kuhl, U; Höhmann, R; Stöckmann, H-J; Gnutzmann, S

    2007-03-01

    Nodal domains are studied both for real psiR and imaginary part psiI of the wave functions of an open microwave cavity and found to show the same behavior as wave functions in closed billiards. In addition we investigate the variation of the number of nodal domains and the signed area correlation by changing the global phase phig according to psiR+ipsiI=eiphig(psiR'+ipsiI'). This variation can be qualitatively, and the correlation quantitatively explained in terms of the phase rigidity characterizing the openness of the billiard.

  13. Nodal domains in open microwave systems

    NASA Astrophysics Data System (ADS)

    Kuhl, U.; Höhmann, R.; Stöckmann, H.-J.; Gnutzmann, S.

    2007-03-01

    Nodal domains are studied both for real ψR and imaginary part ψI of the wave functions of an open microwave cavity and found to show the same behavior as wave functions in closed billiards. In addition we investigate the variation of the number of nodal domains and the signed area correlation by changing the global phase φg according to ψR+iψI=eiφg(ψR'+iψI') . This variation can be qualitatively, and the correlation quantitatively explained in terms of the phase rigidity characterizing the openness of the billiard.

  14. NOKIN1D: one-dimensional neutron kinetics based on a nodal collocation method

    NASA Astrophysics Data System (ADS)

    Verdú, G.; Ginestar, D.; Miró, R.; Jambrina, A.; Barrachina, T.; Soler, Amparo; Concejal, Alberto

    2014-06-01

    The TRAC-BF1 one-dimensional kinetic model is a formulation of the neutron diffusion equation in the two energy groups' approximation, based on the analytical nodal method (ANM). The advantage compared with a zero-dimensional kinetic model is that the axial power profile may vary with time due to thermal-hydraulic parameter changes and/or actions of the control systems but at has the disadvantages that in unusual situations it fails to converge. The nodal collocation method developed for the neutron diffusion equation and applied to the kinetics resolution of TRAC-BF1 thermal-hydraulics, is an adaptation of the traditional collocation methods for the discretization of partial differential equations, based on the development of the solution as a linear combination of analytical functions. It has chosen to use a nodal collocation method based on a development of Legendre polynomials of neutron fluxes in each cell. The qualification is carried out by the analysis of the turbine trip transient from the NEA benchmark in Peach Bottom NPP using both the original 1D kinetics implemented in TRAC-BF1 and the 1D nodal collocation method.

  15. Nodal Green’s Function Method Singular Source Term and Burnable Poison Treatment in Hexagonal Geometry

    SciTech Connect

    A.A. Bingham; R.M. Ferrer; A.M. ougouag

    2009-09-01

    An accurate and computationally efficient two or three-dimensional neutron diffusion model will be necessary for the development, safety parameters computation, and fuel cycle analysis of a prismatic Very High Temperature Reactor (VHTR) design under Next Generation Nuclear Plant Project (NGNP). For this purpose, an analytical nodal Green’s function solution for the transverse integrated neutron diffusion equation is developed in two and three-dimensional hexagonal geometry. This scheme is incorporated into HEXPEDITE, a code first developed by Fitzpatrick and Ougouag. HEXPEDITE neglects non-physical discontinuity terms that arise in the transverse leakage due to the transverse integration procedure application to hexagonal geometry and cannot account for the effects of burnable poisons across nodal boundaries. The test code being developed for this document accounts for these terms by maintaining an inventory of neutrons by using the nodal balance equation as a constraint of the neutron flux equation. The method developed in this report is intended to restore neutron conservation and increase the accuracy of the code by adding these terms to the transverse integrated flux solution and applying the nodal Green’s function solution to the resulting equation to derive a semi-analytical solution.

  16. CASTRO: A NEW COMPRESSIBLE ASTROPHYSICAL SOLVER. II. GRAY RADIATION HYDRODYNAMICS

    SciTech Connect

    Zhang, W.; Almgren, A.; Bell, J.; Howell, L.; Burrows, A.

    2011-10-01

    We describe the development of a flux-limited gray radiation solver for the compressible astrophysics code, CASTRO. CASTRO uses an Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. The gray radiation solver is based on a mixed-frame formulation of radiation hydrodynamics. In our approach, the system is split into two parts, one part that couples the radiation and fluid in a hyperbolic subsystem, and another parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem is solved explicitly with a high-order Godunov scheme, whereas the parabolic part is solved implicitly with a first-order backward Euler method.

  17. Finite Element Interface to Linear Solvers

    SciTech Connect

    Williams, Alan

    2005-03-18

    Sparse systems of linear equations arise in many engineering applications, including finite elements, finite volumes, and others. The solution of linear systems is often the most computationally intensive portion of the application. Depending on the complexity of problems addressed by the application, there may be no single solver capable of solving all of the linear systems that arise. This motivates the desire to switch an application from one solver librwy to another, depending on the problem being solved. The interfaces provided by solver libraries differ greatly, making it difficult to switch an application code from one library to another. The amount of library-specific code in an application Can be greatly reduced by having an abstraction layer between solver libraries and the application, putting a common "face" on various solver libraries. One such abstraction layer is the Finite Element Interface to Linear Solvers (EEl), which has seen significant use by finite element applications at Sandia National Laboratories and Lawrence Livermore National Laboratory.

  18. Enthalpy Diffusion in Multicomponent Flows

    SciTech Connect

    Cook, A W

    2009-01-20

    The conclusions of this paper are: (1) Enthalpy diffusion preserves the second law. (2) Euler solvers will not produce correct temperatures in mixing regions. (3) Navier-Stokes solvers will only produce correct temperatures if q{sub d} is included. (4) Errors from neglecting enthalpy diffusion are most severe when differences in molecular weights are large. (5) In addition to temperature, enthalpy diffusion affects density, dilatation and other fields in subtle ways. (6) Reacting flow simulations that neglect the term are a dubious proposition. (7) Turbulence models for RANS and LES closures should preserve consistency between energy and species diffusion.

  19. Analysis Tools for CFD Multigrid Solvers

    NASA Technical Reports Server (NTRS)

    Mineck, Raymond E.; Thomas, James L.; Diskin, Boris

    2004-01-01

    Analysis tools are needed to guide the development and evaluate the performance of multigrid solvers for the fluid flow equations. Classical analysis tools, such as local mode analysis, often fail to accurately predict performance. Two-grid analysis tools, herein referred to as Idealized Coarse Grid and Idealized Relaxation iterations, have been developed and evaluated within a pilot multigrid solver. These new tools are applicable to general systems of equations and/or discretizations and point to problem areas within an existing multigrid solver. Idealized Relaxation and Idealized Coarse Grid are applied in developing textbook-efficient multigrid solvers for incompressible stagnation flow problems.

  20. Nodal quasiparticle in pseudogapped colossal magnetoresistive manganites

    NASA Astrophysics Data System (ADS)

    Mannella, N.; Yang, W. L.; Zhou, X. J.; Tanaka, K.; Zheng, H.; Mitchell, J. F.; Zaanen, J.; Devereaux, T. P.; Nagaosa, N.; Hussain, Z.; Shen, Z. X.

    2006-03-01

    In this talk, the result of a recent angle-resolved photoemission spectroscopy (ARPES) investigation which allowed elucidating the controversial nature of the ferromagnetic metallic groundstate in the prototypical colossal magnetoresistive manganite bilayer compound La1.2Sr1.8Mn2O7 will be discussed [1]. The distribution of spectral weight in momentum space exhibits a nodal--antinodal dichotomous character. Quasiparticle excitations have been detected for the first time along the nodal direction (i.e. diagonal), and they are found to determine the metallic transport properties of this compound. The weight of the quasiparticle peak diminishes rapidly while crossing over to the antinodal (i.e. parallel to the Mn--O bonds) parallel sections of the Fermi surface, with the spectra strongly resembling those found in heavily underdoped cuprates high temperature superconductors (HTSC) such as Ca2-xNaxCuO2Cl2 [2]. This dichotomy between the electronic excitations along the nodal and antinodal directions in momentum space was so far considered a characteristic unique feature of the copper oxide HTSC. These findings therefore cast doubt on the assumption that the pseudogap state in the cuprate HTSC and the nodal-antinodal dichotomy are hallmarks of the superconductivity state. [1] N. Mannella et al., Nature 438, 474 (2005) [2] K. M Shen et al., Science 307, 901 (2005).

  1. Nodal quasiparticle in pseudogapped colossal magnetoresistivemanganites

    SciTech Connect

    Mannella, Norman; Yang, Wanli L.; Zhou, Xing Jiang; Zheng, Hong; Mitchell, John F.; Zaanen, Jan; Devereaux, Thomas P.; Nagaosa, Naoto; Hussain, Zahid; Shen, Zhi-Xun

    2008-01-17

    A characteristic feature of the copper oxidehigh-temperaturesuperconductors is the dichotomy between the electronicexcitations along the nodal (diagonal) and antinodal (parallel to the CuO bonds) directions in momentum space, generally assumed to be linked tothe 'd-wave' symmetry of the superconducting state. Angle-resolvedphotoemission measurements in the superconducting state have revealed aquasiparticle spectrum with a d-wave gap structure that exhibits amaximum along the antinodal direction and vanishes along the nodaldirection1. Subsequent measurements have shown that, at low dopinglevels, this gap structure persists even in the high-temperature metallicstate, although the nodal points of the superconducting state spread outin finite 'Fermi arcs'2. This is the so-called pseudogap phase, and ithas been assumed that it is closely linked to the superconducting state,either by assigning it to fluctuating superconductivity3 or by invokingorders which are natural competitors of d-wave superconductors4, 5. Herewe report experimental evidence that a very similar pseudogap state witha nodal-antinodal dichotomous character exists in a system that ismarkedly different from a superconductor: the ferromagnetic metallicgroundstate of the colossal magnetoresistive bilayer manganiteLa1.2Sr1.8Mn2O7. Our findings therefore cast doubt on the assumption thatthe pseudogap state in the copper oxides and the nodal-antinodaldichotomy are hallmarks of the superconductivity state.

  2. Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.

    PubMed

    Sako, Keisuke; Pradhan, Saurabh J; Barone, Vanessa; Inglés-Prieto, Álvaro; Müller, Patrick; Ruprecht, Verena; Čapek, Daniel; Galande, Sanjeev; Janovjak, Harald; Heisenberg, Carl-Philipp

    2016-07-19

    During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation. PMID:27396324

  3. EXTENSION OF THE 1D FOUR-GROUP ANALYTIC NODAL METHOD TO FULL MULTIGROUP

    SciTech Connect

    B. D. Ganapol; D. W. Nigg

    2008-09-01

    In the mid 80’s, a four-group/two-region, entirely analytical 1D nodal benchmark appeared. It was readily acknowledged that this special case was as far as one could go in terms of group number and still achieve an analytical solution. In this work, we show that by decomposing the solution to the multigroup diffusion equation into homogeneous and particular solutions, extension to any number of groups is a relatively straightforward exercise using the mathematics of linear algebra.

  4. KLU2 Direct Linear Solver Package

    2012-01-04

    KLU2 is a direct sparse solver for solving unsymmetric linear systems. It is related to the existing KLU solver, (in Amesos package and also as a stand-alone package from University of Florida) but provides template support for scalar and ordinal types. It uses a left looking LU factorization method.

  5. Improving Resource-Unaware SAT Solvers

    NASA Astrophysics Data System (ADS)

    Hölldobler, Steffen; Manthey, Norbert; Saptawijaya, Ari

    The paper discusses cache utilization in state-of-the-art SAT solvers. The aim of the study is to show how a resource-unaware SAT solver can be improved by utilizing the cache sensibly. The analysis is performed on a CDCL-based SAT solver using a subset of the industrial SAT Competition 2009 benchmark. For the analysis, the total cycles, the resource stall cycles, the L2 cache hits and the L2 cache misses are traced using sample based profiling. Based on the analysis, several techniques - some of which have not been used in SAT solvers so far - are proposed resulting in a combined speedup up to 83% without affecting the search path of the solver. The average speedup on the benchmark is 60%. The new techniques are also applied to MiniSAT2.0 improving its runtime by 20% on average.

  6. Belos Block Linear Solvers Package

    2004-03-01

    Belos is an extensible and interoperable framework for large-scale, iterative methods for solving systems of linear equations with multiple right-hand sides. The motivation for this framework is to provide a generic interface to a collection of algorithms for solving large-scale linear systems. Belos is interoperable because both the matrix and vectors are considered to be opaque objects--only knowledge of the matrix and vectors via elementary operations is necessary. An implementation of Balos is accomplished viamore » the use of interfaces. One of the goals of Belos is to allow the user flexibility in specifying the data representation for the matrix and vectors and so leverage any existing software investment. The algorithms that will be included in package are Krylov-based linear solvers, like Block GMRES (Generalized Minimal RESidual) and Block CG (Conjugate-Gradient).« less

  7. ALPS - A LINEAR PROGRAM SOLVER

    NASA Technical Reports Server (NTRS)

    Viterna, L. A.

    1994-01-01

    Linear programming is a widely-used engineering and management tool. Scheduling, resource allocation, and production planning are all well-known applications of linear programs (LP's). Most LP's are too large to be solved by hand, so over the decades many computer codes for solving LP's have been developed. ALPS, A Linear Program Solver, is a full-featured LP analysis program. ALPS can solve plain linear programs as well as more complicated mixed integer and pure integer programs. ALPS also contains an efficient solution technique for pure binary (0-1 integer) programs. One of the many weaknesses of LP solvers is the lack of interaction with the user. ALPS is a menu-driven program with no special commands or keywords to learn. In addition, ALPS contains a full-screen editor to enter and maintain the LP formulation. These formulations can be written to and read from plain ASCII files for portability. For those less experienced in LP formulation, ALPS contains a problem "parser" which checks the formulation for errors. ALPS creates fully formatted, readable reports that can be sent to a printer or output file. ALPS is written entirely in IBM's APL2/PC product, Version 1.01. The APL2 workspace containing all the ALPS code can be run on any APL2/PC system (AT or 386). On a 32-bit system, this configuration can take advantage of all extended memory. The user can also examine and modify the ALPS code. The APL2 workspace has also been "packed" to be run on any DOS system (without APL2) as a stand-alone "EXE" file, but has limited memory capacity on a 640K system. A numeric coprocessor (80X87) is optional but recommended. The standard distribution medium for ALPS is a 5.25 inch 360K MS-DOS format diskette. IBM, IBM PC and IBM APL2 are registered trademarks of International Business Machines Corporation. MS-DOS is a registered trademark of Microsoft Corporation.

  8. SUDOKU A STORY & A SOLVER

    SciTech Connect

    GARDNER, P.R.

    2006-04-01

    Sudoku, also known as Number Place, is a logic-based placement puzzle. The aim of the puzzle is to enter a numerical digit from 1 through 9 in each cell of a 9 x 9 grid made up of 3 x 3 subgrids (called ''regions''), starting with various digits given in some cells (the ''givens''). Each row, column, and region must contain only one instance of each numeral. Completing the puzzle requires patience and logical ability. Although first published in a U.S. puzzle magazine in 1979, Sudoku initially caught on in Japan in 1986 and attained international popularity in 2005. Last fall, after noticing Sudoku puzzles in some newspapers and magazines, I attempted a few just to see how hard they were. Of course, the difficulties varied considerably. ''Obviously'' one could use Trial and Error but all the advice was to ''Use Logic''. Thinking to flex, and strengthen, those powers, I began to tackle the puzzles systematically. That is, when I discovered a new tactical rule, I would write it down, eventually generating a list of ten or so, with some having overlap. They served pretty well except for the more difficult puzzles, but even then I managed to develop an additional three rules that covered all of them until I hit the Oregonian puzzle shown. With all of my rules, I could not seem to solve that puzzle. Initially putting my failure down to rapid mental fatigue (being unable to hold a sufficient quantity of information in my mind at one time), I decided to write a program to implement my rules and see what I had failed to notice earlier. The solver, too, failed. That is, my rules were insufficient to solve that particular puzzle. I happened across a book written by a fellow who constructs such puzzles and who claimed that, sometimes, the only tactic left was trial and error. With a trial and error routine implemented, my solver successfully completed the Oregonian puzzle, and has successfully solved every puzzle submitted to it since.

  9. SIERRA framework version 4 : solver services.

    SciTech Connect

    Williams, Alan B.

    2005-02-01

    Several SIERRA applications make use of third-party libraries to solve systems of linear and nonlinear equations, and to solve eigenproblems. The classes and interfaces in the SIERRA framework that provide linear system assembly services and access to solver libraries are collectively referred to as solver services. This paper provides an overview of SIERRA's solver services including the design goals that drove the development, and relationships and interactions among the various classes. The process of assembling and manipulating linear systems will be described, as well as access to solution methods and other operations.

  10. ALPS: A Linear Program Solver

    NASA Technical Reports Server (NTRS)

    Ferencz, Donald C.; Viterna, Larry A.

    1991-01-01

    ALPS is a computer program which can be used to solve general linear program (optimization) problems. ALPS was designed for those who have minimal linear programming (LP) knowledge and features a menu-driven scheme to guide the user through the process of creating and solving LP formulations. Once created, the problems can be edited and stored in standard DOS ASCII files to provide portability to various word processors or even other linear programming packages. Unlike many math-oriented LP solvers, ALPS contains an LP parser that reads through the LP formulation and reports several types of errors to the user. ALPS provides a large amount of solution data which is often useful in problem solving. In addition to pure linear programs, ALPS can solve for integer, mixed integer, and binary type problems. Pure linear programs are solved with the revised simplex method. Integer or mixed integer programs are solved initially with the revised simplex, and the completed using the branch-and-bound technique. Binary programs are solved with the method of implicit enumeration. This manual describes how to use ALPS to create, edit, and solve linear programming problems. Instructions for installing ALPS on a PC compatible computer are included in the appendices along with a general introduction to linear programming. A programmers guide is also included for assistance in modifying and maintaining the program.

  11. Euler solvers for transonic applications

    NASA Technical Reports Server (NTRS)

    Vanleer, Bram

    1989-01-01

    The 1980s may well be called the Euler era of applied aerodynamics. Computer codes based on discrete approximations of the Euler equations are now routinely used to obtain solutions of transonic flow problems in which the effects of entropy and vorticity production are significant. Such codes can even predict separation from a sharp edge, owing to the inclusion of artificial dissipation, intended to lend numerical stability to the calculation but at the same time enforcing the Kutta condition. One effect not correctly predictable by Euler codes is the separation from a smooth surface, and neither is viscous drag; for these some form of the Navier-Stokes equation is needed. It, therefore, comes as no surprise to observe that the Navier-Stokes has already begun before Euler solutions were fully exploited. Moreover, most numerical developments for the Euler equations are now constrained by the requirement that the techniques introduced, notably artificial dissipation, must not interfere with the new physics added when going from an Euler to a full Navier-Stokes approximation. In order to appreciate the contributions of Euler solvers to the understanding of transonic aerodynamics, it is useful to review the components of these computational tools. Space discretization, time- or pseudo-time marching and boundary procedures, the essential constituents are discussed. The subject of grid generation and grid adaptation to the solution are touched upon only where relevant. A list of unanswered questions and an outlook for the future are covered.

  12. CASTRO: A NEW COMPRESSIBLE ASTROPHYSICAL SOLVER. III. MULTIGROUP RADIATION HYDRODYNAMICS

    SciTech Connect

    Zhang, W.; Almgren, A.; Bell, J.; Howell, L.; Burrows, A.; Dolence, J.

    2013-01-15

    We present a formulation for multigroup radiation hydrodynamics that is correct to order O(v/c) using the comoving-frame approach and the flux-limited diffusion approximation. We describe a numerical algorithm for solving the system, implemented in the compressible astrophysics code, CASTRO. CASTRO uses a Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. In our multigroup radiation solver, the system is split into three parts: one part that couples the radiation and fluid in a hyperbolic subsystem, another part that advects the radiation in frequency space, and a parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem and the frequency space advection are solved explicitly with high-order Godunov schemes, whereas the parabolic part is solved implicitly with a first-order backward Euler method. Our multigroup radiation solver works for both neutrino and photon radiation.

  13. CASTRO: A New Compressible Astrophysical Solver. III. Multigroup Radiation Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Zhang, W.; Howell, L.; Almgren, A.; Burrows, A.; Dolence, J.; Bell, J.

    2013-01-01

    We present a formulation for multigroup radiation hydrodynamics that is correct to order O(v/c) using the comoving-frame approach and the flux-limited diffusion approximation. We describe a numerical algorithm for solving the system, implemented in the compressible astrophysics code, CASTRO. CASTRO uses a Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. In our multigroup radiation solver, the system is split into three parts: one part that couples the radiation and fluid in a hyperbolic subsystem, another part that advects the radiation in frequency space, and a parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem and the frequency space advection are solved explicitly with high-order Godunov schemes, whereas the parabolic part is solved implicitly with a first-order backward Euler method. Our multigroup radiation solver works for both neutrino and photon radiation.

  14. Parallelizing alternating direction implicit solver on GPUs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present a parallel Alternating Direction Implicit (ADI) solver on GPUs. Our implementation significantly improves existing implementations in two aspects. First, we address the scalability issue of existing Parallel Cyclic Reduction (PCR) implementations by eliminating their hardware resource con...

  15. Small renal tumor with lymph nodal enlargement: A histopathological surprise

    PubMed Central

    Thottathil, Mujeeburahiman; Verma, Ashish; D’souza, Nischith; Khan, Altaf

    2016-01-01

    Renal cancer with lymph nodal mass on the investigation is clinically suggestive of an advanced tumor. Small renal cancers are not commonly associated with lymph nodal metastasis. Association of renal cell carcinoma with renal tuberculosis (TB) in the same kidney is also rare. We report here a case of small renal cancer with multiple hilar and paraaortic lymph nodes who underwent radical nephrectomy, and histopathology report showed renal and lymph nodal TB too. PMID:27453671

  16. Development and assessment of the CONTAIN hybrid flow solver

    SciTech Connect

    Murata, K.K.; Stamps, D.W.

    1996-11-01

    A new gravitational head formulation for the treatment of stratified conditions has been developed for CONTAIN 1.2, a control volume code used primarily for the analyses of postulated accidents in nuclear power plants. The new CONTAIN formulation of gravitational heads, termed the hybrid formulation, is described. This method of calculating stratified conditions is compared with the old, average-density formulation used in code versions prior to CONTAIN 1.2. Both formulations are assessed in this report with experimental data from three large-scale experiments in which stratified conditions formed by injection of a buoyant gas were observed. In general, the hybrid formulation gives a substantially higher degree of stratification than the old formulation. For stable, fully developed stratifications, the hybrid formulation also gives much better agreement with the measured degree of stratification than the old formulation. In addition, the predicted degree of stratification is robust and not sensitive to nodalization, provided a set of nodalization guidelines are followed. However, for stratification behavior controlled by special physics not modeled in CONTAIN, such as momentum convection, plume entrainment, or bulk molecular diffusion, one should not expect good agreement with experiment unless special measures to accommodate the missing physics are taken.

  17. Finite Element Interface to Linear Solvers

    2005-03-18

    Sparse systems of linear equations arise in many engineering applications, including finite elements, finite volumes, and others. The solution of linear systems is often the most computationally intensive portion of the application. Depending on the complexity of problems addressed by the application, there may be no single solver capable of solving all of the linear systems that arise. This motivates the desire to switch an application from one solver librwy to another, depending on themore » problem being solved. The interfaces provided by solver libraries differ greatly, making it difficult to switch an application code from one library to another. The amount of library-specific code in an application Can be greatly reduced by having an abstraction layer between solver libraries and the application, putting a common "face" on various solver libraries. One such abstraction layer is the Finite Element Interface to Linear Solvers (EEl), which has seen significant use by finite element applications at Sandia National Laboratories and Lawrence Livermore National Laboratory.« less

  18. A parallel PCG solver for MODFLOW.

    PubMed

    Dong, Yanhui; Li, Guomin

    2009-01-01

    In order to simulate large-scale ground water flow problems more efficiently with MODFLOW, the OpenMP programming paradigm was used to parallelize the preconditioned conjugate-gradient (PCG) solver with in this study. Incremental parallelization, the significant advantage supported by OpenMP on a shared-memory computer, made the solver transit to a parallel program smoothly one block of code at a time. The parallel PCG solver, suitable for both MODFLOW-2000 and MODFLOW-2005, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. Based on the timing results, execution times using the parallel PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree. PMID:19563427

  19. Error analysis of the quadratic nodal expansion method in slab geometry

    SciTech Connect

    Penland, R.C.; Turinsky, P.J.; Azmy, Y.Y.

    1994-10-01

    As part of an effort to develop an adaptive mesh refinement strategy for use in state-of-the-art nodal diffusion codes, the authors derive error bounds on the solution variables of the quadratic Nodal Expansion Method (NEM) in slab geometry. Closure of the system is obtained through flux discontinuity relationships and boundary conditions. In order to verify the analysis presented, the authors compare the quadratic NEM to the analytic solution of a test problem. The test problem for this investigation is a one-dimensional slab [0,20cm] with L{sup 2} = 6.495cm{sup 2} and D = 0.1429cm. The slab has a unit neutron source distributed uniformly throughout and zero flux boundary conditions. The analytic solution to this problem is used to compute the node-average fluxes over a variety of meshes, and these are used to compute the NEM maximum error on each mesh.

  20. Topological surface states in nodal superconductors.

    PubMed

    Schnyder, Andreas P; Brydon, Philip M R

    2015-06-24

    Topological superconductors have become a subject of intense research due to their potential use for technical applications in device fabrication and quantum information. Besides fully gapped superconductors, unconventional superconductors with point or line nodes in their order parameter can also exhibit nontrivial topological characteristics. This article reviews recent progress in the theoretical understanding of nodal topological superconductors, with a focus on Weyl and noncentrosymmetric superconductors and their protected surface states. Using selected examples, we review the bulk topological properties of these systems, study different types of topological surface states, and examine their unusual properties. Furthermore, we survey some candidate materials for topological superconductivity and discuss different experimental signatures of topological surface states.

  1. An essential role for maternal control of Nodal signaling

    PubMed Central

    Kumari, Pooja; Gilligan, Patrick C; Lim, Shimin; Tran, Long Duc; Winkler, Sylke; Philp, Robin; Sampath, Karuna

    2013-01-01

    Growth factor signaling is essential for pattern formation, growth, differentiation, and maintenance of stem cell pluripotency. Nodal-related signaling factors are required for axis formation and germ layer specification from sea urchins to mammals. Maternal transcripts of the zebrafish Nodal factor, Squint (Sqt), are localized to future embryonic dorsal. The mechanisms by which maternal sqt/nodal RNA is localized and regulated have been unclear. Here, we show that maternal control of Nodal signaling via the conserved Y box-binding protein 1 (Ybx1) is essential. We identified Ybx1 via a proteomic screen. Ybx1 recognizes the 3’ untranslated region (UTR) of sqt RNA and prevents premature translation and Sqt/Nodal signaling. Maternal-effect mutations in zebrafish ybx1 lead to deregulated Nodal signaling, gastrulation failure, and embryonic lethality. Implanted Nodal-coated beads phenocopy ybx1 mutant defects. Thus, Ybx1 prevents ectopic Nodal activity, revealing a new paradigm in the regulation of Nodal signaling, which is likely to be conserved. DOI: http://dx.doi.org/10.7554/eLife.00683.001 PMID:24040511

  2. Anomalous thermodynamic power laws in nodal superconductors

    NASA Astrophysics Data System (ADS)

    Quintanilla, Jorge; Mazidian, Bayan; Annett, James F.; Hillier, Adrian D.

    2013-03-01

    Unconventional superconductors are frequently identified by the observation of power law behaviour on low temperature thermodynamic properties such as specific heat. These power laws generally derive from the linear spectrum near points or lines of zeros, or nodes, in the superconducting energy gap on the Fermi surface. Here we show that, in addition to the usual point and line nodes, a much wider class of different nodal types can occur. Some of these new types of nodes typically occur when there are transitions between different types of gap node topology, for example when point or line nodes first appear as a function of some physical parameter. We derive anomalous, non-integer thermodynamic power laws associated with these new nodal types and predict their occurrence in iron pnictide superconductors and in the noncentrosymmetric system Li2Pd3-xPtxB. This works was supported by EPSRC and STFC (U.K.) J.Q. gratefully acknowledges funding from HEFCE and STFC through the South-East Physics network (SEPnet).

  3. Code Verification of the HIGRAD Computational Fluid Dynamics Solver

    SciTech Connect

    Van Buren, Kendra L.; Canfield, Jesse M.; Hemez, Francois M.; Sauer, Jeremy A.

    2012-05-04

    The purpose of this report is to outline code and solution verification activities applied to HIGRAD, a Computational Fluid Dynamics (CFD) solver of the compressible Navier-Stokes equations developed at the Los Alamos National Laboratory, and used to simulate various phenomena such as the propagation of wildfires and atmospheric hydrodynamics. Code verification efforts, as described in this report, are an important first step to establish the credibility of numerical simulations. They provide evidence that the mathematical formulation is properly implemented without significant mistakes that would adversely impact the application of interest. Highly accurate analytical solutions are derived for four code verification test problems that exercise different aspects of the code. These test problems are referred to as: (i) the quiet start, (ii) the passive advection, (iii) the passive diffusion, and (iv) the piston-like problem. These problems are simulated using HIGRAD with different levels of mesh discretization and the numerical solutions are compared to their analytical counterparts. In addition, the rates of convergence are estimated to verify the numerical performance of the solver. The first three test problems produce numerical approximations as expected. The fourth test problem (piston-like) indicates the extent to which the code is able to simulate a 'mild' discontinuity, which is a condition that would typically be better handled by a Lagrangian formulation. The current investigation concludes that the numerical implementation of the solver performs as expected. The quality of solutions is sufficient to provide credible simulations of fluid flows around wind turbines. The main caveat associated to these findings is the low coverage provided by these four problems, and somewhat limited verification activities. A more comprehensive evaluation of HIGRAD may be beneficial for future studies.

  4. MGLab3D: An interactive environment for iterative solvers for elliptic PDEs in two and three dimensions

    SciTech Connect

    Bordner, J.; Saied, F.

    1996-12-31

    GLab3D is an enhancement of an interactive environment (MGLab) for experimenting with iterative solvers and multigrid algorithms. It is implemented in MATLAB. The new version has built-in 3D elliptic pde`s and several iterative methods and preconditioners that were not available in the original version. A sparse direct solver option has also been included. The multigrid solvers have also been extended to 3D. The discretization and pde domains are restricted to standard finite differences on the unit square/cube. The power of this software studies in the fact that no programming is needed to solve, for example, the convection-diffusion equation in 3D with TFQMR and a customized V-cycle preconditioner, for a variety of problem sizes and mesh Reynolds, numbers. In addition to the graphical user interface, some sample drivers are included to show how experiments can be composed using the underlying suite of problems and solvers.

  5. Performance of seminal and nodal roots of wheat in stagnant solution: K+ and P uptake and effects of increasing O2 partial pressures around the shoot on nodal root elongation.

    PubMed

    Wiengweera, Amara; Greenway, Hank

    2004-09-01

    Roots of intact wheat plants were grown for 7-12 d in stagnant nutrient solution, containing 0.1% agar, to mimic the lack of convection in waterlogged soil. Net K+ and P uptakes by seminal and nodal roots were measured separately using a split root system. For seminal roots in stagnant solution, net uptakes as a percentage of aerated roots were between 0% and 16% for P, while K+ ranged between 15% uptake and 54% loss. For the more waterlogging-tolerant nodal roots, net uptakes in stagnant nutrient solution, as a percentage of aerated roots, were 31-73% for P and 69-115% for K+. Elongation rates of nodal roots in stagnant nutrient were about 35-43% of those for roots in aerated solution. This partial inhibition occurred in these nodal roots despite their 15% porosity (v/v). Elevation of O2 partial pressures around the shoots to 40 kPa and then to 80 kPa substantially accelerated nodal root elongation in stagnant solution, demonstrating that most of the inhibition seen with ambient O2 around the shoots was associated with a restricted O2 supply to these nodal roots. Thus, in wheat nodal roots, with a partial pressure of 20 kPa O2 around the shoots, O2 diffusion from the shoots did not completely relieve the restrictions on elongation resulting from stagnancy in the nutrient solution. These results contrast with those in the literature for rice, in which roots function efficiently in stagnant solutions (0.1% agar). So, when wheat roots are aerenchymatous there are still restrictions to O2 diffusion in the gas space continuum between the atmosphere and the functional tissues of the roots. This poor acclimation must have been due to inefficiency of the aerenchymatous axes, which may include persistence of anoxic steles, and/or restricted O2 diffusion in other parts of the gas space continuum, in either the shoots and shoot-root junction or in the root tip.

  6. FETI Prime Domain Decomposition base Parallel Iterative Solver Library Ver.1.0

    2003-09-15

    FETI Prime is a library for the iterative solution of linear equations in solid and structural mechanics. The algorithm employs preconditioned conjugate gradients, with a domain decomposition-based preconditioner. The software is written in C++ and is designed for use with massively parallel computers, using MPI. The algorithm is based on the FETI-DP method, with additional capabilities for handling constraint equations, as well as interfacing with the Salinas structural dynamics code and the Finite Element Interfacemore » (FEI) library. Practical Application: FETI Prime is designed for use with finite element-based simulation codes for solid and structural mechanics. The solver uses element matrices, connectivity information, nodal information, and force vectors computed by the host code and provides back the solution to the linear system of equations, to the user specified level of accuracy, The library is compiled with the host code and becomes an integral part of the host code executable.« less

  7. Using SPARK as a Solver for Modelica

    SciTech Connect

    Wetter, Michael; Wetter, Michael; Haves, Philip; Moshier, Michael A.; Sowell, Edward F.

    2008-06-30

    Modelica is an object-oriented acausal modeling language that is well positioned to become a de-facto standard for expressing models of complex physical systems. To simulate a model expressed in Modelica, it needs to be translated into executable code. For generating run-time efficient code, such a translation needs to employ algebraic formula manipulations. As the SPARK solver has been shown to be competitive for generating such code but currently cannot be used with the Modelica language, we report in this paper how SPARK's symbolic and numerical algorithms can be implemented in OpenModelica, an open-source implementation of a Modelica modeling and simulation environment. We also report benchmark results that show that for our air flow network simulation benchmark, the SPARK solver is competitive with Dymola, which is believed to provide the best solver for Modelica.

  8. New iterative solvers for the NAG Libraries

    SciTech Connect

    Salvini, S.; Shaw, G.

    1996-12-31

    The purpose of this paper is to introduce the work which has been carried out at NAG Ltd to update the iterative solvers for sparse systems of linear equations, both symmetric and unsymmetric, in the NAG Fortran 77 Library. Our current plans to extend this work and include it in our other numerical libraries in our range are also briefly mentioned. We have added to the Library the new Chapter F11, entirely dedicated to sparse linear algebra. At Mark 17, the F11 Chapter includes sparse iterative solvers, preconditioners, utilities and black-box routines for sparse symmetric (both positive-definite and indefinite) linear systems. Mark 18 will add solvers, preconditioners, utilities and black-boxes for sparse unsymmetric systems: the development of these has already been completed.

  9. Topological surface states in nodal superconductors.

    PubMed

    Schnyder, Andreas P; Brydon, Philip M R

    2015-06-24

    Topological superconductors have become a subject of intense research due to their potential use for technical applications in device fabrication and quantum information. Besides fully gapped superconductors, unconventional superconductors with point or line nodes in their order parameter can also exhibit nontrivial topological characteristics. This article reviews recent progress in the theoretical understanding of nodal topological superconductors, with a focus on Weyl and noncentrosymmetric superconductors and their protected surface states. Using selected examples, we review the bulk topological properties of these systems, study different types of topological surface states, and examine their unusual properties. Furthermore, we survey some candidate materials for topological superconductivity and discuss different experimental signatures of topological surface states. PMID:26000466

  10. Experience with advanced nodal codes at YAEC

    SciTech Connect

    Cacciapouti, R.J.

    1990-01-01

    Yankee Atomic Electric Company (YAEC) has been performing reload licensing analysis since 1969. The basic pressurized water reactor (PWR) methodology involves the use of LEOPARD for cross-section generation, PDQ for radial power distributions and integral control rod worth, and SIMULATE for axial power distributions and differential control rod worth. In 1980, YAEC began performing reload licensing analysis for the Vermont Yankee boiling water reactor (BWR). The basic BWR methodology involves the use of CASMO for cross-section generation and SIMULATE for three-dimensional power distributions. In 1986, YAEC began investigating the use of CASMO-3 for cross-section generation and the advanced nodal code SIMULATE-3 for power distribution analysis. Based on the evaluation, the CASMO-3/SIMULATE-3 methodology satisfied all requirements. After careful consideration, the cost of implementing the new methodology is expected to be offset by reduced computing costs, improved engineering productivity, and fuel-cycle performance gains.

  11. Radar response from vegetation with nodal structure

    NASA Technical Reports Server (NTRS)

    Blanchard, B. J.; Oneill, P. E.

    1984-01-01

    Radar images from the SEASAT synthetic aperture radar (SAR) produced unusually high returns from corn and sorghum fields, which seem to indicate a correlation between nodal separation in the stalk and the wavelength of the radar. These images also show no difference in return from standing or harvested corn. Further investigation using images from the Shuttle Imaging Radar (SIR-A) substantiated these observations and showed a degradation of the high return with time after harvest. From portions of corn and sweet sorghum stalks that were sampled to measure stalk water content, it was determined that near and after maturity the water becomes more concentrated in the stalk nodes. The stalk then becomes a linear sequence of alternating dielectrics as opposed to a long slender cylinder with uniform dielectric properties.

  12. An Adaptive Flow Solver for Air-Borne Vehicles Undergoing Time-Dependent Motions/Deformations

    NASA Technical Reports Server (NTRS)

    Singh, Jatinder; Taylor, Stephen

    1997-01-01

    This report describes a concurrent Euler flow solver for flows around complex 3-D bodies. The solver is based on a cell-centered finite volume methodology on 3-D unstructured tetrahedral grids. In this algorithm, spatial discretization for the inviscid convective term is accomplished using an upwind scheme. A localized reconstruction is done for flow variables which is second order accurate. Evolution in time is accomplished using an explicit three-stage Runge-Kutta method which has second order temporal accuracy. This is adapted for concurrent execution using another proven methodology based on concurrent graph abstraction. This solver operates on heterogeneous network architectures. These architectures may include a broad variety of UNIX workstations and PCs running Windows NT, symmetric multiprocessors and distributed-memory multi-computers. The unstructured grid is generated using commercial grid generation tools. The grid is automatically partitioned using a concurrent algorithm based on heat diffusion. This results in memory requirements that are inversely proportional to the number of processors. The solver uses automatic granularity control and resource management techniques both to balance load and communication requirements, and deal with differing memory constraints. These ideas are again based on heat diffusion. Results are subsequently combined for visualization and analysis using commercial CFD tools. Flow simulation results are demonstrated for a constant section wing at subsonic, transonic, and a supersonic case. These results are compared with experimental data and numerical results of other researchers. Performance results are under way for a variety of network topologies.

  13. ODE System Solver W. Krylov Iteration & Rootfinding

    1991-09-09

    LSODKR is a new initial value ODE solver for stiff and nonstiff systems. It is a variant of the LSODPK and LSODE solvers, intended mainly for large stiff systems. The main differences between LSODKR and LSODE are the following: (a) for stiff systems, LSODKR uses a corrector iteration composed of Newton iteration and one of four preconditioned Krylov subspace iteration methods. The user must supply routines for the preconditioning operations, (b) Within the corrector iteration,more » LSODKR does automatic switching between functional (fixpoint) iteration and modified Newton iteration, (c) LSODKR includes the ability to find roots of given functions of the solution during the integration.« less

  14. Enthalpy Diffusion in Multicomponent Flows

    SciTech Connect

    Cook, A W

    2008-11-12

    The enthalpy diffusion flux in the multicomponent energy equation is a well known yet frequently neglected term. It accounts for energy changes, associated with compositional changes, resulting from species diffusion. Enthalpy diffusion is important in flows where significant mixing occurs between species of dissimilar molecular weight. The term plays a critical role in preventing local violations of the entropy condition. In simulations of nonpremixed combustion, omission of the enthalpy flux can lead to anomalous temperature gradients, which may cause mixing regions to exceed ignition conditions. The term can also play a role in generating acoustic noise in turbulent mixing layers. Euler solvers that rely on numerical diffusion to mix fluids cannot accurately predict the temperature in mixed regions. On the other hand, Navier-Stokes solvers that incorporate enthalpy diffusion can provide much more accurate results.

  15. A high-accuracy Eulerian gyrokinetic solver for collisional plasmas

    NASA Astrophysics Data System (ADS)

    Candy, J.; Belli, E. A.; Bravenec, R. V.

    2016-11-01

    We describe a new approach to solve the electromagnetic gyrokinetic equations which is optimized for accurate treatment of multispecies Fokker-Planck collisions including both pitch-angle and energy diffusion. The new algorithm is spectral/pseudospectral in four of the five phase space dimensions, and in the fieldline direction a novel 5th-order conservative upwind scheme is used to permit high-accuracy electromagnetic simulation even in the limit of very high plasma β and vanishingly small perpendicular wavenumber, k⊥ → 0. To our knowledge, this is the first pseudospectral implementation of the collision operator in a gyrokinetic code. We show that the new solver agrees closely with GYRO in the limit of weak Lorentz collisions, but gives a significantly more realistic description of collisions at high collision frequency. The numerical methods are also designed to be efficient and scalable for multiscale simulations that treat ion-scale and electron-scale turbulence simultaneously.

  16. Equation solvers for distributed-memory computers

    NASA Technical Reports Server (NTRS)

    Storaasli, Olaf O.

    1994-01-01

    A large number of scientific and engineering problems require the rapid solution of large systems of simultaneous equations. The performance of parallel computers in this area now dwarfs traditional vector computers by nearly an order of magnitude. This talk describes the major issues involved in parallel equation solvers with particular emphasis on the Intel Paragon, IBM SP-1 and SP-2 processors.

  17. Parallel solvers for reservoir simulation on MIMD computers

    SciTech Connect

    Piault, E.; Willien, F.; Roux, F.X.

    1995-12-01

    We have investigated parallel solvers for reservoir simulation. We compare different solvers and preconditioners using T3D and SP1 parallel computers. We use block diagonal domain decomposition preconditioner with non-overlapping sub-domains.

  18. Tunable Weyl Points in Periodically Driven Nodal Line Semimetals.

    PubMed

    Yan, Zhongbo; Wang, Zhong

    2016-08-19

    Weyl semimetals and nodal line semimetals are characterized by linear band touching at zero-dimensional points and one-dimensional lines, respectively. We predict that a circularly polarized light drives nodal line semimetals into Weyl semimetals. The Floquet Weyl points thus obtained are tunable by the incident light, which enables investigations of them in a highly controllable manner. The transition from nodal line semimetals to Weyl semimetals is accompanied by the emergence of a large and tunable anomalous Hall conductivity. Our predictions are experimentally testable by transport measurement in film samples or by pump-probe angle-resolved photoemission spectroscopy. PMID:27588882

  19. NODAL — The second life of the accelerator control language

    NASA Astrophysics Data System (ADS)

    Cuisinier, G.; Perriollat, F.; Ribeiro, P.; Kagarmanov, A.; Kovaltsov, V.

    1994-12-01

    NODAL has been a popular interpreter language for accelerator controls since the beginning of the 1970s. NODAL has been rewritten in the C language to be easily portable to the different computer platforms which are in use in accelerator controls. The paper describes the major features of this new version of NODAL, the major software packages which are available through this implementation, the platforms on which it is currently running, and some relevant performances. The experience gained during the rejuvenation project of the CERN accelerator control systems is presented. The benefit of this is discussed, in particular in a view of the prevailing strong constraints in personnel and money resources.

  20. Tunable Weyl Points in Periodically Driven Nodal Line Semimetals

    NASA Astrophysics Data System (ADS)

    Yan, Zhongbo; Wang, Zhong

    2016-08-01

    Weyl semimetals and nodal line semimetals are characterized by linear band touching at zero-dimensional points and one-dimensional lines, respectively. We predict that a circularly polarized light drives nodal line semimetals into Weyl semimetals. The Floquet Weyl points thus obtained are tunable by the incident light, which enables investigations of them in a highly controllable manner. The transition from nodal line semimetals to Weyl semimetals is accompanied by the emergence of a large and tunable anomalous Hall conductivity. Our predictions are experimentally testable by transport measurement in film samples or by pump-probe angle-resolved photoemission spectroscopy.

  1. A semianalytic two-group nodal model for SIMULATE-3

    SciTech Connect

    Esser, P.D.; Smith, K.S. )

    1993-01-01

    Light water reactor (LWR) cores containing highly enriched ([ge] 10% Pu) mixed-oxide (MOX) fuel exhibit steep thermal flux gradients near MOX-UO[sub 2] assembly interfaces. The fourth-order polynomial representation of the internodal flux used in many polynomial nodal methods (including the QPANDA nodal model in the SIMULATE-3 core analysis code) has already been verified against low-enriched MOX fuel but cannot accurately portray the severe flux variations near highly enriched MOX interfaces. This paper describes the development of an enhanced nodal model that includes transcendental components in the thermal flux profile.

  2. Designer Nodal/BMP2 Chimeras Mimic Nodal Signaling, Promote Chondrogenesis, and Reveal a BMP2-like Structure

    PubMed Central

    Esquivies, Luis; Blackler, Alissa; Peran, Macarena; Rodriguez-Esteban, Concepcion; Izpisua Belmonte, Juan Carlos; Booker, Evan; Gray, Peter C.; Ahn, Chihoon; Kwiatkowski, Witek; Choe, Senyon

    2014-01-01

    Nodal, a member of the TGF-β superfamily, plays an important role in vertebrate and invertebrate early development. The biochemical study of Nodal and its signaling pathway has been a challenge, mainly because of difficulties in producing the protein in sufficient quantities. We have developed a library of stable, chemically refoldable Nodal/BMP2 chimeric ligands (NB2 library). Three chimeras, named NB250, NB260, and NB264, show Nodal-like signaling properties including dependence on the co-receptor Cripto and activation of the Smad2 pathway. NB250, like Nodal, alters heart looping during the establishment of embryonic left-right asymmetry, and both NB250 and NB260, as well as Nodal, induce chondrogenic differentiation of human adipose-derived stem cells. This Nodal-induced differentiation is shown to be more efficient than BPM2-induced differentiation. Interestingly, the crystal structure of NB250 shows a backbone scaffold similar to that of BMP2. Our results show that these chimeric ligands may have therapeutic implications in cartilage injuries. PMID:24311780

  3. The genetics of nodal marginal zone lymphoma.

    PubMed

    Spina, Valeria; Khiabanian, Hossein; Messina, Monica; Monti, Sara; Cascione, Luciano; Bruscaggin, Alessio; Spaccarotella, Elisa; Holmes, Antony B; Arcaini, Luca; Lucioni, Marco; Tabbò, Fabrizio; Zairis, Sakellarios; Diop, Fary; Cerri, Michaela; Chiaretti, Sabina; Marasca, Roberto; Ponzoni, Maurilio; Deaglio, Silvia; Ramponi, Antonio; Tiacci, Enrico; Pasqualucci, Laura; Paulli, Marco; Falini, Brunangelo; Inghirami, Giorgio; Bertoni, Francesco; Foà, Robin; Rabadan, Raul; Gaidano, Gianluca; Rossi, Davide

    2016-09-01

    Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34%), PTPRD (20%), NOTCH2 (20%), and KLF2 (17%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification.

  4. The genetics of nodal marginal zone lymphoma

    PubMed Central

    Spina, Valeria; Khiabanian, Hossein; Messina, Monica; Monti, Sara; Cascione, Luciano; Bruscaggin, Alessio; Spaccarotella, Elisa; Holmes, Antony B.; Arcaini, Luca; Lucioni, Marco; Tabbò, Fabrizio; Zairis, Sakellarios; Diop, Fary; Cerri, Michaela; Chiaretti, Sabina; Marasca, Roberto; Ponzoni, Maurilio; Deaglio, Silvia; Ramponi, Antonio; Tiacci, Enrico; Pasqualucci, Laura; Paulli, Marco; Falini, Brunangelo; Inghirami, Giorgio; Bertoni, Francesco; Foà, Robin; Rabadan, Raul; Gaidano, Gianluca

    2016-01-01

    Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34%), PTPRD (20%), NOTCH2 (20%), and KLF2 (17%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification. PMID:27335277

  5. The genetics of nodal marginal zone lymphoma.

    PubMed

    Spina, Valeria; Khiabanian, Hossein; Messina, Monica; Monti, Sara; Cascione, Luciano; Bruscaggin, Alessio; Spaccarotella, Elisa; Holmes, Antony B; Arcaini, Luca; Lucioni, Marco; Tabbò, Fabrizio; Zairis, Sakellarios; Diop, Fary; Cerri, Michaela; Chiaretti, Sabina; Marasca, Roberto; Ponzoni, Maurilio; Deaglio, Silvia; Ramponi, Antonio; Tiacci, Enrico; Pasqualucci, Laura; Paulli, Marco; Falini, Brunangelo; Inghirami, Giorgio; Bertoni, Francesco; Foà, Robin; Rabadan, Raul; Gaidano, Gianluca; Rossi, Davide

    2016-09-01

    Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34%), PTPRD (20%), NOTCH2 (20%), and KLF2 (17%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification. PMID:27335277

  6. Nodal Solutions for Supercritical Laplace Equations

    NASA Astrophysics Data System (ADS)

    Dalbono, Francesca; Franca, Matteo

    2016-11-01

    In this paper we study radial solutions for the following equation Δ u(x)+f (u(x), |x|) = 0, where {x in {Rn}}, n > 2, f is subcritical for r small and u large and supercritical for r large and u small, with respect to the Sobolev critical exponent {2^{*} = 2n/n-2}. The solutions are classified and characterized by their asymptotic behaviour and nodal properties. In an appropriate super-linear setting, we give an asymptotic condition sufficient to guarantee the existence of at least one ground state with fast decay with exactly j zeroes for any j ≥ 0. Under the same assumptions, we also find uncountably many ground states with slow decay, singular ground states with fast decay and singular ground states with slow decay, all of them with exactly j zeroes. Our approach, based on Fowler transformation and invariant manifold theory, enables us to deal with a wide family of potentials allowing spatial inhomogeneity and a quite general dependence on u. In particular, for the Matukuma-type potential, we show a kind of structural stability.

  7. Classification, Electrophysiological Features and Therapy of Atrioventricular Nodal Reentrant Tachycardia

    PubMed Central

    Josephson, Mark E

    2016-01-01

    Atrioventricular nodal reentrant tachycardia (AVNRT) should be classified as typical or atypical. The term ‘fast-slow AVNRT’ is rather misleading. Retrograde atrial activation during tachycardia should not be relied upon as a diagnostic criterion. Both typical and atypical atrioventricular nodal reentrant tachycardia are compatible with varying retrograde atrial activation patterns. Attempts at establishing the presence of a ‘lower common pathway’ are probably of no practical significance. When the diagnosis of AVNRT is established, ablation should be only directed towards the anatomic position of the slow pathway. If right septal attempts are unsuccessful, the left septal side should be tried. Ablation targeting earliest atrial activation sites during typical atrioventricular nodal reentrant tachycardia or the fast pathway in general for any kind of typical or atypical atrioventricular nodal reentrant tachycardia, are not justified. In this review we discuss current concepts about the tachycardia circuit, electrophysiologic diagnosis, and ablation of this arrhythmia. PMID:27617092

  8. Classification, Electrophysiological Features and Therapy of Atrioventricular Nodal Reentrant Tachycardia

    PubMed Central

    Josephson, Mark E

    2016-01-01

    Atrioventricular nodal reentrant tachycardia (AVNRT) should be classified as typical or atypical. The term ‘fast-slow AVNRT’ is rather misleading. Retrograde atrial activation during tachycardia should not be relied upon as a diagnostic criterion. Both typical and atypical atrioventricular nodal reentrant tachycardia are compatible with varying retrograde atrial activation patterns. Attempts at establishing the presence of a ‘lower common pathway’ are probably of no practical significance. When the diagnosis of AVNRT is established, ablation should be only directed towards the anatomic position of the slow pathway. If right septal attempts are unsuccessful, the left septal side should be tried. Ablation targeting earliest atrial activation sites during typical atrioventricular nodal reentrant tachycardia or the fast pathway in general for any kind of typical or atypical atrioventricular nodal reentrant tachycardia, are not justified. In this review we discuss current concepts about the tachycardia circuit, electrophysiologic diagnosis, and ablation of this arrhythmia.

  9. Methods for Solving Gas Damping Problems in Perforated Microstructures Using a 2D Finite-Element Solver

    PubMed Central

    Veijola, Timo; Råback, Peter

    2007-01-01

    We present a straightforward method to solve gas damping problems for perforated structures in two dimensions (2D) utilising a Perforation Profile Reynolds (PPR) solver. The PPR equation is an extended Reynolds equation that includes additional terms modelling the leakage flow through the perforations, and variable diffusivity and compressibility profiles. The solution method consists of two phases: 1) determination of the specific admittance profile and relative diffusivity (and relative compressibility) profiles due to the perforation, and 2) solution of the PPR equation with a FEM solver in 2D. Rarefied gas corrections in the slip-flow region are also included. Analytic profiles for circular and square holes with slip conditions are presented in the paper. To verify the method, square perforated dampers with 16–64 holes were simulated with a three-dimensional (3D) Navier-Stokes solver, a homogenised extended Reynolds solver, and a 2D PPR solver. Cases for both translational (in normal to the surfaces) and torsional motion were simulated. The presented method extends the region of accurate simulation of perforated structures to cases where the homogenisation method is inaccurate and the full 3D Navier-Stokes simulation is too time-consuming.

  10. Bilinear nodal transport method in weighted diamond difference form

    SciTech Connect

    Azmy, Y.Y.

    1987-01-01

    Nodal methods have been developed and implemented for the numerical solution of the discrete ordinates neutron transport equation. Numerical testing of these methods and comparison of their results to those obtained by conventional methods have established the high accuracy of nodal methods. Furthermore, it has been suggested that the linear-linear approximation is the most computationally efficient, practical nodal approximation. Indeed, this claim has been substantiated by comparing the accuracy in the solution, and the CPU time required to achieve convergence to that solution by several nodal approximations, as well as the diamond difference scheme. Two types of linear-linear nodal methods have been developed in the literature: analytic linear-linear (NLL) methods, in which the transverse-leakage terms are derived analytically, and approximate linear-linear (PLL) methods, in which these terms are approximated. In spite of their higher accuracy, NLL methods result in very complicated discrete-variable equations that exhibit a high degree of coupling, thus requiring special solution algorithms. On the other hand, the sacrificed accuracy in PLL methods is compensated for by the simple discrete-variable equations and diamond-difference-like solution algorithm. In this paper the authors outline the development of an NLL nodal method, the bilinear method, which can be written in a weighted diamond difference form with one spatial weight per dimension that is analytically derived rather than preassigned in an ad hoc fashion.

  11. VDJSeq-Solver: in silico V(D)J recombination detection tool.

    PubMed

    Paciello, Giulia; Acquaviva, Andrea; Pighi, Chiara; Ferrarini, Alberto; Macii, Enrico; Zamo', Alberto; Ficarra, Elisa

    2015-01-01

    In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(D)J rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/. PMID:25799103

  12. Aleph Field Solver Challenge Problem Results Summary.

    SciTech Connect

    Hooper, Russell; Moore, Stan Gerald

    2015-01-01

    Aleph models continuum electrostatic and steady and transient thermal fields using a finite-element method. Much work has gone into expanding the core solver capability to support enriched mod- eling consisting of multiple interacting fields, special boundary conditions and two-way interfacial coupling with particles modeled using Aleph's complementary particle-in-cell capability. This report provides quantitative evidence for correct implementation of Aleph's field solver via order- of-convergence assessments on a collection of problems of increasing complexity. It is intended to provide Aleph with a pedigree and to establish a basis for confidence in results for more challeng- ing problems important to Sandia's mission that Aleph was specifically designed to address.

  13. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  14. A perspective on unstructured grid flow solvers

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, V.

    1995-01-01

    This survey paper assesses the status of compressible Euler and Navier-Stokes solvers on unstructured grids. Different spatial and temporal discretization options for steady and unsteady flows are discussed. The integration of these components into an overall framework to solve practical problems is addressed. Issues such as grid adaptation, higher order methods, hybrid discretizations and parallel computing are briefly discussed. Finally, some outstanding issues and future research directions are presented.

  15. A multigrid solver for the semiconductor equations

    NASA Technical Reports Server (NTRS)

    Bachmann, Bernhard

    1993-01-01

    We present a multigrid solver for the exponential fitting method. The solver is applied to the current continuity equations of semiconductor device simulation in two dimensions. The exponential fitting method is based on a mixed finite element discretization using the lowest-order Raviart-Thomas triangular element. This discretization method yields a good approximation of front layers and guarantees current conservation. The corresponding stiffness matrix is an M-matrix. 'Standard' multigrid solvers, however, cannot be applied to the resulting system, as this is dominated by an unsymmetric part, which is due to the presence of strong convection in part of the domain. To overcome this difficulty, we explore the connection between Raviart-Thomas mixed methods and the nonconforming Crouzeix-Raviart finite element discretization. In this way we can construct nonstandard prolongation and restriction operators using easily computable weighted L(exp 2)-projections based on suitable quadrature rules and the upwind effects of the discretization. The resulting multigrid algorithm shows very good results, even for real-world problems and for locally refined grids.

  16. Incidental Nodal Lymphangioleiomyomatosis Is Not a Harbinger of Pulmonary Lymphangioleiomyomatosis: A Study of 19 Cases with Evaluation of Diagnostic Immunohistochemistry

    PubMed Central

    Schoolmeester, J. Kenneth; Park, Kay J.

    2016-01-01

    Lymphangioleiomyomatosis (LAM) is a proliferation of perivascular epithelioid cells typically affecting the lung as a low grade, destructive and progressive disease, but may also be found in lymph nodes and other organs. LAM is sometimes seen as an incidental finding in lymph node dissections performed for staging of gynecologic tumors. To our knowledge, no study has investigated the clinical significance of incidental nodal LAM in relation to subsequent development of pulmonary LAM. We identified 19 patients from our institution with LAM in lymph nodes. Follow up was available for 100% of patients and ranged from 3 to 123 months (mean 33.8 months). All were women and ages ranged from 35 to 71 years (mean 56.3). None had a history of tuberous sclerosis, renal angiomyolipoma or pulmonary LAM. LAM involvement spanned 1 to 6 nodes (mean 2) ranging from 1 to 100% of the total excised lymph nodes. The single largest focus of nodal LAM ranged from 1 to 9 mm (mean 4.3) in 18 patients without evidence of persistent or recurrent nodal LAM. In the one patient with persistent local nodal LAM, the greatest diameter was 25 mm. Affected lymph node sites were regional pelvic and retroperitoneal chains routinely sampled in staging operations. An immunohisotchemical panel of HMB45, A103 and β-catenin was evaluated in 18 cases. HMB45 showed strong, but usually focal staining in every case compared to A103 which was very focally expressed (39%) or negative. β-catenin showed strong, diffuse cytoplasmic and membranous (nonnuclear) reactivity in 100% of cases. At last clinic visit, all 19 patients had no manifestations of pulmonary LAM. In an absence of signs of symptoms of extranodal LAM, patients with incidentally discovered nodal LAM smaller than 10 mm are not at risk for developing pulmonary LAM. PMID:26135558

  17. Expression of Nodal and Nodal Receptors in Prostate Stem Cells and Prostate Cancer Cells: Autocrine Effects on Cell Proliferation and Migration

    PubMed Central

    Vo, BaoHan T.; Khan, Shafiq A.

    2010-01-01

    BACKGROUND Nodal, a TGFβ like growth factor, functions as an embryonic morphogen that maintains the pluripotency of embryonic stem cells. Nodal has been implicated in cancer progression; however, there is no information on expression and functions of Nodal in prostate cancer. In this study, we have investigated the expression of Nodal, its receptors, and its effects on proliferation and migration of human prostate cells. METHODS RT-PCR, qPCR, and Western blot analyses were performed to analyze expression of Nodal and Nodal receptors and its effects on phosphorylation of Smad2/3 in prostate cells. The effects on proliferation and migration were determined by 3H-Thymidine incorporation and cell migration assays in the presence or absence of Nodal receptor inhibitor (SB431542). RESULTS Nodal was highly expressed in WPE, DU145, LNCaP, and LNCaP-C81 cells with low expression in RWPE1 and RWPE2 cells, but not in PREC, PC3 and PC3M cells. Nodal receptors are expressed at varying levels in all prostate cells. Treatment with exogenous Nodal induced phosphorylation of Smad2/3 in WPE, DU145, and PC3 cells, which was blocked by SB431542. Nodal dose-dependently inhibited proliferation of WPE, RWPE1 and DU145 cells, but not LNCaP and PC3 cells. Nodal induced cell migration in PC3 cells, which was inhibited by SB431542; Nodal had no effect on cell migration in WPE and DU145 cells. The effects of Nodal on cell proliferation and migration are mediated via ALK4 and ActRII/ActRIIB receptors and Smad 2/3 phosphorylation. CONCLUSIONS Nodal may function as an autocrine regulator of proliferation and migration of prostate cancer cells. PMID:21557273

  18. Development of depletion perturbation theory for a reactor nodal code

    SciTech Connect

    Bowman, S.M.

    1981-09-01

    A generalized depletion perturbation (DPT) theory formulation for light water reactor (LWR) depletion problems is developed and implemented into the three-dimensional LWR nodal code SIMULATE. This development applies the principles of the original derivation by M.L. Williams to the nodal equations solved by SIMULATE. The present formulation is first described in detail, and the nodal coupling methodology in SIMULATE is used to determine partial derivatives of the coupling coefficients. The modifications to the original code and the new DPT options available to the user are discussed. Finally, the accuracy and the applicability of the new DPT capability to LWR design analysis are examined for several LWR depletion test cases. The cases range from simple static cases to a realistic PWR model for an entire fuel cycle. Responses of interest included K/sub eff/, nodal peaking, and peak nodal exposure. The nonlinear behavior of responses with respect to perturbations of the various types of cross sections was also investigated. The time-dependence of the sensitivity coefficients for different responses was examined and compared. Comparison of DPT results for these examples to direct calculations reveals the limited applicability of depletion perturbation theory to LWR design calculations at the present. The reasons for these restrictions are discussed, and several methods which might improve the computational accuracy of DPT are proposed for future research.

  19. Approximate Riemann solvers for the Godunov SPH (GSPH)

    NASA Astrophysics Data System (ADS)

    Puri, Kunal; Ramachandran, Prabhu

    2014-08-01

    The Godunov Smoothed Particle Hydrodynamics (GSPH) method is coupled with non-iterative, approximate Riemann solvers for solutions to the compressible Euler equations. The use of approximate solvers avoids the expensive solution of the non-linear Riemann problem for every interacting particle pair, as required by GSPH. In addition, we establish an equivalence between the dissipative terms of GSPH and the signal based SPH artificial viscosity, under the restriction of a class of approximate Riemann solvers. This equivalence is used to explain the anomalous “wall heating” experienced by GSPH and we provide some suggestions to overcome it. Numerical tests in one and two dimensions are used to validate the proposed Riemann solvers. A general SPH pairing instability is observed for two-dimensional problems when using unequal mass particles. In general, Ducowicz Roe's and HLLC approximate Riemann solvers are found to be suitable replacements for the iterative Riemann solver in the original GSPH scheme.

  20. Unstructured Polyhedral Mesh Thermal Radiation Diffusion

    SciTech Connect

    Palmer, T.S.; Zika, M.R.; Madsen, N.K.

    2000-07-27

    Unstructured mesh particle transport and diffusion methods are gaining wider acceptance as mesh generation, scientific visualization and linear solvers improve. This paper describes an algorithm that is currently being used in the KULL code at Lawrence Livermore National Laboratory to solve the radiative transfer equations. The algorithm employs a point-centered diffusion discretization on arbitrary polyhedral meshes in 3D. We present the results of a few test problems to illustrate the capabilities of the radiation diffusion module.

  1. Development of an efficient multigrid method for the NEM form of the multigroup neutron diffusion equation

    NASA Astrophysics Data System (ADS)

    Al-Chalabi, Rifat M. Khalil

    1997-09-01

    reconstruction methodology. The relaxation method, which is the power method, utilizes a constant coefficient matrix within the NEM non-linear iterative strategy. The choice of the MG nesting within the nested iterative strategy enables the incorporation of other non-linear effects with no additional coding effort. In addition, if an eigenvalue problem is being solved, it remains an eigenvalue problem at all grid levels, simplifying coding implementation. The merit of the developed MG method was tested by incorporating it into the NESTLE iterative solver, and employing it to solve four different benchmark problems. In addition to the base cases, three different sensitivity studies are performed, examining the effects of number of MG levels, homogenized coupling coefficients correction (i.e. restriction operator), and fine-mesh reconstruction algorithm (i.e. prolongation operator). The multilevel acceleration scheme developed in this research provides the foundation for developing adaptive multilevel acceleration methods for steady-state and transient NEM nodal neutron diffusion equations. (Abstract shortened by UMI.)

  2. On the Nodal Lines of Eisenstein Series on Schottky Surfaces

    NASA Astrophysics Data System (ADS)

    Jakobson, Dmitry; Naud, Frédéric

    2016-09-01

    On convex co-compact hyperbolic surfaces {X=Γ backslash H2} , we investigate the behavior of nodal curves of real valued Eisenstein series {F_λ(z,ξ)} , where {λ} is the spectral parameter, {ξ} the direction at infinity. Eisenstein series are (non-{L^2} ) eigenfunctions of the Laplacian {Δ_X} satisfying {Δ_X F_λ=(1/4+λ^2)F_λ} . As {λ} goes to infinity (the high energy limit), we show that, for generic {ξ} , the number of intersections of nodal lines with any compact segment of geodesic grows like {λ} , up to multiplicative constants. Applications to the number of nodal domains inside the convex core of the surface are then derived.

  3. Simulating Weyl points and nodal loops in an optical superlattice

    NASA Astrophysics Data System (ADS)

    Zhang, Dan-Wei

    2016-08-01

    We propose a scheme to simulate Weyl points and nodal loops with ultracold atoms in an optical lattice that is subjected to realizable synthetic magnetic field and synthetic dimension. We show that a Hofstadter-like Hamiltonian with a cyclically parameterized on-site energy term can be realized in a tunable two-dimensional optical superlattice, based on the laser-assisted atomic tunneling method. This model effectively describes a three-dimensional periodic lattice system under magnetic fluxes, where a synthetic dimension is encoded by a cyclical phase of the optical lattice potential. For different atomic hopping configurations, the single-particle bands are demonstrated to, respectively, exhibit Weyl points and nodal loops in the extended three-dimensional Brillouin zone. Furthermore, we illustrate that the mimicked Weyl points and nodal loops can be experimentally detected by measuring the atomic transfer fraction in Bloch-Zener oscillations.

  4. Three-dimensional transport with variational nodal methods

    SciTech Connect

    Lewis, E.E.; Palmiotti, G.; Shalil, H.S.; Laurin-Kovitz, K.; Fanning, T.; Hanebutte, U.R.

    1996-12-31

    The development of the variational nodal method contained in the three-dimensional transport code VARIANT is reviewed. This Argonne National Laboratory code treats two- and three- dimensional multigroup problems with anisotropic scattering in hexagonal and Cartesian geometries. The methodology couples hybrid finite elements in space, which enforce nodal balance, with spherical harmonics expansions in angle. The resulting response matrix equations are solved by red-black or four-color iterations. Several enhancements to VARIANT are discussed: The simplified spherical harmonics option provides near spherical harmonic accuracy for many problems at a fraction of the cost. Adjoint and perturbation calculations are performed without the physical- and mathematical adjoint dichotomy appearing in other nodal methods. Heterogeneous node methods extend the problem classes to which the method may be applied. Computational strategies and trade-offs are discussed and possible future research directions are outlined.

  5. A computational study of nodal-based tetrahedral element behavior.

    SciTech Connect

    Gullerud, Arne S.

    2010-09-01

    This report explores the behavior of nodal-based tetrahedral elements on six sample problems, and compares their solution to that of a corresponding hexahedral mesh. The problems demonstrate that while certain aspects of the solution field for the nodal-based tetrahedrons provide good quality results, the pressure field tends to be of poor quality. Results appear to be strongly affected by the connectivity of the tetrahedral elements. Simulations that rely on the pressure field, such as those which use material models that are dependent on the pressure (e.g. equation-of-state models), can generate erroneous results. Remeshing can also be strongly affected by these issues. The nodal-based test elements as they currently stand need to be used with caution to ensure that their numerical deficiencies do not adversely affect critical values of interest.

  6. Updates to the NEQAIR Radiation Solver

    NASA Technical Reports Server (NTRS)

    Cruden, Brett A.; Brandis, Aaron M.

    2014-01-01

    The NEQAIR code is one of the original heritage solvers for radiative heating prediction in aerothermal environments, and is still used today for mission design purposes. This paper discusses the implementation of the first major revision to the NEQAIR code in the last five years, NEQAIR v14.0. The most notable features of NEQAIR v14.0 are the parallelization of the radiation computation, reducing runtimes by about 30×, and the inclusion of mid-wave CO2 infrared radiation.

  7. DPS--a computerised diagnostic problem solver.

    PubMed

    Bartos, P; Gyárfas, F; Popper, M

    1982-01-01

    The paper contains a short description of the DPS system which is a computerized diagnostic problem solver. The system is under development of the Research Institute of Medical Bionics in Bratislava, Czechoslovakia. Its underlying philosophy yields from viewing the diagnostic process as process of cognitive problem solving. The implementation of the system is based on the methods of Artificial Intelligence and utilisation of production systems and frame theory should be noted in this context. Finally a list of program modules and their characterisation is presented.

  8. Input-output-controlled nonlinear equation solvers

    NASA Technical Reports Server (NTRS)

    Padovan, Joseph

    1988-01-01

    To upgrade the efficiency and stability of the successive substitution (SS) and Newton-Raphson (NR) schemes, the concept of input-output-controlled solvers (IOCS) is introduced. By employing the formal properties of the constrained version of the SS and NR schemes, the IOCS algorithm can handle indefiniteness of the system Jacobian, can maintain iterate monotonicity, and provide for separate control of load incrementation and iterate excursions, as well as having other features. To illustrate the algorithmic properties, the results for several benchmark examples are presented. These define the associated numerical efficiency and stability of the IOCS.

  9. Deformation modes in the finite element absolute nodal coordinate formulation

    NASA Astrophysics Data System (ADS)

    Sugiyama, Hiroyuki; Gerstmayr, Johannes; Shabana, Ahmed A.

    2006-12-01

    The objective of this study is to provide interpretation of the deformation modes in the finite element absolute nodal coordinate formulation using several strain definitions. In this finite element formulation, the nodal coordinates consist of absolute position coordinates and gradients that can be used to define a unique rotation and deformation fields within the element as well as at the nodal points. The results obtained in this study clearly show cross-section deformation modes eliminated when the number of the finite element nodal coordinates is systematically and consistently reduced. Using the procedure discussed in this paper one can obtain a reduced order dynamic model, eliminate position vector gradients that introduce high frequencies to the solution of some problems, achieve the continuity of the remaining gradients at the nodal points, and obtain a formulation that automatically satisfies the principle of work and energy. Furthermore, the resulting dynamic model, unlike large rotation finite element formulations, leads to a unique rotation field, and as a consequence, the obtained formulation does not suffer from the problem of coordinate redundancy that characterizes existing large deformation finite element formulations. In order to accurately define strain components that can have easy physical interpretation, a material coordinate system is introduced to define the material element rotation and deformation. Using the material coordinate system, the Timoshenko-Reissner and Euler -Bernoulli beam models can be systematically obtained as special cases of the absolute nodal coordinate formulation beam models. While a constraint approach is used in this study to eliminate the cross-section deformation modes, it is important to point out as mentioned in this paper that lower-order finite elements, some of which already presented in previous investigations, can be efficiently used in thin and stiff structure applications.

  10. A transient, quadratic nodal method for triangular-Z geometry

    SciTech Connect

    DeLorey, T.F.

    1993-06-01

    Many systematically-derived nodal methods have been developed for Cartesian geometry due to the extensive interest in Light Water Reactors. These methods typically model the transverse-integrated flux as either an analytic or low order polynomial function of position within the node. Recently, quadratic nodal methods have been developed for R-Z and hexagonal geometry. A static and transient quadratic nodal method is developed for triangular-Z geometry. This development is particularly challenging because the quadratic expansion in each node must be performed between the node faces and the triangular points. As a consequence, in the 2-D plane, the flux and current at the points of the triangles must be treated. Quadratic nodal equations are solved using a non-linear iteration scheme, which utilizes the corrected, mesh-centered finite difference equations, and forces these equations to match the quadratic equations by computing discontinuity factors during the solution. Transient nodal equations are solved using the improved quasi-static method, which has been shown to be a very efficient solution method for transient problems. Several static problems are used to compare the quadratic nodal method to the Coarse Mesh Finite Difference (CMFD) method. The quadratic method is shown to give more accurate node-averaged fluxes. However, it appears that the method has difficulty predicting node leakages near reactor boundaries and severe material interfaces. The consequence is that the eigenvalue may be poorly predicted for certain reactor configurations. The transient methods are tested using a simple analytic test problem, a heterogeneous heavy water reactor benchmark problem, and three thermal hydraulic test problems. Results indicate that the transient methods have been implemented correctly.

  11. Variational nodal solution algorithms for multigroup criticality problems

    SciTech Connect

    Carrico, C.B.; Lewis, E.E.

    1991-01-01

    Variational nodal transport methods are generalized for the treatment of multigroup criticality problems. The generation of variational response matrices is streamlined and automated through the use of symbolic manipulation. A new red-black partitioned matrix algorithm for the solution of the within-group equations is formulated and shown to be at once both a regular matrix splitting and a synthetic acceleration method. The methods are implemented in X- Y geometry as a module of the Argonne National Laboratory code DIF3D. For few group problems highly accurate P[sub 3] eigenvalues are obtained with computing times comparable to those of an existing interface-current nodal transport method.

  12. Long period nodal motion of sun synchronous orbits

    NASA Technical Reports Server (NTRS)

    Duck, K. I.

    1975-01-01

    An approximative model is formulated for assessing these perturbations that significantly affect long term modal motion of sun synchronous orbits. Computer simulations with several independent computer programs consider zonal and tesseral gravitational harmonics, third body gravitational disturbances induced by the sun and the moon, and atmospheric drag. A pendulum model consisting of evenzonal harmonics through order 4 and solar gravity dominated nodal motion approximation. This pendulum motion results from solar gravity inducing an inclination oscillation which couples into the nodal precession induced by the earth's oblateness. The pendulum model correlated well with simulations observed flight data.

  13. Chiral Spin-Orbital Liquids with Nodal Lines

    NASA Astrophysics Data System (ADS)

    Natori, W. M. H.; Andrade, E. C.; Miranda, E.; Pereira, R. G.

    2016-07-01

    Strongly correlated materials with strong spin-orbit coupling hold promise for realizing topological phases with fractionalized excitations. Here, we propose a chiral spin-orbital liquid as a stable phase of a realistic model for heavy-element double perovskites. This spin liquid state has Majorana fermion excitations with a gapless spectrum characterized by nodal lines along the edges of the Brillouin zone. We show that the nodal lines are topological defects of a non-Abelian Berry connection and that the system exhibits dispersing surface states. We discuss some experimental signatures of this state and compare them with properties of the spin liquid candidate Ba2YMoO6.

  14. Reflector modelling of small high leakage cores making use of multi-group nodal equivalence theory

    SciTech Connect

    Theron, S. A.; Reitsma, F.

    2012-07-01

    This research focuses on modelling reflectors in typical material testing reactors (MTRs). Equivalence theory is used to homogenise and collapse detailed transport solutions to generate equivalent nodal parameters and albedo boundary conditions for reflectors, for subsequent use in full core nodal diffusion codes. This approach to reflector modelling has been shown to be accurate for two-group large commercial light water reactor (LWR) analysis, but has not been investigated for MTRs. MTRs are smaller, with much larger leakage, environment sensitivity and multi-group spectrum dependencies than LWRs. This study aims to determine if this approach to reflector modelling is an accurate and plausible homogenisation technique for the modelling of small MTR cores. The successful implementation will result in simplified core models, better accuracy and improved efficiency of computer simulations. Codes used in this study include SCALE 6.1, OSCAR-4 and EQUIVA (the last two codes are developed and used at Necsa). The results show a five times reduction in calculational time for the proposed reduced reactor model compared to the traditional explicit model. The calculated equivalent parameters however show some sensitivity to the environment used to generate them. Differences in the results compared to the current explicit model, require more careful investigation including comparisons with a reference result, before its implementation can be recommended. (authors)

  15. Using the scalable nonlinear equations solvers package

    SciTech Connect

    Gropp, W.D.; McInnes, L.C.; Smith, B.F.

    1995-02-01

    SNES (Scalable Nonlinear Equations Solvers) is a software package for the numerical solution of large-scale systems of nonlinear equations on both uniprocessors and parallel architectures. SNES also contains a component for the solution of unconstrained minimization problems, called SUMS (Scalable Unconstrained Minimization Solvers). Newton-like methods, which are known for their efficiency and robustness, constitute the core of the package. As part of the multilevel PETSc library, SNES incorporates many features and options from other parts of PETSc. In keeping with the spirit of the PETSc library, the nonlinear solution routines are data-structure-neutral, making them flexible and easily extensible. This users guide contains a detailed description of uniprocessor usage of SNES, with some added comments regarding multiprocessor usage. At this time the parallel version is undergoing refinement and extension, as we work toward a common interface for the uniprocessor and parallel cases. Thus, forthcoming versions of the software will contain additional features, and changes to parallel interface may result at any time. The new parallel version will employ the MPI (Message Passing Interface) standard for interprocessor communication. Since most of these details will be hidden, users will need to perform only minimal message-passing programming.

  16. A transient, Hex-Z nodal code corrected by discontinuity factors. Volume 1: The transient nodal code; Final report

    SciTech Connect

    Shatilla, Y.A.M.; Henry, A.F.

    1993-12-31

    This document constitutes Volume 1 of the Final Report of a three-year study supported by the special Research Grant Program for Nuclear Energy Research set up by the US Department of Energy. The original motivation for the work was to provide a fast and accurate computer program for the analysis of transients in heavy water or graphite-moderated reactors being considered as candidates for the New Production Reactor. Thus, part of the funding was by way of pass-through money from the Savannah River Laboratory. With this intent in mind, a three-dimensional (Hex-Z), general-energy-group transient, nodal code was created, programmed, and tested. In order to improve accuracy, correction terms, called {open_quotes}discontinuity factors,{close_quotes} were incorporated into the nodal equations. Ideal values of these factors force the nodal equations to provide node-integrated reaction rates and leakage rates across nodal surfaces that match exactly those edited from a more exact reference calculation. Since the exact reference solution is needed to compute the ideal discontinuity factors, the fact that they result in exact nodal equations would be of little practical interest were it not that approximate discontinuity factors, found at a greatly reduced cost, often yield very accurate results. For example, for light-water reactors, discontinuity factors found from two-dimensional, fine-mesh, multigroup transport solutions for two-dimensional cuts of a fuel assembly provide very accurate predictions of three-dimensional, full-core power distributions. The present document (volume 1) deals primarily with the specification, programming and testing of the three-dimensional, Hex-Z computer program. The program solves both the static (eigenvalue) and transient, general-energy-group, nodal equations corrected by user-supplied discontinuity factors.

  17. Extension of the linear nodal method to large concrete building calculations

    SciTech Connect

    Childs, R.L.; Rhoades, W.A.

    1985-01-01

    The implementation of the linear nodal method in the TORT code is described, and the results of a mesh refinement study to test the effectiveness of the linear nodal and weighted diamond difference methods available in TORT are presented.

  18. Nodal Structure and the Partitioning of Equivalence Classes

    ERIC Educational Resources Information Center

    Fields, Lanny; Watanabe-Rose, Mari

    2008-01-01

    By definition, all of the stimuli in an equivalence class have to be functionally interchangeable with each other. The present experiment, however, demonstrated that this was not the case when using post-class-formation dual-option response transfer tests. With college students, two 4-node 6-member equivalence classes with nodal structures of…

  19. PoroTomo Subtask 6.3 Nodal Seismometers Metadata

    DOE Data Explorer

    Lesley Parker

    2016-03-28

    Metadata for the nodal seismometer array deployed at the POROTOMO's Natural Laboratory in Brady Hot Spring, Nevada during the March 2016 testing. Metadata includes location and timing for each instrument as well as file lists of data to be uploaded in a separate submission.

  20. jShyLU Scalable Hybrid Preconditioner and Solver

    2012-09-11

    ShyLU is numerical software to solve sparse linear systems of equations. ShyLU uses a hybrid direct-iterative Schur complement method, and may be used either as a preconditioner or as a solver. ShyLU is parallel and optimized for a single compute Solver node. ShyLU will be a package in the Trilinos software framework.

  1. Experiences with linear solvers for oil reservoir simulation problems

    SciTech Connect

    Joubert, W.; Janardhan, R.; Biswas, D.; Carey, G.

    1996-12-31

    This talk will focus on practical experiences with iterative linear solver algorithms used in conjunction with Amoco Production Company`s Falcon oil reservoir simulation code. The goal of this study is to determine the best linear solver algorithms for these types of problems. The results of numerical experiments will be presented.

  2. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Digital Electronic Message Service Nodal... AND SPECIAL RADIO SERVICES FIXED MICROWAVE SERVICES 24 GHz Service and Digital Electronic Message Service § 101.503 Digital Electronic Message Service Nodal Stations. 10.6 GHz DEMS Nodal Stations may...

  3. Verification and Validation of a Chemical Reaction Solver Coupled to the Piecewise Parabolic Method

    NASA Astrophysics Data System (ADS)

    Attal, Nitesh; Ramaprabhu, Praveen; Hossain, Jahed; Karkhanis, Varad; Roy, Sukesh; Gord, James; Uddin, Mesbah

    2012-11-01

    We present a detailed chemical kinetics reaction solver coupled to the Piecewise Parabolic Method (PPM) embedded in the widely used astrophysical FLASH code. The FLASH code solves the compressible Euler equations with a directionally split, PPM with Adaptive Mesh Refinement (AMR). The reaction network is solved using a library of coupled ODE solvers, specialized for handling stiff systems of equations. Finally, the diffusion of heat, mass, and momentum is handled either through an update of the fluxes of each quantity, or by directly solving a diffusion equation for each. The resulting product is capable of handling a variety of physics such as gas-phase chemical kinetics, diffusive transport of mass, momentum, and heat, shocks, sharp interfaces, multi-species mixtures, and thermal radiation. We will present results from verification and validation of the above capabilities through comparison with analytical solutions, and published numerical and experimental data. Our validation cases include advection of reacting fronts in 1-D and 2D, laminar premixed flames in a Bunsen burner configuration, and shock-driven combustion. We acknowledge funding from Spectral Energies LLC.

  4. Nodal, paranodal and juxtaparanodal axonal proteins during demyelination and remyelination in multiple sclerosis.

    PubMed

    Coman, I; Aigrot, M S; Seilhean, D; Reynolds, R; Girault, J A; Zalc, B; Lubetzki, C

    2006-12-01

    Saltatory conduction in myelinated fibres depends on the specific molecular organization of highly specialized axonal domains at the node of Ranvier, the paranodal and the juxtaparanodal regions. Voltage-gated sodium channels (Na(v)) have been shown to be deployed along the naked demyelinated axon in experimental models of CNS demyelination and in multiple sclerosis lesions. Little is known about aggregation of nodal, paranodal and juxtaparanodal constituents during the repair process. We analysed by immunohistochemistry on free-floating sections from multiple sclerosis brains the expression and distribution of nodal (Na(v) channels), paranodal (paranodin/Caspr) and juxtaparanodal (K(v) channels and Caspr2) molecules in demyelinated and remyelinated lesions. Whereas in demyelinated lesions, paranodal and juxtaparanodal proteins are diffusely distributed on denuded axons, the distribution of Na(v) channels is heterogeneous, with a diffuse immunoreactivity but also few broad Na(v) channel aggregates in all demyelinated lesions. In contrast to the demyelinated plaques, all remyelinated lesions are characterized by the detection of aggregates of Na(v) channels, paranodin/Caspr, K(v) channels and Caspr2. Our data suggest that these aggregates precede remyelination, and that Na(v) channel aggregation is the initial event, followed by aggregation of paranodal and then juxtaparanodal axonal proteins. Remyelination takes place in multiple sclerosis tissue but myelin repair is often incomplete, and the reasons for this remyelination deficit are many. We suggest that a defect of Na(v) channel aggregation might be involved in the remyelination failure in demyelinated lesions with spared axons and oligodendroglial cells. PMID:16766541

  5. Shape reanalysis and sensitivities utilizing preconditioned iterative boundary solvers

    NASA Technical Reports Server (NTRS)

    Guru Prasad, K.; Kane, J. H.

    1992-01-01

    The computational advantages associated with the utilization of preconditined iterative equation solvers are quantified for the reanalysis of perturbed shapes using continuum structural boundary element analysis (BEA). Both single- and multi-zone three-dimensional problems are examined. Significant reductions in computer time are obtained by making use of previously computed solution vectors and preconditioners in subsequent analyses. The effectiveness of this technique is demonstrated for the computation of shape response sensitivities required in shape optimization. Computer times and accuracies achieved using the preconditioned iterative solvers are compared with those obtained via direct solvers and implicit differentiation of the boundary integral equations. It is concluded that this approach employing preconditioned iterative equation solvers in reanalysis and sensitivity analysis can be competitive with if not superior to those involving direct solvers.

  6. A real-time impurity solver for DMFT

    NASA Astrophysics Data System (ADS)

    Kim, Hyungwon; Aron, Camille; Han, Jong E.; Kotliar, Gabriel

    Dynamical mean-field theory (DMFT) offers a non-perturbative approach to problems with strongly correlated electrons. The method heavily relies on the ability to numerically solve an auxiliary Anderson-type impurity problem. While powerful Matsubara-frequency solvers have been developed over the past two decades to tackle equilibrium situations, the status of real-time impurity solvers that could compete with Matsubara-frequency solvers and be readily generalizable to non-equilibrium situations is still premature. We present a real-time solver which is based on a quantum Master equation description of the dissipative dynamics of the impurity and its exact diagonalization. As a benchmark, we illustrate the strengths of our solver in the context of the equilibrium Mott-insulator transition of the one-band Hubbard model and compare it with iterative perturbation theory (IPT) method. Finally, we discuss its direct application to a nonequilibrium situation.

  7. Premixed flame response to pressure fluctuations using an implicit solver with detailed chemistry

    NASA Astrophysics Data System (ADS)

    Malik, Nadeem

    2015-11-01

    A major challenge in combustion research is the coupling of the compressible flow field to the detailed thermochemistry. Recent advances in numerical solvers has met this challenge within an implicit numerical framework, retaining the full stiffness of the realistic comprehensive chemistry and multicomponent transport properties in the system. Here, the solver TARDIS (Transient Advection Reaction Diffusion Implicit Simulations) is demonstrated, first, by investigating the laminar flame speed in stoichiometric H2/air and CH4/air flames as a function of the flame curvature and found to follow non-linear regimes, contrary to previous thinking. Second, planar and curved laminar flames are subjected to pressure and equivalence ratio oscillations and found to respond through a spectrum of time and length scales. TARDIS has the potential to elucidate fundamental aspects of flame structure and thermochemistry, and could be the basis for a new generation of implicit DNS solvers. The author acknowledge financial support from SABIC, #SB101018, through the Dean of Scientific Research at KFUPM.

  8. Two-Dimensional Riemann Solver for Euler Equations of Gas Dynamics

    NASA Astrophysics Data System (ADS)

    Brio, M.; Zakharian, A. R.; Webb, G. M.

    2001-02-01

    We construct a Riemann solver based on two-dimensional linear wave contributions to the numerical flux that generalizes the one-dimensional method due to Roe (1981, J. Comput. Phys.43, 157). The solver is based on a multistate Riemann problem and is suitable for arbitrary triangular grids or any other finite volume tessellations of the plane. We present numerical examples illustrating the performance of the method using both first- and second-order-accurate numerical solutions. The numerical flux contributions are due to one-dimensional waves and multidimensional waves originating from the corners of the computational cell. Under appropriate CFL restrictions, the contributions of one-dimensional waves dominate the flux, which explains good performance of dimensionally split solvers in practice. The multidimensional flux corrections increase the accuracy and stability, allowing a larger time step. The improvements are more pronounced on a coarse mesh and for large CFL numbers. For the second-order method, the improvements can be comparable to the improvements resulting from a less diffusive limiter.

  9. Parallel solver for trajectory optimization search directions

    NASA Technical Reports Server (NTRS)

    Psiaki, M. L.; Park, K. H.

    1992-01-01

    A key algorithmic element of a real-time trajectory optimization hardware/software implementation is presented, the search step solver. This is one piece of an algorithm whose overall goal is to make nonlinear trajectory optimization fast enough to provide real-time commands during guidance of a vehicle such as an aeromaneuvering orbiter or the National Aerospace Plane. Many methods of nonlinear programming require the solution of a quadratic program (QP) at each iteration to determine the search step. In the trajectory optimization case, the QP has a special dynamic programming structure. The algorithm exploits this special structure with a divide- and conquer type of parallel implementation. The algorithm solves a (p.N)-stage problem on N processors in O(p + log2 N) operations. The algorithm yields a factor of 8 speed-up over the fastest known serial algorithm when solving a 1024-stage test problem on 32 processors.

  10. Scalable Adaptive Multilevel Solvers for Multiphysics Problems

    SciTech Connect

    Xu, Jinchao

    2014-12-01

    In this project, we investigated adaptive, parallel, and multilevel methods for numerical modeling of various real-world applications, including Magnetohydrodynamics (MHD), complex fluids, Electromagnetism, Navier-Stokes equations, and reservoir simulation. First, we have designed improved mathematical models and numerical discretizaitons for viscoelastic fluids and MHD. Second, we have derived new a posteriori error estimators and extended the applicability of adaptivity to various problems. Third, we have developed multilevel solvers for solving scalar partial differential equations (PDEs) as well as coupled systems of PDEs, especially on unstructured grids. Moreover, we have integrated the study between adaptive method and multilevel methods, and made significant efforts and advances in adaptive multilevel methods of the multi-physics problems.

  11. Optimising a parallel conjugate gradient solver

    SciTech Connect

    Field, M.R.

    1996-12-31

    This work arises from the introduction of a parallel iterative solver to a large structural analysis finite element code. The code is called FEX and it was developed at Hitachi`s Mechanical Engineering Laboratory. The FEX package can deal with a large range of structural analysis problems using a large number of finite element techniques. FEX can solve either stress or thermal analysis problems of a range of different types from plane stress to a full three-dimensional model. These problems can consist of a number of different materials which can be modelled by a range of material models. The structure being modelled can have the load applied at either a point or a surface, or by a pressure, a centrifugal force or just gravity. Alternatively a thermal load can be applied with a given initial temperature. The displacement of the structure can be constrained by having a fixed boundary or by prescribing the displacement at a boundary.

  12. General purpose nonlinear system solver based on Newton-Krylov method.

    SciTech Connect

    2013-12-01

    KINSOL is part of a software family called SUNDIALS: SUite of Nonlinear and Differential/Algebraic equation Solvers [1]. KINSOL is a general-purpose nonlinear system solver based on Newton-Krylov and fixed-point solver technologies [2].

  13. Algebraic multigrid preconditioning within parallel finite-element solvers for 3-D electromagnetic modelling problems in geophysics

    NASA Astrophysics Data System (ADS)

    Koldan, Jelena; Puzyrev, Vladimir; de la Puente, Josep; Houzeaux, Guillaume; Cela, José María

    2014-06-01

    We present an elaborate preconditioning scheme for Krylov subspace methods which has been developed to improve the performance and reduce the execution time of parallel node-based finite-element (FE) solvers for 3-D electromagnetic (EM) numerical modelling in exploration geophysics. This new preconditioner is based on algebraic multigrid (AMG) that uses different basic relaxation methods, such as Jacobi, symmetric successive over-relaxation (SSOR) and Gauss-Seidel, as smoothers and the wave front algorithm to create groups, which are used for a coarse-level generation. We have implemented and tested this new preconditioner within our parallel nodal FE solver for 3-D forward problems in EM induction geophysics. We have performed series of experiments for several models with different conductivity structures and characteristics to test the performance of our AMG preconditioning technique when combined with biconjugate gradient stabilized method. The results have shown that, the more challenging the problem is in terms of conductivity contrasts, ratio between the sizes of grid elements and/or frequency, the more benefit is obtained by using this preconditioner. Compared to other preconditioning schemes, such as diagonal, SSOR and truncated approximate inverse, the AMG preconditioner greatly improves the convergence of the iterative solver for all tested models. Also, when it comes to cases in which other preconditioners succeed to converge to a desired precision, AMG is able to considerably reduce the total execution time of the forward-problem code-up to an order of magnitude. Furthermore, the tests have confirmed that our AMG scheme ensures grid-independent rate of convergence, as well as improvement in convergence regardless of how big local mesh refinements are. In addition, AMG is designed to be a black-box preconditioner, which makes it easy to use and combine with different iterative methods. Finally, it has proved to be very practical and efficient in the

  14. Comparison of open-source linear programming solvers.

    SciTech Connect

    Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.; Jones, Katherine A.; Martin, Nathaniel; Detry, Richard Joseph

    2013-10-01

    When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modular In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.

  15. Chiral Spin-Orbital Liquids with Nodal Lines.

    PubMed

    Natori, W M H; Andrade, E C; Miranda, E; Pereira, R G

    2016-07-01

    Strongly correlated materials with strong spin-orbit coupling hold promise for realizing topological phases with fractionalized excitations. Here, we propose a chiral spin-orbital liquid as a stable phase of a realistic model for heavy-element double perovskites. This spin liquid state has Majorana fermion excitations with a gapless spectrum characterized by nodal lines along the edges of the Brillouin zone. We show that the nodal lines are topological defects of a non-Abelian Berry connection and that the system exhibits dispersing surface states. We discuss some experimental signatures of this state and compare them with properties of the spin liquid candidate Ba_{2}YMoO_{6}. PMID:27419588

  16. Anomalous contagion and renormalization in networks with nodal mobility

    NASA Astrophysics Data System (ADS)

    Manrique, Pedro D.; Qi, Hong; Zheng, Minzhang; Xu, Chen; Hui, Pak Ming; Johnson, Neil F.

    2016-07-01

    A common occurrence in everyday human activity is where people join, leave and possibly rejoin clusters of other individuals —whether this be online (e.g. social media communities) or in real space (e.g. popular meeting places such as cafes). In the steady state, the resulting interaction network would appear static over time if the identities of the nodes are ignored. Here we show that even in this static steady-state limit, a non-zero nodal mobility leads to a diverse set of outbreak profiles that is dramatically different from known forms, and yet matches well with recent real-world social outbreaks. We show how this complication of nodal mobility can be renormalized away for a particular class of networks.

  17. Anomalous thermodynamic power laws near topological transitions in nodal superconductors

    NASA Astrophysics Data System (ADS)

    Mazidian, B.; Quintanilla, J.; Hillier, A. D.; Annett, J. F.

    2013-12-01

    Unconventional superconductors are most frequently identified by the observation of power-law behavior on low-temperature thermodynamic or transport properties, such as specific heat. Here, we show that, in addition to the usual point and line nodes, a much wider class of different nodal types can occur. These new types of nodes typically occur when there are transitions between different types of gap node topology, for example, when point or line nodes first appear as a function of some physical parameter. We identify anomalous, noninteger thermodynamic power laws associated with these new nodal types, and give physical examples of superconductors in which they might be observed experimentally, including the noncentrosymmetric superconductor Li2Pd3-xPtxB.

  18. Nodal failure index approach to groundwater remediation design

    USGS Publications Warehouse

    Lee, J.; Reeves, H.W.; Dowding, C.H.

    2008-01-01

    Computer simulations often are used to design and to optimize groundwater remediation systems. We present a new computationally efficient approach that calculates the reliability of remedial design at every location in a model domain with a single simulation. The estimated reliability and other model information are used to select a best remedial option for given site conditions, conceptual model, and available data. To evaluate design performance, we introduce the nodal failure index (NFI) to determine the number of nodal locations at which the probability of success is below the design requirement. The strength of the NFI approach is that selected areas of interest can be specified for analysis and the best remedial design determined for this target region. An example application of the NFI approach using a hypothetical model shows how the spatial distribution of reliability can be used for a decision support system in groundwater remediation design. ?? 2008 ASCE.

  19. A non-conforming 3D spherical harmonic transport solver

    SciTech Connect

    Van Criekingen, S.

    2006-07-01

    A new 3D transport solver for the time-independent Boltzmann transport equation has been developed. This solver is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux in spherical harmonics (PN method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations such as the ones based on Raviart-Thomas finite elements. Encouraging numerical results are presented. (authors)

  20. Multi-GPU kinetic solvers using MPI and CUDA

    NASA Astrophysics Data System (ADS)

    Zabelok, Sergey; Arslanbekov, Robert; Kolobov, Vladimir

    2014-12-01

    This paper describes recent progress towards porting a Unified Flow Solver (UFS) to heterogeneous parallel computing. The main challenge of porting UFS to graphics processing units (GPUs) comes from the dynamically adapted mesh, which causes irregular data access. We describe the implementation of CUDA kernels for three modules in UFS: the direct Boltzmann solver using discrete velocity method (DVM), the DSMC module, and the Lattice Boltzmann Method (LBM) solver, all using octree Cartesian mesh with adaptive Mesh Refinement (AMR). Double digit speedup on single GPU and good scaling for multi-GPU has been demonstrated.

  1. Atrioventricular nodal reentrant tachycardia ablation and inferior vena cava agenesis.

    PubMed

    Galand, Vincent; Pavin, Dominique; Behar, Nathalie; Mabo, Philippe; Martins, Raphaël P

    2016-10-01

    Congenital anomalies of the inferior vena cava (IVC) are rare and very often diagnosed in asymptomatic patients during computed tomography performed for other purposes. These anomalies can have significant clinical implications, for example if electrophysiology procedures are needed. Diagnostic and ablation procedures are difficult since catheter manipulation and positioning are more complex. We present here a case of successful atrioventricular nodal reentrant tachycardia ablation in a patient with unexpected IVC agenesis, using an azygos route. PMID:27633734

  2. Nodal Basin Recurrence After Sentinel Lymph Node Biopsy for Melanoma

    PubMed Central

    Kretschmer, Lutz; Bertsch, Hans Peter; Zapf, Antonia; Mitteldorf, Christina; Satzger, Imke; Thoms, Kai-Martin; Völker, Bernward; Schön, Michael Peter; Gutzmer, Ralf; Starz, Hans

    2015-01-01

    Abstract The objective of this study was to analyze different types of nodal basin recurrence after sentinel lymph node biopsy (SLNB) for melanoma. Patients and Methods: Kaplan–Meier estimates and the Cox proportional hazards model were used to study 2653 patients from 3 German melanoma centers retrospectively. The estimated 5-year negative predictive value of SLNB was 96.4%. The estimated false-negative (FN) rates after 1, 2, 3, 5, and 10 years were 2.5%, 4.6%, 6.4%, 8.7%, and 12.6%, respectively. Independent factors associated with false negativity were older age, fewer SLNs excised, and head or neck location of the primary tumor. Compared with SLN-positive patients, the FNs had a significantly lower survival. In SLN-positive patients undergoing completion lymphadenectomy (CLND), the 5-year nodal basin recurrence rate was 18.3%. The recurrence rates for axilla, groin, and neck were 17.2%, 15.5%, and 44.1%, respectively. Significant factors predicting local relapse after CLND were older age, head, or neck location of the primary tumor, ulceration, deeper penetration of the metastasis into the SLN, tumor-positive CLND, and >2 lymph node metastases. All kinds of nodal relapse were associated with a higher prevalence of in-transit metastases. The FN rate after SLNB steadily increases over the observation period and should, therefore, be estimated by the Kaplan–Meier method. False-negativity is associated with fewer SLNs excised. The beneficial effect of CLND on nodal basin disease control varies considerably across different risk groups. This should be kept in mind about SLN-positive patients when individual decisions on prophylactic CLND are taken. PMID:26356697

  3. Topological Phase Transitions in Line-nodal Superconductors

    NASA Astrophysics Data System (ADS)

    Cho, Gil Young; Han, Sangeun; Moon, Eun-Gook

    Fathoming interplay between symmetry and topology of many-electron wave-functions deepens our understanding in quantum nature of many particle systems. Topology often protects zero-energy excitation, and in a certain class, symmetry is intrinsically tied to the topological protection. Namely, unless symmetry is broken, topological nature is intact. We study one specific case of such class, symmetry-protected line-nodal superconductors in three spatial dimensions (3d). Mismatch between phase spaces of order parameter fluctuation and line-nodal fermion excitation induces an exotic universality class in a drastic contrast to one of the conventional ϕ4 theory in 3d. Hyper-scaling violation and relativistic dynamic scaling with unusually large quantum critical region are main characteristics, and their implication in experiments is discussed. For example, continuous phase transition out of line-nodal superconductors has a linear phase boundary in a temperature-tuning parameter phase-diagram. This work was supported by the Brain Korea 21 PLUS Project of Korea Government and KAIST start-up funding.

  4. Anomalous scaling of the penetration depth in nodal superconductors

    NASA Astrophysics Data System (ADS)

    She, Jian-Huang; Lawler, Michael J.; Kim, Eun-Ah

    2015-07-01

    Recent findings of anomalous superlinear scaling of low-temperature (T ) penetration depth (PD) in several nodal superconductors near putative quantum critical points suggest that the low-temperature PD can be a useful probe of quantum critical fluctuations in a superconductor. On the other hand, cuprates, which are poster child nodal superconductors, have not shown any such anomalous scaling of PD, despite growing evidence of quantum critical points (QCP). Then it is natural to ask when and how can quantum critical fluctuations cause anomalous scaling of PD? Carrying out the renormalization group calculation for the problem of two-dimensional superconductors with point nodes, we show that quantum critical fluctuations associated with a point group symmetry reduction result in nonuniversal logarithmic corrections to the T dependence of the PD. The resulting apparent power law depends on the bare velocity anisotropy ratio. We then compare our results to data sets from two distinct nodal superconductors: YBa2Cu3O6.95 and CeCoIn5. Considering all symmetry-lowering possibilities of the point group of interest, C4 v, we find our results to be remarkably consistent with YBa2Cu3O6.95 being near a vertical nematic QCP and CeCoIn5 being near a diagonal nematic QCP. Our results motivate a search for diagonal nematic fluctuations in CeCoIn5.

  5. LSST Telescope Alignment Plan Based on Nodal Aberration Theory

    NASA Astrophysics Data System (ADS)

    Sebag, J.; Gressler, W.; Schmid, T.; Rolland, J. P.; Thompson, K. P.

    2012-04-01

    The optical alignment of the Large Synoptic Survey Telescope (LSST) is potentially challenging, due to its fast three-mirror optical design and its large 3.5° field of view (FOV). It is highly advantageous to align the three-mirror optical system prior to the integration of the complex science camera on the telescope, which corrects the FOV via three refractive elements and includes the operational wavefront sensors. A telescope alignment method based on nodal aberration theory (NAT) is presented here to address this challenge. Without the science camera installed on the telescope, the on-axis imaging performance of the telescope is diffraction-limited, but the field of view is not corrected. The nodal properties of the three-mirror telescope design have been analyzed and an alignment approach has been developed using the intrinsically linear nodal behavior, which is linked via sensitivities to the misalignment parameters. Since mirror figure errors will exist in any real application, a methodology to introduce primary-mirror figure errors into the analysis has been developed and is also presented.

  6. A nodal domain theorem for integrable billiards in two dimensions

    SciTech Connect

    Samajdar, Rhine; Jain, Sudhir R.

    2014-12-15

    Eigenfunctions of integrable planar billiards are studied — in particular, the number of nodal domains, ν of the eigenfunctions with Dirichlet boundary conditions are considered. The billiards for which the time-independent Schrödinger equation (Helmholtz equation) is separable admit trivial expressions for the number of domains. Here, we discover that for all separable and non-separable integrable billiards, ν satisfies certain difference equations. This has been possible because the eigenfunctions can be classified in families labelled by the same value of mmodkn, given a particular k, for a set of quantum numbers, m,n. Further, we observe that the patterns in a family are similar and the algebraic representation of the geometrical nodal patterns is found. Instances of this representation are explained in detail to understand the beauty of the patterns. This paper therefore presents a mathematical connection between integrable systems and difference equations. - Highlights: • We find that the number of nodal domains of eigenfunctions of integrable, planar billiards satisfy a class of difference equations. • The eigenfunctions labelled by quantum numbers (m,n) can be classified in terms of mmodkn. • A theorem is presented, realising algebraic representations of geometrical patterns exhibited by the domains. • This work presents a connection between integrable systems and difference equations.

  7. Generic task problem solvers in Soar

    NASA Technical Reports Server (NTRS)

    Johnson, Todd R.; Smith, Jack W., Jr.; Chandrasekaran, B.

    1989-01-01

    Two trends can be discerned in research in problem solving architectures in the last few years. On one hand, interest in task-specific architectures has grown, wherein types of problems of general utility are identified, and special architectures that support the development of problem solving systems for those types of problems are proposed. These architectures help in the acquisition and specification of knowledge by providing inference methods that are appropriate for the type of problem. However, knowledge based systems which use only one type of problem solving method are very brittle, and adding more types of methods requires a principled approach to integrating them in a flexible way. Contrasting with this trend is the proposal for a flexible, general architecture contained in the work on Soar. Soar has features which make it attractive for flexible use of all potentially relevant knowledge or methods. But as the theory Soar does not make commitments to specific types of problem solvers or provide guidance for their construction. It was investigated how task-specific architectures can be constructed in Soar to retain as many of the advantages as possible of both approaches. Examples were used from the Generic Task approach for building knowledge based systems. Though this approach was developed and applied for a number of problems, the ideas are applicable to other task-specific approaches as well.

  8. Elliptic Solvers for Adaptive Mesh Refinement Grids

    SciTech Connect

    Quinlan, D.J.; Dendy, J.E., Jr.; Shapira, Y.

    1999-06-03

    We are developing multigrid methods that will efficiently solve elliptic problems with anisotropic and discontinuous coefficients on adaptive grids. The final product will be a library that provides for the simplified solution of such problems. This library will directly benefit the efforts of other Laboratory groups. The focus of this work is research on serial and parallel elliptic algorithms and the inclusion of our black-box multigrid techniques into this new setting. The approach applies the Los Alamos object-oriented class libraries that greatly simplify the development of serial and parallel adaptive mesh refinement applications. In the final year of this LDRD, we focused on putting the software together; in particular we completed the final AMR++ library, we wrote tutorials and manuals, and we built example applications. We implemented the Fast Adaptive Composite Grid method as the principal elliptic solver. We presented results at the Overset Grid Conference and other more AMR specific conferences. We worked on optimization of serial and parallel performance and published several papers on the details of this work. Performance remains an important issue and is the subject of continuing research work.

  9. Optimization of hydraulic turbine diffuser

    NASA Astrophysics Data System (ADS)

    Moravec, Prokop; Hliník, Juraj; Rudolf, Pavel

    2016-03-01

    Hydraulic turbine diffuser recovers pressure energy from residual kinetic energy on turbine runner outlet. Efficiency of this process is especially important for high specific speed turbines, where almost 50% of available head is utilized within diffuser. Magnitude of the coefficient of pressure recovery can be significantly influenced by designing its proper shape. Present paper focuses on mathematical shape optimization method coupled with CFD. First method is based on direct search Nelder-Mead algorithm, while the second method employs adjoint solver and morphing. Results obtained with both methods are discussed and their advantages/disadvantages summarized.

  10. LSPRAY: Lagrangian Spray Solver for Applications With Parallel Computing and Unstructured Gas-Phase Flow Solvers

    NASA Technical Reports Server (NTRS)

    Raju, Manthena S.

    1998-01-01

    Sprays occur in a wide variety of industrial and power applications and in the processing of materials. A liquid spray is a phase flow with a gas as the continuous phase and a liquid as the dispersed phase (in the form of droplets or ligaments). Interactions between the two phases, which are coupled through exchanges of mass, momentum, and energy, can occur in different ways at different times and locations involving various thermal, mass, and fluid dynamic factors. An understanding of the flow, combustion, and thermal properties of a rapidly vaporizing spray requires careful modeling of the rate-controlling processes associated with the spray's turbulent transport, mixing, chemical kinetics, evaporation, and spreading rates, as well as other phenomena. In an attempt to advance the state-of-the-art in multidimensional numerical methods, we at the NASA Lewis Research Center extended our previous work on sprays to unstructured grids and parallel computing. LSPRAY, which was developed by M.S. Raju of Nyma, Inc., is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo probability density function (PDF) solver. The LSPRAY solver accommodates the use of an unstructured mesh with mixed triangular, quadrilateral, and/or tetrahedral elements in the gas-phase solvers. It is used specifically for fuel sprays within gas turbine combustors, but it has many other uses. The spray model used in LSPRAY provided favorable results when applied to stratified-charge rotary combustion (Wankel) engines and several other confined and unconfined spray flames. The source code will be available with the National Combustion Code (NCC) as a complete package.

  11. A Radiation Transfer Solver for Athena Using Short Characteristics

    NASA Astrophysics Data System (ADS)

    Davis, Shane W.; Stone, James M.; Jiang, Yan-Fei

    2012-03-01

    We describe the implementation of a module for the Athena magnetohydrodynamics (MHD) code that solves the time-independent, multi-frequency radiative transfer (RT) equation on multidimensional Cartesian simulation domains, including scattering and non-local thermodynamic equilibrium (LTE) effects. The module is based on well known and well tested algorithms developed for modeling stellar atmospheres, including the method of short characteristics to solve the RT equation, accelerated Lambda iteration to handle scattering and non-LTE effects, and parallelization via domain decomposition. The module serves several purposes: it can be used to generate spectra and images, to compute a variable Eddington tensor (VET) for full radiation MHD simulations, and to calculate the heating and cooling source terms in the MHD equations in flows where radiation pressure is small compared with gas pressure. For the latter case, the module is combined with the standard MHD integrators using operator splitting: we describe this approach in detail, including a new constraint on the time step for stability due to radiation diffusion modes. Implementation of the VET method for radiation pressure dominated flows is described in a companion paper. We present results from a suite of test problems for both the RT solver itself and for dynamical problems that include radiative heating and cooling. These tests demonstrate that the radiative transfer solution is accurate and confirm that the operator split method is stable, convergent, and efficient for problems of interest. We demonstrate there is no need to adopt ad hoc assumptions of questionable accuracy to solve RT problems in concert with MHD: the computational cost for our general-purpose module for simple (e.g., LTE gray) problems can be comparable to or less than a single time step of Athena's MHD integrators, and only few times more expensive than that for more general (non-LTE) problems.

  12. Performance of NASA Equation Solvers on Computational Mechanics Applications

    NASA Technical Reports Server (NTRS)

    Storaasli, Olaf O.

    1996-01-01

    This paper describes the performance of a new family of NASA-developed equation solvers used for large-scale (i.e. 551,705 equations) structural analysis. To minimize computer time and memory, the solvers are divided by application and matrix characteristics (sparse/dense, real/complex, symmetric/nonsymmetric, size: in-core/out of core) and exploit the hardware features of current and future computers. In this paper, the equation solvers, which are written in FORTRAN, and are therefore easily transportable, are shown to be faster than specialized computer library routines utilizing assembly code. Twenty NASA structural benchmark models with NASA solver timings reside on World Wide Web with a challenge to beat them.

  13. Two-dimensional time dependent Riemann solvers for neutron transport

    SciTech Connect

    Brunner, Thomas A. . E-mail: tabrunn@sandia.gov; Holloway, James Paul

    2005-11-20

    A two-dimensional Riemann solver is developed for the spherical harmonics approximation to the time dependent neutron transport equation. The eigenstructure of the resulting equations is explored, giving insight into both the spherical harmonics approximation and the Riemann solver. The classic Roe-type Riemann solver used here was developed for one-dimensional problems, but can be used in multidimensional problems by treating each face of a two-dimensional computation cell in a locally one-dimensional way. Several test problems are used to explore the capabilities of both the Riemann solver and the spherical harmonics approximation. The numerical solution for a simple line source problem is compared to the analytic solution to both the P{sub 1} equation and the full transport solution. A lattice problem is used to test the method on a more challenging problem.

  14. Parallel iterative solvers and preconditioners using approximate hierarchical methods

    SciTech Connect

    Grama, A.; Kumar, V.; Sameh, A.

    1996-12-31

    In this paper, we report results of the performance, convergence, and accuracy of a parallel GMRES solver for Boundary Element Methods. The solver uses a hierarchical approximate matrix-vector product based on a hybrid Barnes-Hut / Fast Multipole Method. We study the impact of various accuracy parameters on the convergence and show that with minimal loss in accuracy, our solver yields significant speedups. We demonstrate the excellent parallel efficiency and scalability of our solver. The combined speedups from approximation and parallelism represent an improvement of several orders in solution time. We also develop fast and paralellizable preconditioners for this problem. We report on the performance of an inner-outer scheme and a preconditioner based on truncated Green`s function. Experimental results on a 256 processor Cray T3D are presented.

  15. A survey of deterministic solvers for rarefied flows (Invited)

    NASA Astrophysics Data System (ADS)

    Mieussens, Luc

    2014-12-01

    Numerical simulations of rarefied gas flows are generally made with DSMC methods. Up to a recent period, deterministic numerical methods based on a discretization of the Boltzmann equation were restricted to simple problems (1D, linearized flows, or simple geometries, for instance). In the last decade, several deterministic solvers have been developed in different teams to tackle more complex problems like 2D and 3D flows. Some of them are based on the full Boltzmann equation. Solving this equation numerically is still very challenging, and 3D solvers are still restricted to monoatomic gases, even if recent works have proved it was possible to simulate simple flows for polyatomic gases. Other solvers are based on simpler BGK like models: they allow for much more intensive simulations on 3D flows for realistic geometries, but treating complex gases requires extended BGK models that are still under development. In this paper, we discuss the main features of these existing solvers, and we focus on their strengths and inefficiencies. We will also review some recent results that show how these solvers can be improved: - higher accuracy (higher order finite volume methods, discontinuous Galerkin approaches) - lower memory and CPU costs with special velocity discretization (adaptive grids, spectral methods) - multi-scale simulations by using hybrid and asymptotic preserving schemes - efficient implementation on high performance computers (parallel computing, hybrid parallelization) Finally, we propose some perspectives to make these solvers more efficient and more popular.

  16. Nodal Follicular Lymphomas: A Clinicopathological Study from a Tertiary Care Centre in South India.

    PubMed

    Supari, Divya; Ananthamurthy, Anuradha

    2016-06-01

    The aim of this study was to assess the distribution of nodal follicular lymphomas (FL) among various subtypes of non- Hodgkin lymphoma and to study their clinico-pathological features. Clinical details, histomorphology including grading & patterns and immunoprofile of 44 cases were studied. Majority of the cases were grade 1 (61 %) FL. BCL2 positivity was higher in low grade FLs (97 %). An associated diffuse large B cell lymphoma component was seen in 18 % and was present only in conjunction with grade 3 FL. Majority of our patients (76 %) had a high FLIPI score and belonged to the high risk group. Our study showed that the incidence of FLs is much lower in the Indian population (14.5 %) when compared to western studies and majority were of low grade. Although there was complete initial response to treatment, relapse was common and was much higher in low grade FLs with diffuse areas on histology, Ann Arbor stage III/IV and FLIPI scores of 3-5. PMID:27065580

  17. A robust multilevel simultaneous eigenvalue solver

    NASA Technical Reports Server (NTRS)

    Costiner, Sorin; Taasan, Shlomo

    1993-01-01

    Multilevel (ML) algorithms for eigenvalue problems are often faced with several types of difficulties such as: the mixing of approximated eigenvectors by the solution process, the approximation of incomplete clusters of eigenvectors, the poor representation of solution on coarse levels, and the existence of close or equal eigenvalues. Algorithms that do not treat appropriately these difficulties usually fail, or their performance degrades when facing them. These issues motivated the development of a robust adaptive ML algorithm which treats these difficulties, for the calculation of a few eigenvectors and their corresponding eigenvalues. The main techniques used in the new algorithm include: the adaptive completion and separation of the relevant clusters on different levels, the simultaneous treatment of solutions within each cluster, and the robustness tests which monitor the algorithm's efficiency and convergence. The eigenvectors' separation efficiency is based on a new ML projection technique generalizing the Rayleigh Ritz projection, combined with a technique, the backrotations. These separation techniques, when combined with an FMG formulation, in many cases lead to algorithms of O(qN) complexity, for q eigenvectors of size N on the finest level. Previously developed ML algorithms are less focused on the mentioned difficulties. Moreover, algorithms which employ fine level separation techniques are of O(q(sub 2)N) complexity and usually do not overcome all these difficulties. Computational examples are presented where Schrodinger type eigenvalue problems in 2-D and 3-D, having equal and closely clustered eigenvalues, are solved with the efficiency of the Poisson multigrid solver. A second order approximation is obtained in O(qN) work, where the total computational work is equivalent to only a few fine level relaxations per eigenvector.

  18. A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing

    NASA Technical Reports Server (NTRS)

    Takaki, Mitsuo; Cavalcanti, Diego; Gheyi, Rohit; Iyoda, Juliano; dAmorim, Marcelo; Prudencio, Ricardo

    2009-01-01

    The complexity of constraints is a major obstacle for constraint-based software verification. Automatic constraint solvers are fundamentally incomplete: input constraints often build on some undecidable theory or some theory the solver does not support. This paper proposes and evaluates several randomized solvers to address this issue. We compare the effectiveness of a symbolic solver (CVC3), a random solver, three hybrid solvers (i.e., mix of random and symbolic), and two heuristic search solvers. We evaluate the solvers on two benchmarks: one consisting of manually generated constraints and another generated with a concolic execution of 8 subjects. In addition to fully decidable constraints, the benchmarks include constraints with non-linear integer arithmetic, integer modulo and division, bitwise arithmetic, and floating-point arithmetic. As expected symbolic solving (in particular, CVC3) subsumes the other solvers for the concolic execution of subjects that only generate decidable constraints. For the remaining subjects the solvers are complementary.

  19. Response of millet and sorghum to a varying water supply around the primary and nodal roots

    PubMed Central

    Rostamza, M.; Richards, R. A.; Watt, M.

    2013-01-01

    Background and Aims Cereals have two root systems. The primary system originates from the embryo when the seed germinates and can support the plant until it produces grain. The nodal system can emerge from stem nodes throughout the plant's life; its value for yield is unclear and depends on the environment. The aim of this study was to test the role of nodal roots of sorghum and millet in plant growth in response to variation in soil moisture. Sorghum and millet were chosen as both are adapted to dry conditions. Methods Sorghum and millet were grown in a split-pot system that allowed the primary and nodal roots to be watered separately. Key Results When primary and nodal roots were watered (12 % soil water content; SWC), millet nodal roots were seven times longer than those of sorghum and six times longer than millet plants in dry treatments, mainly from an 8-fold increase in branch root length. When soil was allowed to dry in both compartments, millet nodal roots responded and grew 20 % longer branch roots than in the well-watered control. Sorghum nodal roots were unchanged. When only primary roots received water, nodal roots of both species emerged and elongated into extremely dry soil (0·6–1·5 % SWC), possibly with phloem-delivered water from the primary roots in the moist inner pot. Nodal roots were thick, short, branchless and vertical, indicating a tropism that was more pronounced in millet. Total nodal root length increased in both species when the dry soil was covered with plastic, suggesting that stubble retention or leaf mulching could facilitate nodal roots reaching deeper moist layers in dry climates. Greater nodal root length in millet than in sorghum was associated with increased shoot biomass, water uptake and water use efficiency (shoot mass per water). Millet had a more plastic response than sorghum to moisture around the nodal roots due to (1) faster growth and progression through ontogeny for earlier nodal root branch length and (2

  20. Quantitative analysis of numerical solvers for oscillatory biomolecular system models

    PubMed Central

    Quo, Chang F; Wang, May D

    2008-01-01

    Background This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, the ODEs can be stiff and ill-conditioned, resulting in non-unique, non-existing, or non-reproducible modeling solutions. Previous studies have not examined in depth how to best select numerical solvers for biomolecular system models, which makes it difficult to experimentally validate the modeling results. To address this problem, we have chosen one of the well-known stiff initial value problems with limit cycle behavior as a test-bed system model. Solving this model, we have illustrated that different answers may result from different numerical solvers. We use MATLAB numerical solvers because they are optimized and widely used by the modeling community. We have also conducted a systematic study of numerical solver performances by using qualitative and quantitative measures such as convergence, accuracy, and computational cost (i.e. in terms of function evaluation, partial derivative, LU decomposition, and "take-off" points). The results show that the modeling solutions can be drastically different using different numerical solvers. Thus, it is important to intelligently select numerical solvers when solving biomolecular system models. Results The classic Belousov-Zhabotinskii (BZ) reaction is described by the Oregonator model and is used as a case study. We report two guidelines in selecting optimal numerical solver(s) for stiff, complex oscillatory systems: (i) for problems with unknown parameters, ode45 is the optimal choice regardless of the relative error tolerance; (ii) for known stiff problems, both ode113 and ode15s are good choices under strict relative tolerance conditions. Conclusions For any given biomolecular model, by building a library of numerical solvers with quantitative performance assessment metric, we show that it is possible

  1. Elsevier Trophoblast Research Award lecture: The multifaceted role of Nodal signaling during mammalian reproduction.

    PubMed

    Park, C B; Dufort, D

    2011-03-01

    Nodal, a secreted signaling protein in the transforming growth factor-beta (TGF-β) superfamily, has established roles in vertebrate development. However, components of the Nodal signaling pathway are also expressed at the maternal-fetal interface and have been implicated in many processes of mammalian reproduction. Emerging evidence indicates that Nodal and its extracellular inhibitor Lefty are expressed in the uterus and complex interactions between the two proteins mediate menstruation, decidualization and embryo implantation. Furthermore, several studies have shown that Nodal from both fetal and maternal sources may regulate trophoblast cell fate and facilitate placentation as both embryonic and uterine-specific Nodal knockout mouse strains exhibit disrupted placenta morphology. Here we review the established and prospective roles of Nodal signaling in facilitating successful pregnancy, including recent evidence supporting a potential link to parturition and preterm birth.

  2. A Nodal Kinetics and Thermohydraulics Analysis (NOKTA) Code for Analyzing Rod-Ejection Accidents and Other Transients in Nuclear Power Reactor Cores

    SciTech Connect

    Kaya, Sadi; Yavuz, Hasbi

    2000-01-15

    For analyzing nuclear power reactor core transients, a three-dimensional nodal kinetics and thermohydraulics code, NOKTA, was developed. Nodal kinetics calculation is based on a one-group neutron diffusion approach. Thermal-hydraulics analysis is handled as in the COBRA-IV-I code. The NOKTA code was designed for analyzing especially large reactivity accidents, such as sudden rod ejection. It can also analyze intermediate transients, such as sharp power changes that may initiate xenon oscillations, and slow transients, such as boric acid density changes in the flow. The code dimensions are set at 125 subchannels and 30 axial levels. Calculation starts with a saturated xenon density, one-group neutronics parameters, and a flux profile, which is required as an input. Initially, k{sub eff} of each computation cell is set to unity.

  3. Approximate Schur complement preconditioning of the lowest order nodal discretizations

    SciTech Connect

    Moulton, J.D.; Ascher, U.M.; Morel, J.E.

    1996-12-31

    Particular classes of nodal methods and mixed hybrid finite element methods lead to equivalent, robust and accurate discretizations of 2nd order elliptic PDEs. However, widespread popularity of these discretizations has been hindered by the awkward linear systems which result. The present work exploits this awkwardness, which provides a natural partitioning of the linear system, by defining two optimal preconditioners based on approximate Schur complements. Central to the optimal performance of these preconditioners is their sparsity structure which is compatible with Dendy`s black box multigrid code.

  4. Topological insulating phases from two-dimensional nodal loop semimetals

    NASA Astrophysics Data System (ADS)

    Li, Linhu; Araújo, Miguel A. N.

    2016-10-01

    Starting from a minimal model for a two-dimensional nodal loop semimetal, we study the effect of chiral mass gap terms. The resulting Dirac loop anomalous Hall insulator's Chern number is the phase-winding number of the mass gap terms on the loop. We provide simple lattice models, analyze the topological phases, and generalize a previous index characterizing topological transitions. The responses of the Dirac loop anomalous Hall and quantum spin Hall insulators to a magnetic field's vector potential are also studied both in weak- and strong-field regimes, as well as the edge states in a ribbon geometry.

  5. Evaluation of the use of nodal methods for MTR neutronic analysis

    SciTech Connect

    Reitsma, F.; Mueller, E.Z.

    1997-08-01

    Although modern nodal methods are used extensively in the nuclear power industry, their use for research reactor analysis has been very limited. The suitability of nodal methods for material testing reactor analysis is investigated with the emphasis on the modelling of the core region (fuel assemblies). The nodal approach`s performance is compared with that of the traditional finite-difference fine mesh approach. The advantages of using nodal methods coupled with integrated cross section generation systems are highlighted, especially with respect to data preparation, simplicity of use and the possibility of performing a great variety of reactor calculations subject to strict time limitations such as are required for the RERTR program.

  6. Nodal line optimization and its application to violin top plate design

    NASA Astrophysics Data System (ADS)

    Yu, Yonggyun; Jang, In Gwun; Kim, In Kyum; Kwak, Byung Man

    2010-10-01

    In the literature, most problems of structural vibration have been formulated to adjust a specific natural frequency: for example, to maximize the first natural frequency. In musical instruments like a violin; however, mode shapes are equally important because they are related to sound quality in the way that natural frequencies are related to the octave. The shapes of nodal lines, which represent the natural mode shapes, are generally known to have a unique feature for good violins. Among the few studies on mode shape optimization, one typical study addresses the optimization of nodal point location for reducing vibration in a one-dimensional beam structure. However, nodal line optimization, which is required in violin plate design, has not yet been considered. In this paper, the central idea of controlling the shape of the nodal lines is proposed and then applied to violin top plate design. Finite element model for a violin top plate was constructed using shell elements. Then, optimization was performed to minimize the square sum of the displacement of selected nodes located along the target nodal lines by varying the thicknesses of the top plate. We conducted nodal line optimization for the second and the fifth modes together at the same time, and the results showed that the nodal lines obtained match well with the target nodal lines. The information on plate thickness distribution from nodal line optimization would be valuable for tailored trimming of a violin top plate for the given performances.

  7. Performance Models for the Spike Banded Linear System Solver

    DOE PAGES

    Manguoglu, Murat; Saied, Faisal; Sameh, Ahmed; Grama, Ananth

    2011-01-01

    With availability of large-scale parallel platforms comprised of tens-of-thousands of processors and beyond, there is significant impetus for the development of scalable parallel sparse linear system solvers and preconditioners. An integral part of this design process is the development of performance models capable of predicting performance and providing accurate cost models for the solvers and preconditioners. There has been some work in the past on characterizing performance of the iterative solvers themselves. In this paper, we investigate the problem of characterizing performance and scalability of banded preconditioners. Recent work has demonstrated the superior convergence properties and robustness of banded preconditioners,more » compared to state-of-the-art ILU family of preconditioners as well as algebraic multigrid preconditioners. Furthermore, when used in conjunction with efficient banded solvers, banded preconditioners are capable of significantly faster time-to-solution. Our banded solver, the Truncated Spike algorithm is specifically designed for parallel performance and tolerance to deep memory hierarchies. Its regular structure is also highly amenable to accurate performance characterization. Using these characteristics, we derive the following results in this paper: (i) we develop parallel formulations of the Truncated Spike solver, (ii) we develop a highly accurate pseudo-analytical parallel performance model for our solver, (iii) we show excellent predication capabilities of our model – based on which we argue the high scalability of our solver. Our pseudo-analytical performance model is based on analytical performance characterization of each phase of our solver. These analytical models are then parameterized using actual runtime information on target platforms. An important consequence of our performance models is that they reveal underlying performance bottlenecks in both serial and parallel formulations. All of our results are validated

  8. The novel high-performance 3-D MT inverse solver

    NASA Astrophysics Data System (ADS)

    Kruglyakov, Mikhail; Geraskin, Alexey; Kuvshinov, Alexey

    2016-04-01

    We present novel, robust, scalable, and fast 3-D magnetotelluric (MT) inverse solver. The solver is written in multi-language paradigm to make it as efficient, readable and maintainable as possible. Separation of concerns and single responsibility concepts go through implementation of the solver. As a forward modelling engine a modern scalable solver extrEMe, based on contracting integral equation approach, is used. Iterative gradient-type (quasi-Newton) optimization scheme is invoked to search for (regularized) inverse problem solution, and adjoint source approach is used to calculate efficiently the gradient of the misfit. The inverse solver is able to deal with highly detailed and contrasting models, allows for working (separately or jointly) with any type of MT responses, and supports massive parallelization. Moreover, different parallelization strategies implemented in the code allow optimal usage of available computational resources for a given problem statement. To parameterize an inverse domain the so-called mask parameterization is implemented, which means that one can merge any subset of forward modelling cells in order to account for (usually) irregular distribution of observation sites. We report results of 3-D numerical experiments aimed at analysing the robustness, performance and scalability of the code. In particular, our computational experiments carried out at different platforms ranging from modern laptops to HPC Piz Daint (6th supercomputer in the world) demonstrate practically linear scalability of the code up to thousands of nodes.

  9. Adaptive kinetic-fluid solvers for heterogeneous computing architectures

    NASA Astrophysics Data System (ADS)

    Zabelok, Sergey; Arslanbekov, Robert; Kolobov, Vladimir

    2015-12-01

    We show feasibility and benefits of porting an adaptive multi-scale kinetic-fluid code to CPU-GPU systems. Challenges are due to the irregular data access for adaptive Cartesian mesh, vast difference of computational cost between kinetic and fluid cells, and desire to evenly load all CPUs and GPUs during grid adaptation and algorithm refinement. Our Unified Flow Solver (UFS) combines Adaptive Mesh Refinement (AMR) with automatic cell-by-cell selection of kinetic or fluid solvers based on continuum breakdown criteria. Using GPUs enables hybrid simulations of mixed rarefied-continuum flows with a million of Boltzmann cells each having a 24 × 24 × 24 velocity mesh. We describe the implementation of CUDA kernels for three modules in UFS: the direct Boltzmann solver using the discrete velocity method (DVM), the Direct Simulation Monte Carlo (DSMC) solver, and a mesoscopic solver based on the Lattice Boltzmann Method (LBM), all using adaptive Cartesian mesh. Double digit speedups on single GPU and good scaling for multi-GPUs have been demonstrated.

  10. Descents and nodal load in scale-free networks

    NASA Astrophysics Data System (ADS)

    Bareinboim, Elias; Barbosa, Valmir C.

    2008-04-01

    The load of a node in a network is the total traffic going through it when every node pair sustains a uniform bidirectional traffic between them on shortest paths. We express nodal load in terms of the more elementary notion of a node’s descents in breadth-first-search [(BFS) or shortest-path] trees and study both the descent and nodal-load distributions in the case of scale-free networks. Our treatment is both semianalytical (combining a generating-function formalism with simulation-derived BFS branching probabilities) and computational for the descent distribution; it is exclusively computational in the case of the load distribution. Our main result is that the load distribution, even though it can be disguised as a power law through subtle (but inappropriate) binning of the raw data, is in fact a succession of sharply delineated probability peaks, each of which can be clearly interpreted as a function of the underlying BFS descents. This find is in stark contrast with previously held belief, based on which a power law of exponent -2.2 was conjectured to be valid regardless of the exponent of the power-law distribution of node degrees.

  11. Regional non-nodal metastases of cutaneous melanoma.

    PubMed

    Cascinelli, N; Bufalino, R; Marolda, R; Belli, F; Nava, M; Galluzzo, D; Santinami, M; Levene, A

    1986-06-01

    The authors studied the prognosis of patients with so called local recurrences, satellites and in-transit metastases from cutaneous melanoma on the basis of 291 patients. These are the 19.3% of the 1503 patients with stage I and II melanoma originally submitted to surgical treatment at the National Cancer Institute of Milano (Italy). The majority of patients were males (M/F = 0.7): 102 had local recurrence, 99 in-transit metastases, 24 satellites and 66 both local and in-transit metastases. Regional non-nodal metastases were not related with the site of origin, and inadequate treatment of primary. These metastases were more frequently observed in patients who were submitted to regional node dissection no matter whether in discontinuity or in continuity with primary tumor. The frequency of regional non-nodal metastases was found to increase with increasing thickness of primary melanoma or, in stage II patients, with the number of involved nodes. Local and in-transit metastases were related with prognostic criteria in the same way. The overall survival was very close between in-transit and local metastases. Similar survival rates were observed comparing regional non-nodes and disseminated cutaneous and subcutaneous metastases. The authors conclude that the distinction between local recurrences, satellites and in-transit metastases is artificial and that these metastatic events are not prognostically dissimilar from metastases in distant skin areas.

  12. Symmetry Breaking in a Model for Nodal Cilia

    NASA Astrophysics Data System (ADS)

    Brokaw, Charles J.

    2005-03-01

    Nodal cilia are very short cilia found in the embryonic node on the ventral surface of early mammalian embryos. They create a right to left fluid flow that is responsible for determining the normal asymmetry of the internal organs of the mammalian body. To do this, the distal end of the cilium must circle in a counterclockwise sense. Computer simulations with 3-dimensional models of flagella allow examination of 3-dimensional movements such as those of nodal cilia. 3-dimensional circling motions of short cilia can be achieved with velocity controlled models, in which dynein activity is regulated by sliding velocity. If dyneins on one outer doublet are controlled by the sliding velocity experienced by that doublet, the system is symmetric, and the 3-dimensional models can show either clockwise or counterclockwise circling. My computer simulations have examined two possible symmetry breaking mechanisms: 1) dyneins on doublet N are regulated by a mixture of the sliding velocities experienced by doublets N and N+1 (numbered in a clockwise direction, looking from the base). or 2) symmetry is broken by an off-axis force that produces a right-handed twist of the axoneme, consistent with observations that some dyneins can rotate their substrate microtubules in a clockwise direction.

  13. Extrapolation of critical Rayleigh values using static nodal integral methods

    SciTech Connect

    Wilson, G.L.; Rydin, R.A.

    1988-01-01

    The Benard problem is the study of the convective motion of a fluid in a rectangular cavity that is uniformly heated form below. Flow bifurcation in the cavity is a function of the Rayleigh number (Ra). The time-dependent nodal integral method (TDNIM) has been reported previously; its development leads to a set of 11 equations per node. The static nodal integral method (SNIM) was derived from the TDNIM by forcing the dependent variable at adjacent time steps (one of the velocity components or temperature) to take on the node integral average value. The paper summarizes the SNIM calculation of Ra for mesh sizes ranging from 4 x 4 to 24 x 24. The numerical calculation of Ra is within plus or minus one-half unit. The relative errors are calculated based on the obtained extrapolated value of Ra{sub best}* = 2584. The paper also summarizes three-point schemes used with increasingly finer mesh combinations. This approach avoids the contamination of the results with a coarse mesh; however, the calculation on n is very sensitive to small changes in the numerical values obtained for Ra*. In this approach, the extrapolated values quickly converge to Ra*{sub e} between 2583 and 2584 with n {approx}2.0 as desired, and give a best value of Ra*{sub best} = 2584.

  14. The effects of nodality on the formation of equivalence classes.

    PubMed

    Fields, L; Adams, B J; Verhave, T; Newman, S

    1990-05-01

    A four-member equivalence class (A----B----C----D) can be formed by training AB, BC, and CD. The nodal stimuli, B and C, mediate all of the derivative (transitive and equivalence) relations in the class. The derivative relations AC, CA, BD, and DB are separated by one node, whereas AD and DA are separated by two nodes. How do the number of nodes that separate the stimuli in a derivative relation influence the induction of stimulus control exerted by that relation? Seven college students learned two four-member classes made up of nonsense syllables. After training, all derivative relations were presented repeatedly without informative feedback. Stimulus control exerted by each derivative relation was assessed concurrently. For the 7 subjects, control exerted by the derivative relations increased gradually with repeated presentations. With 6 of the 7 subjects, the one-node relations exerted more control than the two-node relations during the process. However, the disparity between the one- and two-node relations decreased with repeated presentations. Eventually, all derivative relations exerted complete control. The control exerted by derivative relations during induction was inversely related to the number of nodes separating the terms in the derivative relations. These results demonstrate that nodal distance is a determinant of the relatedness of stimuli in equivalence classes. The findings are discussed in terms of remote association, semantic memory networks, and the study of transitive inference.

  15. A multiple right hand side iterative solver for history matching

    SciTech Connect

    Killough, J.E.; Sharma, Y.; Dupuy, A.; Bissell, R.; Wallis, J.

    1995-12-31

    History matching of oil and gas reservoirs can be accelerated by directly calculating the gradients of observed quantities (e.g., well pressure) with respect to the adjustable reserve parameters (e.g., permeability). This leads to a set of linear equations which add a significant overhead to the full simulation run without gradients. Direct Gauss elimination solvers can be used to address this problem by performing the factorization of the matrix only once and then reusing the factor matrix for the solution of the multiple right hand sides. This is a limited technique, however. Experience has shown that problems with greater than few thousand cells may not be practical for direct solvers because of computation time and memory limitations. This paper discusses the implementation of a multiple right hand side iterative linear equation solver (MRHS) for a system of adjoint equations to significantly enhance the performance of a gradient simulator.

  16. Gpu Implementation of a Viscous Flow Solver on Unstructured Grids

    NASA Astrophysics Data System (ADS)

    Xu, Tianhao; Chen, Long

    2016-06-01

    Graphics processing units have gained popularities in scientific computing over past several years due to their outstanding parallel computing capability. Computational fluid dynamics applications involve large amounts of calculations, therefore a latest GPU card is preferable of which the peak computing performance and memory bandwidth are much better than a contemporary high-end CPU. We herein focus on the detailed implementation of our GPU targeting Reynolds-averaged Navier-Stokes equations solver based on finite-volume method. The solver employs a vertex-centered scheme on unstructured grids for the sake of being capable of handling complex topologies. Multiple optimizations are carried out to improve the memory accessing performance and kernel utilization. Both steady and unsteady flow simulation cases are carried out using explicit Runge-Kutta scheme. The solver with GPU acceleration in this paper is demonstrated to have competitive advantages over the CPU targeting one.

  17. Two Solvers for Tractable Temporal Constraints with Preferences

    NASA Technical Reports Server (NTRS)

    Rossi, F.; Khatib,L.; Morris, P.; Morris, R.; Clancy, Daniel (Technical Monitor)

    2002-01-01

    A number of reasoning problems involving the manipulation of temporal information can naturally be viewed as implicitly inducing an ordering of potential local decisions involving time on the basis of preferences. Soft temporal constraints problems allow to describe in a natural way scenarios where events happen over time and preferences are associated to event distances and durations. In general, solving soft temporal problems require exponential time in the worst case, but there are interesting subclasses of problems which are polynomially solvable. We describe two solvers based on two different approaches for solving the same tractable subclass. For each solver we present the theoretical results it stands on, a description of the algorithm and some experimental results. The random generator used to build the problems on which tests are performed is also described. Finally, we compare the two solvers highlighting the tradeoff between performance and representational power.

  18. Distal end of the atrioventricular nodal artery predicts the risk of atrioventricular block during slow pathway catheter ablation of atrioventricular nodal re-entrant tachycardia

    PubMed Central

    Lin, J; Huang, S; Lai, L; Lin, L; Chen, J; Tseng, Y; Lien, W

    2000-01-01

    OBJECTIVE—To search for a reliable anatomical landmark within Koch's triangle to predict the risk of atrioventricular (AV) block during radiofrequency slow pathway catheter ablation of AV nodal re-entrant tachycardia (AVNRT).
PATIENTS AND METHODS—To test the hypothesis that the distal end of the AV nodal artery represents the anatomical location of the AV node, and thus could be a useful landmark for predicting the risk of AV block, 128 consecutive patients with AVNRT receiving slow pathway catheter ablation were prospectively studied in two phases. In phase I (77 patients), angiographic demonstration of the AV nodal artery and its ending was performed at the end of the ablation procedure, whereas in the subsequent phase II study (51 patients), the angiography was performed immediately before catheter ablation to assess the value of identifying this new landmark in reducing the risk of AV block. Multiple electrophysiologic and anatomical parameters were analysed. The former included the atrial activation sequence between the His bundle recording site (HBE) and the coronary sinus orifice or the catheter ablation site, either during AVNRT or during sinus rhythm. The latter included the spatial distances between the distal end of the AV nodal artery and the HBE and the final catheter ablation site, and the distance between the HBE and the tricuspid border at the coronary sinus orifice floor.
RESULTS—In phase I, nine of the 77 patients had complications of transient (seven patients) or permanent (two patients) complete AV block during stepwise, anatomy guided slow pathway catheter ablation. These nine patients had a wider distance between the HBE and the distal end of the AV nodal artery, and a closer approximation of the catheter ablation site to the distal end of the AV nodal artery, which independently predicted the risk of AV block. In contrast, none of the available electrophysiologic parameters were shown to be reliable. When the distance between

  19. LAPACKrc: Fast linear algebra kernels/solvers for FPGA accelerators

    NASA Astrophysics Data System (ADS)

    Gonzalez, Juan; Núñez, Rafael C.

    2009-07-01

    We present LAPACKrc, a family of FPGA-based linear algebra solvers able to achieve more than 100x speedup per commodity processor on certain problems. LAPACKrc subsumes some of the LAPACK and ScaLAPACK functionalities, and it also incorporates sparse direct and iterative matrix solvers. Current LAPACKrc prototypes demonstrate between 40x-150x speedup compared against top-of-the-line hardware/software systems. A technology roadmap is in place to validate current performance of LAPACKrc in HPC applications, and to increase the computational throughput by factors of hundreds within the next few years.

  20. Numerical System Solver Developed for the National Cycle Program

    NASA Technical Reports Server (NTRS)

    Binder, Michael P.

    1999-01-01

    As part of the National Cycle Program (NCP), a powerful new numerical solver has been developed to support the simulation of aeropropulsion systems. This software uses a hierarchical object-oriented design. It can provide steady-state and time-dependent solutions to nonlinear and even discontinuous problems typically encountered when aircraft and spacecraft propulsion systems are simulated. It also can handle constrained solutions, in which one or more factors may limit the behavior of the engine system. Timedependent simulation capabilities include adaptive time-stepping and synchronization with digital control elements. The NCP solver is playing an important role in making the NCP a flexible, powerful, and reliable simulation package.

  1. Profile solver in C for finite element equations

    NASA Astrophysics Data System (ADS)

    Hededal, O.; Krenk, S.

    1994-08-01

    This paper presents an efficient, pointer based profile solver with standard matrix indexing. Constrained equations Ax = b where x contains known and unknown values are solved and the full vectors x and b are obtained. Pseudo-code algorithms are formulated for a row oriented form of the LDL(sup T) factorization and implemented directly as a C code. The solver is implemented in C because of the close relation between two-dimensional arrays and pointers which makes it possible to write a clear and efficient code.

  2. Beam Elements with Trapezoidal Cross Section Deformation Modes Based on the Absolute Nodal Coordinate Formulation

    NASA Astrophysics Data System (ADS)

    Matikainen, Marko K.; Dmitrochenko, Oleg; Mikkola, Aki

    2010-09-01

    In this study, higher order beam elements are developed based on the absolute nodal coordinate formulation. The absolute nodal coordinate formulation is a finite element procedure that was recently proposed for flexible multibody applications. Many different elements based on the absolute nodal coordinate formulation are introduced, but still the beam elements are not able to describe the trapezoidal cross section mode. This leads to the locking phenomena, and therefore, the beam elements based on the absolute nodal coordinate formulation with three dimensional elasticity converge to an inexact solution. In order to avoid the locking phenomena, the trapezoidal cross section deformation mode is included in the beam elements based on the absolute nodal coordinate with additional degrees of freedom. The proper description for the trapezoidal cross section deformation is important for the continuum beam elements based on three-dimensional elasticity where the material model is often based on general continuum mechanics.

  3. Embryonic and tumorigenic pathways converge via Nodal signaling: role in melanoma aggressiveness.

    PubMed

    Topczewska, Jolanta M; Postovit, Lynne-Marie; Margaryan, Naira V; Sam, Anthony; Hess, Angela R; Wheaton, William W; Nickoloff, Brian J; Topczewski, Jacek; Hendrix, Mary J C

    2006-08-01

    Bidirectional cellular communication is integral to both cancer progression and embryological development. In addition, aggressive tumor cells are phenotypically plastic, sharing many properties with embryonic cells. Owing to the similarities between these two types of cells, the developing zebrafish can be used as a biosensor for tumor-derived signals. Using this system, we show that aggressive melanoma cells secrete Nodal (a potent embryonic morphogen) and consequently can induce ectopic formation of the embryonic axis. We further show that Nodal is present in human metastatic tumors, but not in normal skin, and thus may be involved in melanoma pathogenesis. Inhibition of Nodal signaling reduces melanoma cell invasiveness, colony formation and tumorigenicity. Nodal inhibition also promotes the reversion of melanoma cells toward a melanocytic phenotype. These data suggest that Nodal signaling has a key role in melanoma cell plasticity and tumorigenicity, thereby providing a previously unknown molecular target for regulating tumor progression. PMID:16892036

  4. Diffusion in Colocation Contact Networks: The Impact of Nodal Spatiotemporal Dynamics.

    PubMed

    Thomas, Bryce; Jurdak, Raja; Zhao, Kun; Atkinson, Ian

    2016-01-01

    Temporal contact networks are studied to understand dynamic spreading phenomena such as communicable diseases or information dissemination. To establish how spatiotemporal dynamics of nodes impact spreading potential in colocation contact networks, we propose "inducement-shuffling" null models which break one or more correlations between times, locations and nodes. By reconfiguring the time and/or location of each node's presence in the network, these models induce alternative sets of colocation events giving rise to contact networks with varying spreading potential. This enables second-order causal reasoning about how correlations in nodes' spatiotemporal preferences not only lead to a given contact network but ultimately influence the network's spreading potential. We find the correlation between nodes and times to be the greatest impediment to spreading, while the correlation between times and locations slightly catalyzes spreading. Under each of the presented null models we measure both the number of contacts and infection prevalence as a function of time, with the surprising finding that the two have no direct causality. PMID:27501240

  5. Diffusion in Colocation Contact Networks: The Impact of Nodal Spatiotemporal Dynamics

    PubMed Central

    Thomas, Bryce; Jurdak, Raja; Zhao, Kun; Atkinson, Ian

    2016-01-01

    Temporal contact networks are studied to understand dynamic spreading phenomena such as communicable diseases or information dissemination. To establish how spatiotemporal dynamics of nodes impact spreading potential in colocation contact networks, we propose “inducement-shuffling” null models which break one or more correlations between times, locations and nodes. By reconfiguring the time and/or location of each node’s presence in the network, these models induce alternative sets of colocation events giving rise to contact networks with varying spreading potential. This enables second-order causal reasoning about how correlations in nodes’ spatiotemporal preferences not only lead to a given contact network but ultimately influence the network’s spreading potential. We find the correlation between nodes and times to be the greatest impediment to spreading, while the correlation between times and locations slightly catalyzes spreading. Under each of the presented null models we measure both the number of contacts and infection prevalence as a function of time, with the surprising finding that the two have no direct causality. PMID:27501240

  6. Coupling the beam tracing code TORBEAM and the Fokker-Planck solver RELAX for fast electrons

    NASA Astrophysics Data System (ADS)

    Maj, O.; Poli, E.; Westerhof, E.

    2012-12-01

    In this paper the interface between the beam tracing code TORBEAM [Poli, Peeters and Pereverzev, Comp. Phys. Comm. 136, 90 (2001)] and the quasi-linear Fokker-Planck solver RELAX [Westerhof, Peeters and Schippers, Rijnhuizen Report No. RR 92-211 CA, 1992] is presented together with preliminary testing results for electron cyclotron waves in ITER plasmas and their effects on the electron distribution function. The resulting numerical package allows us to account for diffraction effects in the construction of the quasi-linear wave-particle diffusion operator. The coupling of the paraxial-WKB code TORBEAM to the ray-based code RELAX requires a reinterpretation of the paraxial wave field in terms of extended rays, which are addressed in details.

  7. Nodal promotes invasive phenotypes via a Mitogen Activated Protein Kinase-dependent pathway

    PubMed Central

    Quail, DF; Zhang, G; Findlay, SD; Hess, DA; Postovit, LM

    2016-01-01

    The progression of cancer from localized to invasive disease is requisite for metastasis, and is often characterized by epithelial-to-mesenchymal transition (EMT) and alterations in cellular adhesion and migration. Studies have shown that this transition is associated with an up-regulation of embryonic stem cell-associated genes, resulting in a dedifferentiated phenotype and poor patient prognosis. Nodal is an embryonic factor that plays a critical role in promoting early invasive events during development. Nodal is silenced as stem cells differentiate; however, it re-emerges in adult life during placentation and mammary gland development, and is aberrantly expressed in many cancers. Here, we show that Nodal over-expression, in poorly-invasive breast cancer and choriocarcinoma cells, causes increased invasion and migration in vitro. Furthermore, we show that Nodal over-expression in these epithelial cancer types induces an EMT-like event concomitant with the internalization of E-Cadherin. This ability of Nodal to promote cellular invasion and EMT-like phenomena is dependent upon the phosphorylation of ERK1/2. Since Nodal normally signals through SMADs, these findings lend insight into an alternative pathway that is hijacked by this protein in cancer. To evaluate the clinical implications of our results, we show that Nodal inhibition reduces liver tumor burden in a model of spontaneous breast cancer metastasis in vivo, and that Nodal loss-of-function in aggressive breast cancer lines results in a decrease in invasive phenotypes. Our results demonstrate that Nodal is involved in promoting invasion in multiple cellular contexts, and that Nodal inhibition may be useful as a therapeutic target for patients with progressive disease. PMID:23334323

  8. Magnetic response in three-dimensional nodal semimetals

    NASA Astrophysics Data System (ADS)

    Koshino, Mikito; Hizbullah, Intan Fatimah

    We study the magnetic response in various three-dimensional gapless systems, including Dirac and Weyl semimetals and a line-node semimetal. We show that the susceptibility is decomposed into the orbital term, the spin term and also the spin-orbit cross term which is caused by the spin-orbit interaction. We show that the orbital susceptibility logarithmically diverges at the band touching energy in the point-node case, while it exhibits a stronger delta-function singularity in the line node case. The spin-orbit cross term is shown to be paramagnetic in the electron side while diamagnetic in the hole side, in contrast with other two terms which are both even functions in Fermi energy. The spin-orbit cross term in the nodal semimetal is found to be directly related to the chiral surface current induced by the topological surface modes.

  9. Magnetic susceptibility in three-dimensional nodal semimetals

    NASA Astrophysics Data System (ADS)

    Koshino, Mikito; Hizbullah, Intan Fatimah

    2016-01-01

    We study the magnetic susceptibility in various three-dimensional gapless systems, including Dirac and Weyl semimetals, and a line-node semimetal. The susceptibility is decomposed into the orbital term, the spin term and also the spin-orbit cross term, which is caused by the spin-orbit interaction. We show that the orbital susceptibility logarithmically diverges at the band touching energy in the point-node case, while it exhibits a stronger δ -function singularity in the line node case. The spin-orbit cross term is shown to be paramagnetic in the electron side while diamagnetic in the hole side, in contrast with other two terms which are both even functions in Fermi energy. The spin-orbit cross term in the nodal semimetal is found to be directly related to the chiral surface current induced by the topological surface modes.

  10. Typical nodal calcifications in the maxillofacial region: a case report

    PubMed Central

    Wu, Guomin; Sun, Xiumei; Ni, Shilei; Zhang, Zhimin

    2014-01-01

    Multiple nodal calcifications in the maxillofacial region are very rare. This case report described a 49-year-old female patient diagnosed with calcified lymph nodes due to chronic inflammation of the lymphatic nodes, including the parotid lymphatic nodes, the posterior auricular lymphatic nodes and submandibular lymphatic nodes in the right maxillofacial region. In clinical practice, we conducted ultrasonography, three-dimensional reconstruction of CT and sialography make a preliminary diagnosis. Then we took surgery, while removing the calcified blocks within the lymphatic node and cleaning the wound cavity. After surgery, we used anti-inflammatory therapy for one week. Six months follow-up indicated no evidence of other calcified lymph nodes infection. PMID:25356188

  11. Contemporary Management of Recurrent Nodal Disease in Differentiated Thyroid Carcinoma.

    PubMed

    Na'ara, Shorook; Amit, Moran; Fridman, Eran; Gil, Ziv

    2016-01-28

    Differentiated thyroid carcinoma (DTC) comprises over 90% of thyroid tumors and includes papillary and follicular carcinomas. Patients with DTC have an excellent prognosis, with a 10-year survival rate of over 90%. However, the risk of recurrent tumor ranges between 5% and 30% within 10 years of the initial diagnosis. Cervical lymph node disease accounts for the majority of recurrences and in most cases is detected during follow-up by ultrasound or elevated levels of serum thyroglobulin. Recurrent disease is accompanied by increased morbidity. The mainstay of treatment of nodal recurrence is surgical management. We provide an overview of the literature addressing surgical management of recurrent or persistent lymph node disease in patients with DTC.

  12. Coexistence of Weyl fermion and massless triply degenerate nodal points

    NASA Astrophysics Data System (ADS)

    Weng, Hongming; Fang, Chen; Fang, Zhong; Dai, Xi

    2016-10-01

    By using first-principles calculations, we propose that WC-type ZrTe is a new type of topological semimetal (TSM). It has six pairs of chiral Weyl nodes in its first Brillouin zone, but it is distinguished from other existing TSMs by having an additional two paris of massless fermions with triply degenerate nodal points as proposed in the isostructural compounds TaN and NbN. The mirror symmetry, threefold rotational symmetry, and time-reversal symmetry require all of the Weyl nodes to have the same velocity vectors and locate at the same energy level. The Fermi arcs on different surfaces are shown, which may be measured by future experiments. It demonstrates that the "material universe" can support more intriguing particles simultaneously.

  13. Computations of two-fluid models based on a simple and robust hybrid primitive variable Riemann solver with AUSMD

    NASA Astrophysics Data System (ADS)

    Niu, Yang-Yao

    2016-03-01

    This paper is to continue our previous work in 2008 on solving a two-fluid model for compressible liquid-gas flows. We proposed a pressure-velocity based diffusion term original derived from AUSMD scheme of Wada and Liou in 1997 to enhance its robustness. The proposed AUSMD schemes have been applied to gas and liquid fluids universally to capture fluid discontinuities, such as the fluid interfaces and shock waves, accurately for the Ransom's faucet problem, air-water shock tube problems and 2D shock-water liquid interaction problems. However, the proposed scheme failed at computing liquid-gas interfaces in problems under large ratios of pressure, density and volume of fraction. The numerical instability has been remedied by Chang and Liou in 2007 using the exact Riemann solver to enhance the accuracy and stability of numerical flux across the liquid-gas interface. Here, instead of the exact Riemann solver, we propose a simple AUSMD type primitive variable Riemann solver (PVRS) which can successfully solve 1D stiffened water-air shock tube and 2D shock-gas interaction problems under large ratios of pressure, density and volume of fraction without the expensive cost of tedious computer time. In addition, the proposed approach is shown to deliver a good resolution of the shock-front, rarefaction and cavitation inside the evolution of high-speed droplet impact on the wall.

  14. ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm.

    PubMed

    Ellis, Pamela S; Burbridge, Sarah; Soubes, Sandrine; Ohyama, Kyoji; Ben-Haim, Nadav; Chen, Canhe; Dale, Kim; Shen, Michael M; Constam, Daniel; Placzek, Marysia

    2015-11-15

    The secreted glycoprotein sonic hedgehog (Shh) is expressed in the prechordal mesoderm, where it plays a crucial role in induction and patterning of the ventral forebrain. Currently little is known about how Shh is regulated in prechordal tissue. Here we show that in the embryonic chick, Shh is expressed transiently in prechordal mesoderm, and is governed by unprocessed Nodal. Exposure of prechordal mesoderm microcultures to Nodal-conditioned medium, the Nodal inhibitor CerS, or to an ALK4/5/7 inhibitor reveals that Nodal is required to maintain both Shh and Gsc expression, but whereas Gsc is largely maintained through canonical signalling, Nodal signals through a non-canonical route to maintain Shh. Further, Shh expression can be maintained by a recombinant Nodal cleavage mutant, proNodal, but not by purified mature Nodal. A number of lines of evidence suggest that proNodal acts via FGFR3. ProNodal and FGFR3 co-immunoprecipitate and proNodal increases FGFR3 tyrosine phosphorylation. In microcultures, soluble FGFR3 abolishes Shh without affecting Gsc expression. Further, prechordal mesoderm cells in which Fgfr3 expression is reduced by Fgfr3 siRNA fail to bind to proNodal. Finally, targeted electroporation of Fgfr3 siRNA to prechordal mesoderm in vivo results in premature Shh downregulation without affecting Gsc. We report an inverse correlation between proNodal-FGFR3 signalling and pSmad1/5/8, and show that proNodal-FGFR3 signalling antagonises BMP-mediated pSmad1/5/8 signalling, which is poised to downregulate Shh. Our studies suggest that proNodal/FGFR3 signalling governs Shh duration by repressing canonical BMP signalling, and that local BMPs rapidly silence Shh once endogenous Nodal-FGFR3 signalling is downregulated.

  15. ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm

    PubMed Central

    Ellis, Pamela S.; Burbridge, Sarah; Soubes, Sandrine; Ohyama, Kyoji; Ben-Haim, Nadav; Chen, Canhe; Dale, Kim; Shen, Michael M.; Constam, Daniel; Placzek, Marysia

    2015-01-01

    The secreted glycoprotein sonic hedgehog (Shh) is expressed in the prechordal mesoderm, where it plays a crucial role in induction and patterning of the ventral forebrain. Currently little is known about how Shh is regulated in prechordal tissue. Here we show that in the embryonic chick, Shh is expressed transiently in prechordal mesoderm, and is governed by unprocessed Nodal. Exposure of prechordal mesoderm microcultures to Nodal-conditioned medium, the Nodal inhibitor CerS, or to an ALK4/5/7 inhibitor reveals that Nodal is required to maintain both Shh and Gsc expression, but whereas Gsc is largely maintained through canonical signalling, Nodal signals through a non-canonical route to maintain Shh. Further, Shh expression can be maintained by a recombinant Nodal cleavage mutant, proNodal, but not by purified mature Nodal. A number of lines of evidence suggest that proNodal acts via FGFR3. ProNodal and FGFR3 co-immunoprecipitate and proNodal increases FGFR3 tyrosine phosphorylation. In microcultures, soluble FGFR3 abolishes Shh without affecting Gsc expression. Further, prechordal mesoderm cells in which Fgfr3 expression is reduced by Fgfr3 siRNA fail to bind to proNodal. Finally, targeted electroporation of Fgfr3 siRNA to prechordal mesoderm in vivo results in premature Shh downregulation without affecting Gsc. We report an inverse correlation between proNodal-FGFR3 signalling and pSmad1/5/8, and show that proNodal-FGFR3 signalling antagonises BMP-mediated pSmad1/5/8 signalling, which is poised to downregulate Shh. Our studies suggest that proNodal/FGFR3 signalling governs Shh duration by repressing canonical BMP signalling, and that local BMPs rapidly silence Shh once endogenous Nodal-FGFR3 signalling is downregulated. PMID:26417042

  16. Navier-Stokes Solvers and Generalizations for Reacting Flow Problems

    SciTech Connect

    Elman, Howard C

    2013-01-27

    This is an overview of our accomplishments during the final term of this grant (1 September 2008 -- 30 June 2012). These fall mainly into three categories: fast algorithms for linear eigenvalue problems; solution algorithms and modeling methods for partial differential equations with uncertain coefficients; and preconditioning methods and solvers for models of computational fluid dynamics (CFD).

  17. Intellectual Abilities That Discriminate Good and Poor Problem Solvers.

    ERIC Educational Resources Information Center

    Meyer, Ruth Ann

    1981-01-01

    This study compared good and poor fourth-grade problem solvers on a battery of 19 "reference" tests for verbal, induction, numerical, word fluency, memory, perceptual speed, and simple visualization abilities. Results suggest verbal, numerical, and especially induction abilities are important to successful mathematical problem solving. (MP)

  18. Coordinate Projection-based Solver for ODE with Invariants

    2008-04-08

    CPODES is a general purpose (serial and parallel) solver for systems of ordinary differential equation (ODE) with invariants. It implements a coordinate projection approach using different types of projection (orthogonal or oblique) and one of several methods for the decompositon of the Jacobian of the invariant equations.

  19. An Extension of the Athena++ Code Framework for GRMHD Based on Advanced Riemann Solvers and Staggered-mesh Constrained Transport

    NASA Astrophysics Data System (ADS)

    White, Christopher J.; Stone, James M.; Gammie, Charles F.

    2016-08-01

    We present a new general relativistic magnetohydrodynamics (GRMHD) code integrated into the Athena++ framework. Improving upon the techniques used in most GRMHD codes, ours allows the use of advanced, less diffusive Riemann solvers, in particular HLLC and HLLD. We also employ a staggered-mesh constrained transport algorithm suited for curvilinear coordinate systems in order to maintain the divergence-free constraint of the magnetic field. Our code is designed to work with arbitrary stationary spacetimes in one, two, or three dimensions, and we demonstrate its reliability through a number of tests. We also report on its promising performance and scalability.

  20. Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

    NASA Astrophysics Data System (ADS)

    Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em

    2015-09-01

    Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM).

  1. Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

    SciTech Connect

    Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em

    2015-09-15

    Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)

  2. Migration of vectorized iterative solvers to distributed memory architectures

    SciTech Connect

    Pommerell, C.; Ruehl, R.

    1994-12-31

    Both necessity and opportunity motivate the use of high-performance computers for iterative linear solvers. Necessity results from the size of the problems being solved-smaller problems are often better handled by direct methods. Opportunity arises from the formulation of the iterative methods in terms of simple linear algebra operations, even if this {open_quote}natural{close_quotes} parallelism is not easy to exploit in irregularly structured sparse matrices and with good preconditioners. As a result, high-performance implementations of iterative solvers have attracted a lot of interest in recent years. Most efforts are geared to vectorize or parallelize the dominating operation-structured or unstructured sparse matrix-vector multiplication, or to increase locality and parallelism by reformulating the algorithm-reducing global synchronization in inner products or local data exchange in preconditioners. Target architectures for iterative solvers currently include mostly vector supercomputers and architectures with one or few optimized (e.g., super-scalar and/or super-pipelined RISC) processors and hierarchical memory systems. More recently, parallel computers with physically distributed memory and a better price/performance ratio have been offered by vendors as a very interesting alternative to vector supercomputers. However, programming comfort on such distributed memory parallel processors (DMPPs) still lags behind. Here the authors are concerned with iterative solvers and their changing computing environment. In particular, they are considering migration from traditional vector supercomputers to DMPPs. Application requirements force one to use flexible and portable libraries. They want to extend the portability of iterative solvers rather than reimplementing everything for each new machine, or even for each new architecture.

  3. Decision Engines for Software Analysis Using Satisfiability Modulo Theories Solvers

    NASA Technical Reports Server (NTRS)

    Bjorner, Nikolaj

    2010-01-01

    The area of software analysis, testing and verification is now undergoing a revolution thanks to the use of automated and scalable support for logical methods. A well-recognized premise is that at the core of software analysis engines is invariably a component using logical formulas for describing states and transformations between system states. The process of using this information for discovering and checking program properties (including such important properties as safety and security) amounts to automatic theorem proving. In particular, theorem provers that directly support common software constructs offer a compelling basis. Such provers are commonly called satisfiability modulo theories (SMT) solvers. Z3 is a state-of-the-art SMT solver. It is developed at Microsoft Research. It can be used to check the satisfiability of logical formulas over one or more theories such as arithmetic, bit-vectors, lists, records and arrays. The talk describes some of the technology behind modern SMT solvers, including the solver Z3. Z3 is currently mainly targeted at solving problems that arise in software analysis and verification. It has been applied to various contexts, such as systems for dynamic symbolic simulation (Pex, SAGE, Vigilante), for program verification and extended static checking (Spec#/Boggie, VCC, HAVOC), for software model checking (Yogi, SLAM), model-based design (FORMULA), security protocol code (F7), program run-time analysis and invariant generation (VS3). We will describe how it integrates support for a variety of theories that arise naturally in the context of the applications. There are several new promising avenues and the talk will touch on some of these and the challenges related to SMT solvers. Proceedings

  4. 2d PDE Linear Symmetric Matrix Solver

    1983-10-01

    ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  5. 2d PDE Linear Asymmetric Matrix Solver

    1983-10-01

    ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  6. Efficient three-dimensional Poisson solvers in open rectangular conducting pipe

    NASA Astrophysics Data System (ADS)

    Qiang, Ji

    2016-06-01

    Three-dimensional (3D) Poisson solver plays an important role in the study of space-charge effects on charged particle beam dynamics in particle accelerators. In this paper, we propose three new 3D Poisson solvers for a charged particle beam in an open rectangular conducting pipe. These three solvers include a spectral integrated Green function (IGF) solver, a 3D spectral solver, and a 3D integrated Green function solver. These solvers effectively handle the longitudinal open boundary condition using a finite computational domain that contains the beam itself. This saves the computational cost of using an extra larger longitudinal domain in order to set up an appropriate finite boundary condition. Using an integrated Green function also avoids the need to resolve rapid variation of the Green function inside the beam. The numerical operational cost of the spectral IGF solver and the 3D IGF solver scales as O(N log(N)) , where N is the number of grid points. The cost of the 3D spectral solver scales as O(Nn N) , where Nn is the maximum longitudinal mode number. We compare these three solvers using several numerical examples and discuss the advantageous regime of each solver in the physical application.

  7. Nicalin and its binding partner Nomo are novel Nodal signaling antagonists.

    PubMed

    Haffner, Christof; Frauli, Mélanie; Topp, Stephanie; Irmler, Martin; Hofmann, Kay; Regula, Jörg T; Bally-Cuif, Laure; Haass, Christian

    2004-08-01

    Nodals are signaling factors of the transforming growth factor-beta (TGFbeta) superfamily with a key role in vertebrate development. They control a variety of cell fate decisions required for the establishment of the embryonic body plan. We have identified two highly conserved transmembrane proteins, Nicalin and Nomo (Nodal modulator, previously known as pM5), as novel antagonists of Nodal signaling. Nicalin is distantly related to Nicastrin, a component of the Alzheimer's disease-associated gamma-secretase, and forms a complex with Nomo. Ectopic expression of both proteins in zebrafish embryos causes cyclopia, a phenotype that can arise from a defect in mesendoderm patterning mediated by the Nodal signaling pathway. Accordingly, downregulation of Nomo resulted in an increase in anterior axial mesendoderm and the development of an enlarged hatching gland. Inhibition of Nodal signaling by ectopic expression of Lefty was rescued by reducing Nomo levels. Furthermore, Nodal- as well as Activin-induced signaling was inhibited by Nicalin and Nomo in a cell-based reporter assay. Our data demonstrate that the Nicalin/Nomo complex antagonizes Nodal signaling during mesendodermal patterning in zebrafish. PMID:15257293

  8. Application of the Absolute Nodal Co-Ordinate Formulation to Multibody System Dynamics

    NASA Astrophysics Data System (ADS)

    Escalona, J. L.; Hussien, H. A.; Shabana, A. A.

    1998-07-01

    The floating frame of reference formulation is currently the most widely used approach in flexible multibody simulations. The use of this approach, however, has been limited to small deformation problems. In this investigation, the computer implementation of the newabsolute nodal co-ordinate formulationand its use in the small and large deformation analysis of flexible multibody systems that consist of interconnected bodies are discussed. While in the floating frame of reference formulation a mixed set of absolute reference and local elastic co-ordinates are used, in the absolute nodal co-ordinate formulation only absolute co-ordinates are used. In the absolute nodal co-ordinate formulation, new interpretation of the nodal co-ordinates of the finite elements is used. No infinitesimal or finite rotations are used as nodal co-ordinates from beams and plates, instead, global slopes are used to define the element nodal co-ordinates. Using this interpretation of the element co-ordinates, beams and plates can be considered as isoparametric elements, and as a result, exact modelling of the rigid body dynamics can be obtained using the element shape function and the absolute nodal co-ordinates. Unlike the floating frame of reference approach, no co-ordinate transformation is required in order to determine the element inertia. The mass matrix of the finite elements is a constant matrix, and therefore, the centrifugal and Coriolis forces are equal to zero when the absolute nodal co-ordinate formulation is used. Another advantage of using the absolute nodal co-ordinate formulation in the dynamic simulation of multibody systems is its simplicity in imposing some of the joint constraints and also its simplicity in formulating the generalized forces due to spring-damper elements. The results obtained in this investigation show an excellent agreement with the results obtained using the floating frame of reference formulation when large rotation-small deformation problems are

  9. Nodal signaling is required for closure of the anterior neural tube in zebrafish

    PubMed Central

    Aquilina-Beck, Allisan; Ilagan, Kristine; Liu, Qin; Liang, Jennifer O

    2007-01-01

    Background Nodals are secreted signaling proteins with many roles in vertebrate development. Here, we identify a new role for Nodal signaling in regulating closure of the rostral neural tube of zebrafish. Results We find that the neural tube in the presumptive forebrain fails to close in zebrafish Nodal signaling mutants. For instance, the cells that will give rise to the pineal organ fail to move from the lateral edges of the neural plate to the midline of the diencephalon. The open neural tube in Nodal signaling mutants may be due in part to reduced function of N-cadherin, a cell adhesion molecule expressed in the neural tube and required for neural tube closure. N-cadherin expression and localization to the membrane are reduced in fish that lack Nodal signaling. Further, N-cadherin mutants and morphants have a pineal phenotype similar to that of mutants with deficiencies in the Nodal pathway. Overexpression of an activated form of the TGFβ Type I receptor Taram-A (Taram-A*) cell autonomously rescues mesendoderm formation in fish with a severe decrease in Nodal signaling. We find that overexpression of Taram-A* also corrects their open neural tube defect. This suggests that, as in mammals, the mesoderm and endoderm have an important role in regulating closure of the anterior neural tube of zebrafish. Conclusion This work helps establish a role for Nodal signals in neurulation, and suggests that defects in Nodal signaling could underlie human neural tube defects such as exencephaly, a fatal condition characterized by an open neural tube in the anterior brain. PMID:17996054

  10. The accuracy of preoperative axillary nodal staging in primary breast cancer by ultrasound is modified by nodal metastatic load and tumor biology

    PubMed Central

    Dihge, Looket; Grabau, Dorthe A.; Rasmussen, Rogvi W.; Bendahl, Pär-Ola; Rydén, Lisa

    2016-01-01

    Abstract Background The outcome of axillary ultrasound (AUS) with fine-needle aspiration biopsy (FNAB) in the diagnostic work-up of primary breast cancer has an impact on therapy decisions. We hypothesize that the accuracy of AUS is modified by nodal metastatic burden and clinico-pathological characteristics. Material and methods The performance of AUS and AUS-guided FNAB for predicting nodal metastases was assessed in a prospective breast cancer cohort subjected for surgery during 2009–2012. Predictors of accuracy were included in multivariate analysis. Results AUS had a sensitivity of 23% and a specificity of 95%, while AUS-guided FNAB obtained 73% and 100%, respectively. AUS-FNAB exclusively detected macro-metastases (median four metastases) and identified patients with more extensive nodal metastatic burden in comparison with sentinel node biopsy. The accuracy of AUS was affected by metastatic size (OR 1.11), obesity (OR 2.46), histological grade (OR 4.43), and HER2-status (OR 3.66); metastatic size and histological grade were significant in the multivariate analysis. Conclusions The clinical utility of AUS in low-risk breast cancer deserves further evaluation as the accuracy decreased with a low nodal metastatic burden. The diagnostic performance is modified by tumor and clinical characteristics. Patients with nodal disease detected by AUS-FNAB represent a group for whom neoadjuvant therapy should be considered. PMID:27050668

  11. Embryonic Morphogen Nodal Is Associated with Progression and Poor Prognosis of Hepatocellular Carcinoma

    PubMed Central

    Jia, Wei-Dong; Xu, Ge-Liang; Ma, Jin-Liang; Ren, Yun; Chen, Hao; Sun, Si-Nan; Huang, Mei; Li, Jian-Sheng

    2014-01-01

    Background Nodal, a TGF-β-related embryonic morphogen, is involved in multiple biologic processes. However, the expression of Nodal in hepatocellular carcinoma (HCC) and its correlation with tumor angiogenesis, epithelial-mesenchymal transition, and prognosis is unclear. Methods We used real-time PCR and Western blotting to investigate Nodal expression in 6 HCC cell lines and 1 normal liver cell line, 16 pairs of tumor and corresponding paracarcinomatous tissues from HCC patients. Immunohistochemistry was performed to examine Nodal expression in HCC and corresponding paracarcinomatous tissues from 96 patients. CD34 and Vimentin were only examined in HCC tissues of patients mentioned above. Nodal gene was silenced by shRNA in MHCC97H and HCCLM3 cell lines, and cell migration and invasion were detected. Statistical analyses were applied to evaluate the prognostic value and associations of Nodal expression with clinical parameters. Results Nodal expression was detected in HCC cell lines with high metastatic potential alone. Nodal expression is up-regulated in HCC tissues compared with paracarcinomatous and normal liver tissues. Nodal protein was expressed in 70 of the 96 (72.9%) HCC tumors, and was associated with vascular invasion (P = 0.000), status of metastasis (P = 0.004), AFP (P = 0.049), ICGR15 (indocyanine green retention rate at 15 min) (P = 0.010) and tumor size (P = 0.000). High Nodal expression was positively correlated with high MVD (microvessal density) (P = 0.006), but not with Vimentin expression (P = 0.053). Significantly fewer migrated and invaded cells were seen in shRNA group compared with blank group and negative control group (P<0.05). High Nodal expression was found to be an independent factor for predicting overall survival of HCC. Conclusions Our study demonstrated that Nodal expression is associated with aggressive characteristics of HCC. Its aberrant expression may be a predictive factor of unfavorable prognosis

  12. A parallel-vector equation solver for unsymmetric matrices on supercomputers

    NASA Technical Reports Server (NTRS)

    Qin, J.; Mei, C.; Nguyen, D. T.; Gray, C. E., Jr.

    1991-01-01

    A parallel-vector unsymmetric equation solver is presented. The solver exploits both vector and parallel capabilities provided by modern, high-performance supercomputers. A special storage scheme and loop-unrolling technique are used to optimize the vector performance. A parallel FORTRAN language is used to develop the solver on the CRAY 2 and CRAY Y-MP multiple processing computer environment. Three numerical examples are presented which demonstrate the efficiency and accuracy of this equation solver. The first two examples demonstrate the improved performance, and the third example utilizes the proposed solver to solve a highly nonlinear, unsymmetric finite element formulation for panel flutter.

  13. Rethinking Electrostatic Solvers in Particle Simulations for the Exascale Era

    NASA Astrophysics Data System (ADS)

    Deca, Jan; Markidis, Stefano; Lapenta, Giovanni; Járleberg, Erik; Apostolov, Rossen; Laure, Erwin

    2012-10-01

    In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by solving the Poisson equation, in the new approach the electric field is calculated by solving Ampère's law. When the Ampere's law is discretized explicitly in time, the electric field values on the mesh are simply updated from the previous values. In this way, the electrostatic solver becomes an embarrassingly parallel problem, making the algorithm extremely scalable and suitable for exascale computing platforms. An implementation PM code with the new electrostatic solver is presented to show that the proposed method produces correct results. It is a very promising algorithm for exascale PM simulations.

  14. LDRD report : parallel repartitioning for optimal solver performance.

    SciTech Connect

    Heaphy, Robert; Devine, Karen Dragon; Preis, Robert; Hendrickson, Bruce Alan; Heroux, Michael Allen; Boman, Erik Gunnar

    2004-02-01

    We have developed infrastructure, utilities and partitioning methods to improve data partitioning in linear solvers and preconditioners. Our efforts included incorporation of data repartitioning capabilities from the Zoltan toolkit into the Trilinos solver framework, (allowing dynamic repartitioning of Trilinos matrices); implementation of efficient distributed data directories and unstructured communication utilities in Zoltan and Trilinos; development of a new multi-constraint geometric partitioning algorithm (which can generate one decomposition that is good with respect to multiple criteria); and research into hypergraph partitioning algorithms (which provide up to 56% reduction of communication volume compared to graph partitioning for a number of emerging applications). This report includes descriptions of the infrastructure and algorithms developed, along with results demonstrating the effectiveness of our approaches.

  15. Benchmarking ICRF Full-wave Solvers for ITER

    SciTech Connect

    R. V. Budny, L. Berry, R. Bilato, P. Bonoli, M. Brambilla, R. J. Dumont, A. Fukuyama, R. Harvey, E. F. Jaeger, K. Indireshkumar, E. Lerche, D. McCune, C. K. Phillips, V. Vdovin, J. Wright, and members of the ITPA-IOS

    2011-01-06

    Abstract Benchmarking of full-wave solvers for ICRF simulations is performed using plasma profiles and equilibria obtained from integrated self-consistent modeling predictions of four ITER plasmas. One is for a high performance baseline (5.3 T, 15 MA) DT H-mode. The others are for half-field, half-current plasmas of interest for the pre-activation phase with bulk plasma ion species being either hydrogen or He4. The predicted profiles are used by six full-wave solver groups to simulate the ICRF electromagnetic fields and heating, and by three of these groups to simulate the current-drive. Approximate agreement is achieved for the predicted heating power for the DT and He4 cases. Factor of two disagreements are found for the cases with second harmonic He3 heating in bulk H cases. Approximate agreement is achieved simulating the ICRF current drive.

  16. An exact solver for the DCJ median problem.

    PubMed

    Zhang, Meng; Arndt, William; Tang, Jijun

    2009-01-01

    The "double-cut-and-join" (DCJ) model of genome rearrangement proposed by Yancopoulos et al. uses the single DCJ operation to account for all genome rearrangement events. Given three signed permutations, the DCJ median problem is to find a fourth permutation that minimizes the sum of the pairwise DCJ distances between it and the three others. In this paper, we present a branch-and-bound method that provides accurate solution to the multichromosomal DCJ median problems. We conduct extensive simulations and the results show that the DCJ median solver performs better than other median solvers for most of the test cases. These experiments also suggest that DCJ model is more suitable for real datasets where both reversals and transpositions occur.

  17. Elliptic Solvers with Adaptive Mesh Refinement on Complex Geometries

    SciTech Connect

    Phillip, B.

    2000-07-24

    Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.

  18. Scalable Out-of-Core Solvers on Xeon Phi Cluster

    SciTech Connect

    D'Azevedo, Ed F; Chan, Ki Shing; Su, Shiquan; Wong, Kwai

    2015-01-01

    This paper documents the implementation of a distributive out-of-core (OOC) solver for performing LU and Cholesky factorizations of a large dense matrix on clusters of many-core programmable co-processors. The out-of- core algorithm combines both the left-looking and right-looking schemes aimed to minimize the movement of data between the CPU host and the co-processor, optimizing data locality as well as computing throughput. The OOC solver is built to align with the format of the ScaLAPACK software library, making it readily portable to any existing codes using ScaLAPACK. A runtime analysis conducted on Beacon (an Intel Xeon plus Intel Xeon Phi cluster which composed of 48 nodes of multi-core CPU and MIC) at the Na- tional Institute for Computational Sciences is presented. Comparison of the performance on the Intel Xeon Phi and GPU clusters are also provided.

  19. A functional implementation of the Jacobi eigen-solver

    SciTech Connect

    Boehm, A.P.W. . Dept. of Computer Science); Hiromoto, R.E. )

    1993-01-01

    In this paper, we describe the systematic development of two implementations of the Jacobi eigen-solver and give performance results for the MIT/Motorola Monsoon dataflow machine. Our study is carried out using MINT, the MIT Monsoon simulator. The design of these implementations follows from the mathematics of the Jacobi method, and not from a translation of an existing sequential code. The functional semantics with respect to array updates, which cause excessive array copying, has lead us to a new implementation of a parallel group-rotations'' algorithm first described by Sameh. Our version of this algorithm requires 0(n[sup 3]) operations, whereas Sameh's original version requires 0(n[sup 4]) operations. The implementations are programmed in the language Id, and although Id has non-functional features, we have restricted the development of our eigen-solvers to the functional sub-set of the language.

  20. A functional implementation of the Jacobi eigen-solver

    SciTech Connect

    Boehm, A.P.W.; Hiromoto, R.E.

    1993-02-01

    In this paper, we describe the systematic development of two implementations of the Jacobi eigen-solver and give performance results for the MIT/Motorola Monsoon dataflow machine. Our study is carried out using MINT, the MIT Monsoon simulator. The design of these implementations follows from the mathematics of the Jacobi method, and not from a translation of an existing sequential code. The functional semantics with respect to array updates, which cause excessive array copying, has lead us to a new implementation of a parallel ``group-rotations`` algorithm first described by Sameh. Our version of this algorithm requires 0(n{sup 3}) operations, whereas Sameh`s original version requires 0(n{sup 4}) operations. The implementations are programmed in the language Id, and although Id has non-functional features, we have restricted the development of our eigen-solvers to the functional sub-set of the language.

  1. A spectral Poisson solver for kinetic plasma simulation

    NASA Astrophysics Data System (ADS)

    Szeremley, Daniel; Obberath, Jens; Brinkmann, Ralf

    2011-10-01

    Plasma resonance spectroscopy is a well established plasma diagnostic method, realized in several designs. One of these designs is the multipole resonance probe (MRP). In its idealized - geometrically simplified - version it consists of two dielectrically shielded, hemispherical electrodes to which an RF signal is applied. A numerical tool is under development which is capable of simulating the dynamics of the plasma surrounding the MRP in electrostatic approximation. In this contribution we concentrate on the specialized Poisson solver for that tool. The plasma is represented by an ensemble of point charges. By expanding both the charge density and the potential into spherical harmonics, a largely analytical solution of the Poisson problem can be employed. For a practical implementation, the expansion must be appropriately truncated. With this spectral solver we are able to efficiently solve the Poisson equation in a kinetic plasma simulation without the need of introducing a spatial discretization.

  2. A Nonlinear Modal Aeroelastic Solver for FUN3D

    NASA Technical Reports Server (NTRS)

    Goldman, Benjamin D.; Bartels, Robert E.; Biedron, Robert T.; Scott, Robert C.

    2016-01-01

    A nonlinear structural solver has been implemented internally within the NASA FUN3D computational fluid dynamics code, allowing for some new aeroelastic capabilities. Using a modal representation of the structure, a set of differential or differential-algebraic equations are derived for general thin structures with geometric nonlinearities. ODEPACK and LAPACK routines are linked with FUN3D, and the nonlinear equations are solved at each CFD time step. The existing predictor-corrector method is retained, whereby the structural solution is updated after mesh deformation. The nonlinear solver is validated using a test case for a flexible aeroshell at transonic, supersonic, and hypersonic flow conditions. Agreement with linear theory is seen for the static aeroelastic solutions at relatively low dynamic pressures, but structural nonlinearities limit deformation amplitudes at high dynamic pressures. No flutter was found at any of the tested trajectory points, though LCO may be possible in the transonic regime.

  3. On improving linear solver performance: a block variant of GMRES

    SciTech Connect

    Baker, A H; Dennis, J M; Jessup, E R

    2004-05-10

    The increasing gap between processor performance and memory access time warrants the re-examination of data movement in iterative linear solver algorithms. For this reason, we explore and establish the feasibility of modifying a standard iterative linear solver algorithm in a manner that reduces the movement of data through memory. In particular, we present an alternative to the restarted GMRES algorithm for solving a single right-hand side linear system Ax = b based on solving the block linear system AX = B. Algorithm performance, i.e. time to solution, is improved by using the matrix A in operations on groups of vectors. Experimental results demonstrate the importance of implementation choices on data movement as well as the effectiveness of the new method on a variety of problems from different application areas.

  4. Verification and Validation Studies for the LAVA CFD Solver

    NASA Technical Reports Server (NTRS)

    Moini-Yekta, Shayan; Barad, Michael F; Sozer, Emre; Brehm, Christoph; Housman, Jeffrey A.; Kiris, Cetin C.

    2013-01-01

    The verification and validation of the Launch Ascent and Vehicle Aerodynamics (LAVA) computational fluid dynamics (CFD) solver is presented. A modern strategy for verification and validation is described incorporating verification tests, validation benchmarks, continuous integration and version control methods for automated testing in a collaborative development environment. The purpose of the approach is to integrate the verification and validation process into the development of the solver and improve productivity. This paper uses the Method of Manufactured Solutions (MMS) for the verification of 2D Euler equations, 3D Navier-Stokes equations as well as turbulence models. A method for systematic refinement of unstructured grids is also presented. Verification using inviscid vortex propagation and flow over a flat plate is highlighted. Simulation results using laminar and turbulent flow past a NACA 0012 airfoil and ONERA M6 wing are validated against experimental and numerical data.

  5. An Upwind Solver for the National Combustion Code

    NASA Technical Reports Server (NTRS)

    Sockol, Peter M.

    2011-01-01

    An upwind solver is presented for the unstructured grid National Combustion Code (NCC). The compressible Navier-Stokes equations with time-derivative preconditioning and preconditioned flux-difference splitting of the inviscid terms are used. First order derivatives are computed on cell faces and used to evaluate the shear stresses and heat fluxes. A new flux limiter uses these same first order derivatives in the evaluation of left and right states used in the flux-difference splitting. The k-epsilon turbulence equations are solved with the same second-order method. The new solver has been installed in a recent version of NCC and the resulting code has been tested successfully in 2D on two laminar cases with known solutions and one turbulent case with experimental data.

  6. Parallel Auxiliary Space AMG Solver for $H(div)$ Problems

    SciTech Connect

    Kolev, Tzanio V.; Vassilevski, Panayot S.

    2012-12-18

    We present a family of scalable preconditioners for matrices arising in the discretization of $H(div)$ problems using the lowest order Raviart--Thomas finite elements. Our approach belongs to the class of “auxiliary space''--based methods and requires only the finite element stiffness matrix plus some minimal additional discretization information about the topology and orientation of mesh entities. Also, we provide a detailed algebraic description of the theory, parallel implementation, and different variants of this parallel auxiliary space divergence solver (ADS) and discuss its relations to the Hiptmair--Xu (HX) auxiliary space decomposition of $H(div)$ [SIAM J. Numer. Anal., 45 (2007), pp. 2483--2509] and to the auxiliary space Maxwell solver AMS [J. Comput. Math., 27 (2009), pp. 604--623]. Finally, an extensive set of numerical experiments demonstrates the robustness and scalability of our implementation on large-scale $H(div)$ problems with large jumps in the material coefficients.

  7. Brittle Solvers: Lessons and insights into effective solvers for visco-plasticity in geodynamics

    NASA Astrophysics Data System (ADS)

    Spiegelman, M. W.; May, D.; Wilson, C. R.

    2014-12-01

    Plasticity/Fracture and rock failure are essential ingredients in geodynamic models as terrestrial rocks do not possess an infinite yield strength. Numerous physical mechanisms have been proposed to limit the strength of rocks, including low temperature plasticity and brittle fracture. While ductile and creep behavior of rocks at depth is largely accepted, the constitutive relations associated with brittle failure, or shear localisation, are more controversial. Nevertheless, there are really only a few macroscopic constitutive laws for visco-plasticity that are regularly used in geodynamics models. Independent of derivation, all of these can be cast as simple effective viscosities which act as stress limiters with different choices for yield surfaces; the most common being a von Mises (constant yield stress) or Drucker-Prager (pressure dependent yield-stress) criterion. The choice of plasticity model, however, can have significant consequences for the degree of non-linearity in a problem and the choice and efficiency of non-linear solvers. Here we describe a series of simplified 2 and 3-D model problems to elucidate several issues associated with obtaining accurate description and solution of visco-plastic problems. We demonstrate that1) Picard/Successive substitution schemes for solution of the non-linear problems can often stall at large values of the non-linear residual, thus producing spurious solutions2) Combined Picard/Newton schemes can be effective for a range of plasticity models, however, they can produce serious convergence problems for strongly pressure dependent plasticity models such as Drucker-Prager.3) Nevertheless, full Drucker-Prager may not be the plasticity model of choice for strong materials as the dynamic pressures produced in these layers can develop pathological behavior with Drucker-Prager, leading to stress strengthening rather than stress weakening behavior.4) In general, for any incompressible Stoke's problem, it is highly advisable to

  8. Micropropagation of Calophyllum brasiliense (Cambess.) from nodal segments.

    PubMed

    Silveira, S S; Cordeiro-Silva, R; Degenhardt-Goldbach, J; Quoirin, M

    2016-05-01

    Micropropagation of Calophyllum brasiliense Cambess. (Clusiaceae) is a way to overcome difficulties in achieving large-scale plant production, given the recalcitrant nature of the seeds, irregular fructification and absence of natural vegetative propagation of the species. Cultures were established using nodal segments 2 cm in length, obtained from 1-2 year old seedlings, maintained in a greenhouse. Mercury chloride and Plant Preservative Mixture™ were used in the surface sterilizing stage, better results being achieved with Plant Preservative Mixture™ incorporation in culture medium, at any concentration. Polyvinylpyrrolidone, activated charcoal, cysteine, ascorbic acid or citric acid were added to the culture medium to avoid oxidation. After 30 days of culture, polyvinylpirrolidone and ascorbic acid gave better results, eliminating oxidation in most explants. For shoot multiplication, benzylaminopurine was used in concentrations of 4.4 and 8.8 µM in Woody Plant Medium, resulting in an average of 4.43 and 4.68 shoots per explant, respectively, after 90 days. Indole-3-butyric acid and α-naphthalene acetic acid were used to induce root formation, reaching a maximum rooting rate of 24% with 20µM α-naphthalene acetic acid. For acclimatization. the rooted plants were transferred to Plantmax® substrate and cultured in a greenhouse, reaching 79% of survival after 30 days and 60% after one year.

  9. Micropropagation of commercially cultivated Henna (Lawsonia inermis) using nodal explants.

    PubMed

    Ram, Kheta; Shekhawat, N S

    2011-07-01

    Lawsonia inermis Linn. (Mehandi) is cultivated as cash crop in India particularly in Sojat area of Pali district, Rajasthan. Present investigation describes an efficient regeneration system for elite genotype of L. inermis using nodal segments. Optimum response in terms of percent cultures responding, days to bud break and average shoot length was observed on MS medium supplemented with 6-benzylaminopurine (BA; 2.0 mg l(-1)). Shoot multiplication was influenced by plant growth regulators, repeated transfer of explants and addition of ammonium sulphate. Maximum shoots were regenerated on MS medium supplemented with BA (0.25 mg l(-1)), kinetin (Kn; 0.25 mg l(-1)), indole-3-acetic acid (IAA; 0.1 mg l(-1)) and ammonium sulphate (150 mg l(-1)). To reduce resources, time and labours costs, we have also attempted ex vitro rooting of shoots. About 95 % shoots were rooted ex vitro on soilrite after treatment with indole-3-butyric acid (IBA; 300 mg l(-1)) and 2-naphthoxy acetic acid (NOA; 100 mg l(-1)) and establishment in soil successfully.

  10. Heterogeneous nodal responses in cascade dynamics on multiplex networks

    NASA Astrophysics Data System (ADS)

    Lee, Kyu-Min; Brummitt, Charles D.; Goh, Kwang-Il

    2014-03-01

    Structure and dynamics of multiplex network systems have been intensively studied recently, revealing nontrivial results such as facilitated cascading failures and new type of phase transitions unforeseen in the single-level systems. However, most studies about multi-layered, network of networks have mainly considered the case of single nodal response to multiple layers, that is, every node responds to the multiple layers in identical way. Most complex systems like human society, however, function not only through various kinds of relations but also through heterogeneous response behavior across agents, indicating a new level of complexity. To address it, here we formulate a threshold cascade model on multiplex networks with a mixture of two response functions: OR and AND rules. For the OR response, nodes are activated if enough neighbors in any layer are active, whereas for the AND response, the nodes activate only if enough neighbors in all layers are active. Coexistence of these two response rules is shown to control between facilitation and inhibition of cascading failures, and moreover, it can also control the type of transitions to global cascades between continuous and discontinuous ones. We will discuss the implication of the results in the context of social dynamics.

  11. Micropropagation of Calophyllum brasiliense (Cambess.) from nodal segments.

    PubMed

    Silveira, S S; Cordeiro-Silva, R; Degenhardt-Goldbach, J; Quoirin, M

    2016-05-01

    Micropropagation of Calophyllum brasiliense Cambess. (Clusiaceae) is a way to overcome difficulties in achieving large-scale plant production, given the recalcitrant nature of the seeds, irregular fructification and absence of natural vegetative propagation of the species. Cultures were established using nodal segments 2 cm in length, obtained from 1-2 year old seedlings, maintained in a greenhouse. Mercury chloride and Plant Preservative Mixture™ were used in the surface sterilizing stage, better results being achieved with Plant Preservative Mixture™ incorporation in culture medium, at any concentration. Polyvinylpyrrolidone, activated charcoal, cysteine, ascorbic acid or citric acid were added to the culture medium to avoid oxidation. After 30 days of culture, polyvinylpirrolidone and ascorbic acid gave better results, eliminating oxidation in most explants. For shoot multiplication, benzylaminopurine was used in concentrations of 4.4 and 8.8 µM in Woody Plant Medium, resulting in an average of 4.43 and 4.68 shoots per explant, respectively, after 90 days. Indole-3-butyric acid and α-naphthalene acetic acid were used to induce root formation, reaching a maximum rooting rate of 24% with 20µM α-naphthalene acetic acid. For acclimatization. the rooted plants were transferred to Plantmax® substrate and cultured in a greenhouse, reaching 79% of survival after 30 days and 60% after one year. PMID:27143061

  12. Scaling Algebraic Multigrid Solvers: On the Road to Exascale

    SciTech Connect

    Baker, A H; Falgout, R D; Gamblin, T; Kolev, T; Schulz, M; Yang, U M

    2010-12-12

    Algebraic Multigrid (AMG) solvers are an essential component of many large-scale scientific simulation codes. Their continued numerical scalability and efficient implementation is critical for preparing these codes for exascale. Our experiences on modern multi-core machines show that significant challenges must be addressed for AMG to perform well on such machines. We discuss our experiences and describe the techniques we have used to overcome scalability challenges for AMG on hybrid architectures in preparation for exascale.

  13. A chemical reaction network solver for the astrophysics code NIRVANA

    NASA Astrophysics Data System (ADS)

    Ziegler, U.

    2016-02-01

    Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes

  14. An automatic ordering method for incomplete factorization iterative solvers

    SciTech Connect

    Forsyth, P.A.; Tang, W.P. . Dept. of Computer Science); D'Azevedo, E.F.D. )

    1991-01-01

    The minimum discarded fill (MDF) ordering strategy for incomplete factorization iterative solvers is developed. MDF ordering is demonstrated for several model son-symmetric problems, as well as a water-flooding simulation which uses an unstructured grid. The model problems show a three to five fold decrease in the number of iterations compared to natural orderings. Greater than twofold improvement was observed for the waterflooding simulation. 26 refs., 7 figs., 3 tabs.

  15. A contribution to the great Riemann solver debate

    NASA Technical Reports Server (NTRS)

    Quirk, James J.

    1992-01-01

    The aims of this paper are threefold: to increase the level of awareness within the shock capturing community to the fact that many Godunov-type methods contain subtle flaws that can cause spurious solutions to be computed; to identify one mechanism that might thwart attempts to produce very high resolution simulations; and to proffer a simple strategy for overcoming the specific failings of individual Riemann solvers.

  16. Boltzmann Solver with Adaptive Mesh in Velocity Space

    SciTech Connect

    Kolobov, Vladimir I.; Arslanbekov, Robert R.; Frolova, Anna A.

    2011-05-20

    We describe the implementation of direct Boltzmann solver with Adaptive Mesh in Velocity Space (AMVS) using quad/octree data structure. The benefits of the AMVS technique are demonstrated for the charged particle transport in weakly ionized plasmas where the collision integral is linear. We also describe the implementation of AMVS for the nonlinear Boltzmann collision integral. Test computations demonstrate both advantages and deficiencies of the current method for calculations of narrow-kernel distributions.

  17. Direct linear programming solver in C for structural applications

    NASA Astrophysics Data System (ADS)

    Damkilde, L.; Hoyer, O.; Krenk, S.

    1994-08-01

    An optimization problem can be characterized by an object-function, which is maximized, and restrictions, which limit the variation of the variables. A subclass of optimization is Linear Programming (LP), where both the object-function and the restrictions are linear functions of the variables. The traditional solution methods for LP problems are based on the simplex method, and it is customary to allow only non-negative variables. Compared to other optimization routines the LP solvers are more robust and the optimum is reached in a finite number of steps and is not sensitive to the starting point. For structural applications many optimization problems can be linearized and solved by LP routines. However, the structural variables are not always non-negative, and this requires a reformation, where a variable x is substituted by the difference of two non-negative variables, x(sup + ) and x(sup - ). The transformation causes a doubling of the number of variables, and in a computer implementation the memory allocation doubles and for a typical problem the execution time at least doubles. This paper describes a LP solver written in C, which can handle a combination of non-negative variables and unlimited variables. The LP solver also allows restart, and this may reduce the computational costs if the solution to a similar LP problem is known a priori. The algorithm is based on the simplex method, and differs only in the logical choices. Application of the new LP solver will at the same time give both a more direct problem formulation and a more efficient program.

  18. Interactive visualization of volumetric white matter connectivity in DT-MRI using a parallel-hardware Hamilton-Jacobi solver.

    PubMed

    Jeong, Won-Ki; Fletcher, P Thomas; Tao, Ran; Whitaker, Ross

    2007-01-01

    In this paper we present a method to compute and visualize volumetric white matter connectivity in diffusion tensor magnetic resonance imaging (DT-MRI) using a Hamilton-Jacobi (H-J) solver on the GPU (Graphics Processing Unit). Paths through the volume are assigned costs that are lower if they are consistent with the preferred diffusion directions. The proposed method finds a set of voxels in the DTI volume that contain paths between two regions whose costs are within a threshold of the optimal path. The result is a volumetric optimal path analysis, which is driven by clinical and scientific questions relating to the connectivity between various known anatomical regions of the brain. To solve the minimal path problem quickly, we introduce a novel numerical algorithm for solving H-J equations, which we call the Fast Iterative Method (FIM). This algorithm is well-adapted to parallel architectures, and we present a GPU-based implementation, which runs roughly 50-100 times faster than traditional CPU-based solvers for anisotropic H-J equations. The proposed system allows users to freely change the endpoints of interesting pathways and to visualize the optimal volumetric path between them at an interactive rate. We demonstrate the proposed method on some synthetic and real DT-MRI datasets and compare the performance with existing methods. PMID:17968100

  19. Recommendations for Radiotherapy Technique and Dose in Extra-nodal Lymphoma.

    PubMed

    Hoskin, P J; Díez, P; Gallop-Evans, E; Syndikus, I; Bates, A; Bayne, M

    2016-01-01

    Extra-nodal sites may be involved in around 40% of patients with non-Hodgkin lymphoma. The general principles for target volume delineation in this setting are presented, together with specific examples. In general, the entire organ affected should be encompassed in the clinical target volume with an expansion of at least 10 mm, increased in some instances to account for patterns of potential lymphatic flow. Adjacent lymph nodes may be treated using standard techniques for nodal irradiation. Doses for extra-nodal lymphoma follow the same principles as nodal lymphoma, delivering 30 Gy in 15 fractions for Hodgkin and aggressive non-Hodgkin lymphoma and 24 Gy in 12 fractions for indolent lymphomas, with the exception of certain palliative situations, mycosis fungoides, central nervous system lymphoma and natural killer/T-cell lymphoma.

  20. Relation between finite element methods and nodal methods in transport theory

    SciTech Connect

    Walters, W.F.

    1985-01-01

    This paper examines the relationship between nodal methods and finite-element methods for solving the discrete-ordinates form of the transport equation in x-y geometry. Specifically, we will examine the relation of three finite-element schemes to the linear-linear (LL) and linear-nodal (LN) nodal schemes. The three finite-element schemes are the linear-continuous-diamond-difference (DD) scheme, the linear-discontinuous (LD) scheme, and the quadratic-discontinuous (QD) scheme. A brief derivation of the (LL) and (LN) nodal schemes is given in the third section of this paper. The approximations that cause the LL scheme to reduce to the DD, LD, and QD schemes are then indicated. An extremely simple method of deriving the finite-element schemes is then introduced.

  1. Dose-dependent Nodal/Smad signals pattern the early mouse embryo.

    PubMed

    Robertson, Elizabeth J

    2014-08-01

    Nodal signals in the early post-implantation stage embryo are essential to establish initial proximal-distal (P-D) polarity and generate the final anterior-posterior (A-P) body axis. Nodal signaling in the epiblast results in the phosphorylation of Smad2 in the overlying visceral endoderm necessary to induce the AVE, in part via Smad2-dependent activation of the T-box gene Eomesodermin. Slightly later following mesoderm induction a continuum of dose-dependent Nodal signaling during the process of gastrulation underlies specification of mesodermal and definitive endoderm progenitors. Dynamic Nodal expression during the critical 72 h time window immediately following implantation, accomplished by a series of feed-back and feed-forward mechanisms serves to provide key positional cues required for establishment of the body plan and controls cell fate decisions in the early mammalian embryo. PMID:24704361

  2. Recommendations for Radiotherapy Technique and Dose in Extra-nodal Lymphoma.

    PubMed

    Hoskin, P J; Díez, P; Gallop-Evans, E; Syndikus, I; Bates, A; Bayne, M

    2016-01-01

    Extra-nodal sites may be involved in around 40% of patients with non-Hodgkin lymphoma. The general principles for target volume delineation in this setting are presented, together with specific examples. In general, the entire organ affected should be encompassed in the clinical target volume with an expansion of at least 10 mm, increased in some instances to account for patterns of potential lymphatic flow. Adjacent lymph nodes may be treated using standard techniques for nodal irradiation. Doses for extra-nodal lymphoma follow the same principles as nodal lymphoma, delivering 30 Gy in 15 fractions for Hodgkin and aggressive non-Hodgkin lymphoma and 24 Gy in 12 fractions for indolent lymphomas, with the exception of certain palliative situations, mycosis fungoides, central nervous system lymphoma and natural killer/T-cell lymphoma. PMID:26456507

  3. Modeling of photon migration in the human lung using a finite volume solver

    NASA Astrophysics Data System (ADS)

    Sikorski, Zbigniew; Furmanczyk, Michal; Przekwas, Andrzej J.

    2006-02-01

    The application of the frequency domain and steady-state diffusive optical spectroscopy (DOS) and steady-state near infrared spectroscopy (NIRS) to diagnosis of the human lung injury challenges many elements of these techniques. These include the DOS/NIRS instrument performance and accurate models of light transport in heterogeneous thorax tissue. The thorax tissue not only consists of different media (e.g. chest wall with ribs, lungs) but its optical properties also vary with time due to respiration and changes in thorax geometry with contusion (e.g. pneumothorax or hemothorax). This paper presents a finite volume solver developed to model photon migration in the diffusion approximation in heterogeneous complex 3D tissues. The code applies boundary conditions that account for Fresnel reflections. We propose an effective diffusion coefficient for the void volumes (pneumothorax) based on the assumption of the Lambertian diffusion of photons entering the pleural cavity and accounting for the local pleural cavity thickness. The code has been validated using the MCML Monte Carlo code as a benchmark. The code environment enables a semi-automatic preparation of 3D computational geometry from medical images and its rapid automatic meshing. We present the application of the code to analysis/optimization of the hybrid DOS/NIRS/ultrasound technique in which ultrasound provides data on the localization of thorax tissue boundaries. The code effectiveness (3D complex case computation takes 1 second) enables its use to quantitatively relate detected light signal to absorption and reduced scattering coefficients that are indicators of the pulmonary physiologic state (hemoglobin concentration and oxygenation).

  4. Transonic Drag Prediction Using an Unstructured Multigrid Solver

    NASA Technical Reports Server (NTRS)

    Mavriplis, D. J.; Levy, David W.

    2001-01-01

    This paper summarizes the results obtained with the NSU-3D unstructured multigrid solver for the AIAA Drag Prediction Workshop held in Anaheim, CA, June 2001. The test case for the workshop consists of a wing-body configuration at transonic flow conditions. Flow analyses for a complete test matrix of lift coefficient values and Mach numbers at a constant Reynolds number are performed, thus producing a set of drag polars and drag rise curves which are compared with experimental data. Results were obtained independently by both authors using an identical baseline grid and different refined grids. Most cases were run in parallel on commodity cluster-type machines while the largest cases were run on an SGI Origin machine using 128 processors. The objective of this paper is to study the accuracy of the subject unstructured grid solver for predicting drag in the transonic cruise regime, to assess the efficiency of the method in terms of convergence, cpu time, and memory, and to determine the effects of grid resolution on this predictive ability and its computational efficiency. A good predictive ability is demonstrated over a wide range of conditions, although accuracy was found to degrade for cases at higher Mach numbers and lift values where increasing amounts of flow separation occur. The ability to rapidly compute large numbers of cases at varying flow conditions using an unstructured solver on inexpensive clusters of commodity computers is also demonstrated.

  5. Fast linear solvers for variable density turbulent flows

    NASA Astrophysics Data System (ADS)

    Pouransari, Hadi; Mani, Ali; Darve, Eric

    2015-11-01

    Variable density flows are ubiquitous in variety of natural and industrial systems. Two-phase and multi-phase flows in natural and industrial processes, astrophysical flows, and flows involved in combustion processes are such examples. For an ideal gas subject to low-Mach approximation, variations in temperature can lead to a non-uniform density field. In this work, we consider radiatively heated particle-laden turbulent flows as an example application in which density variability is resulted from inhomogeneities in the heat absorption by an inhomogeneous particle field. Under such conditions, the divergence constraint of the fluid is enforced through a variable coefficient Poisson equation. Inversion of the discretized variable coefficient Poisson operator is difficult using the conventional linear solvers as the size of the problem grows. We apply a novel hierarchical linear solve algorithm based on low-rank approximations. The proposed linear solver could be applied to variety of linear systems arising from discretized partial differential equations. It can be used as a standalone direct-solver with tunable accuracy and linear complexity, or as a high-accuracy pre-conditioner in conjunction with other iterative methods.

  6. A Survey of Solver-Related Geometry and Meshing Issues

    NASA Technical Reports Server (NTRS)

    Masters, James; Daniel, Derick; Gudenkauf, Jared; Hine, David; Sideroff, Chris

    2016-01-01

    There is a concern in the computational fluid dynamics community that mesh generation is a significant bottleneck in the CFD workflow. This is one of several papers that will help set the stage for a moderated panel discussion addressing this issue. Although certain general "rules of thumb" and a priori mesh metrics can be used to ensure that some base level of mesh quality is achieved, inadequate consideration is often given to the type of solver or particular flow regime on which the mesh will be utilized. This paper explores how an analyst may want to think differently about a mesh based on considerations such as if a flow is compressible vs. incompressible or hypersonic vs. subsonic or if the solver is node-centered vs. cell-centered. This paper is a high-level investigation intended to provide general insight into how considering the nature of the solver or flow when performing mesh generation has the potential to increase the accuracy and/or robustness of the solution and drive the mesh generation process to a state where it is no longer a hindrance to the analysis process.

  7. QED multi-dimensional vacuum polarization finite-difference solver

    NASA Astrophysics Data System (ADS)

    Carneiro, Pedro; Grismayer, Thomas; Silva, Luís; Fonseca, Ricardo

    2015-11-01

    The Extreme Light Infrastructure (ELI) is expected to deliver peak intensities of 1023 - 1024 W/cm2 allowing to probe nonlinear Quantum Electrodynamics (QED) phenomena in an unprecedented regime. Within the framework of QED, the second order process of photon-photon scattering leads to a set of extended Maxwell's equations [W. Heisenberg and H. Euler, Z. Physik 98, 714] effectively creating nonlinear polarization and magnetization terms that account for the nonlinear response of the vacuum. To model this in a self-consistent way, we present a multi dimensional generalized Maxwell equation finite difference solver with significantly enhanced dispersive properties, which was implemented in the OSIRIS particle-in-cell code [R.A. Fonseca et al. LNCS 2331, pp. 342-351, 2002]. We present a detailed numerical analysis of this electromagnetic solver. As an illustration of the properties of the solver, we explore several examples in extreme conditions. We confirm the theoretical prediction of vacuum birefringence of a pulse propagating in the presence of an intense static background field [arXiv:1301.4918 [quant-ph

  8. NITSOL: A Newton iterative solver for nonlinear systems

    SciTech Connect

    Pernice, M.; Walker, H.F.

    1996-12-31

    Newton iterative methods, also known as truncated Newton methods, are implementations of Newton`s method in which the linear systems that characterize Newton steps are solved approximately using iterative linear algebra methods. Here, we outline a well-developed Newton iterative algorithm together with a Fortran implementation called NITSOL. The basic algorithm is an inexact Newton method globalized by backtracking, in which each initial trial step is determined by applying an iterative linear solver until an inexact Newton criterion is satisfied. In the implementation, the user can specify inexact Newton criteria in several ways and select an iterative linear solver from among several popular {open_quotes}transpose-free{close_quotes} Krylov subspace methods. Jacobian-vector products used by the Krylov solver can be either evaluated analytically with a user-supplied routine or approximated using finite differences of function values. A flexible interface permits a wide variety of preconditioning strategies and allows the user to define a preconditioner and optionally update it periodically. We give details of these and other features and demonstrate the performance of the implementation on a representative set of test problems.

  9. The Method of Space-time Conservation Element and Solution Element: Development of a New Implicit Solver

    NASA Technical Reports Server (NTRS)

    Chang, S. C.; Wang, X. Y.; Chow, C. Y.; Himansu, A.

    1995-01-01

    The method of space-time conservation element and solution element is a nontraditional numerical method designed from a physicist's perspective, i.e., its development is based more on physics than numerics. It uses only the simplest approximation techniques and yet is capable of generating nearly perfect solutions for a 2-D shock reflection problem used by Helen Yee and others. In addition to providing an overall view of the new method, we introduce a new concept in the design of implicit schemes, and use it to construct a highly accurate solver for a convection-diffusion equation. It is shown that, in the inviscid case, this new scheme becomes explicit and its amplification factors are identical to those of the Leapfrog scheme. On the other hand, in the pure diffusion case, its principal amplification factor becomes the amplification factor of the Crank-Nicolson scheme.

  10. Nodal signaling in Xenopus gastrulae is cell-autonomous and patterned by beta-catenin.

    PubMed

    Hashimoto-Partyka, Minako K; Yuge, Masahiro; Cho, Ken W Y

    2003-01-01

    The classical three-signal model of amphibian mesoderm induction and more recent modifications together propose that an activin-like signaling activity is uniformly distributed across the vegetal half of the Xenopus blastula and that this activity contributes to mesoderm induction. In support of this, we have previously shown that the activin-response element (DE) of the goosecoid promoter is uniformly activated across the vegetal half of midgastrula-stage embryos. Here, we further examine the nature of this activity by measuring DE activation by endogenous signals over time. We find that the spatiotemporal pattern of DE activation is much more dynamic than was previously appreciated and also conclude that DE(6X)Luc activity reflects endogenous nodal signaling in the embryo. Using both the DE(6X)Luc construct and endogenous Xbra and Xgsc expression as read-outs for nodal activity, and the cleavage-mutant version of Xnr2 (CmXnr2) to regionally suppress endogenous nodal activity, we demonstrate that nodal signals act cell-autonomously in Xenopus gastrulae. Nodal-expressing cells are unable to rescue either reporter gene activation or target gene expression in distant nodal-deficient cells, suggesting that nodals function at short range in this context. Finally, we show that DE activation by endogenous signals occurs in the absence of dorsal beta-catenin-mediated signaling, but that the timing of dorsal initiation is altered. We conclude that nodal signals in Xenopus gastrulae function cell autonomously at short ranges and that the spatiotemporal pattern of this signaling along the dorsoventral axis is regulated by maternal Wnt-like signaling. PMID:12490202

  11. High Risk of Lateral Nodal Metastasis in Lateral Solitary Solid Papillary Thyroid Cancer.

    PubMed

    Lai, Xing-Jian; Zhang, Bo; Jiang, Yu-Xin; Li, Jian-Chu; Zhao, Rui-Na; Yang, Xiao; Zhang, Qing; Zhang, Xiao-Yan; Li, Wen-Bo; Zhu, Shen-Ling

    2016-01-01

    We explored the relationship between ultrasonic intra-thyroidal location and neck node metastasis pattern in solitary solid papillary thyroid cancer (PTC). Data on 186 patients were retrospectively reviewed. The association between several characteristics and neck node metastasis pattern were analyzed. Among the 186 thyroid nodules, age ≥45 y (p = 0.005), mass size ≥2 cm (p = 0.001), presence of calcifications (p < 0.001) and lateral nodal metastasis (p = 0.001) were significantly related to central nodal metastasis in multivariate analysis. Mass size ≥2 cm (p = 0.046) and central nodal metastasis (p = 0.002) were significantly related to lateral nodal metastasis in multivariate analysis. Location of an intra-thyroidal solitary solid PTC located non-adjacent to the trachea (lateral) was significantly related to lateral nodal metastasis (p = 0.043) compared with location of an intra-thyroidal solitary solid PTC adjacent to the trachea (medial or isthmus). Lateral lesions have a high risk of lateral nodal metastasis in solitary solid PTC.

  12. Solution and Study of the Two-Dimensional Nodal Neutron Transport Equation

    SciTech Connect

    Panta Pazos, Ruben; Biasotto Hauser, Eliete; Tullio de Vilhena, Marco

    2002-07-01

    In the last decade Vilhena and coworkers reported an analytical solution to the two-dimensional nodal discrete-ordinates approximations of the neutron transport equation in a convex domain. The key feature of these works was the application of the combined collocation method of the angular variable and nodal approach in the spatial variables. By nodal approach we mean the transverse integration of the SN equations. This procedure leads to a set of one-dimensional S{sub N} equations for the average angular fluxes in the variables x and y. These equations were solved by the old version of the LTS{sub N} method, which consists in the application of the Laplace transform to the set of nodal S{sub N} equations and solution of the resulting linear system by symbolic computation. It is important to recall that this procedure allow us to increase N the order of S{sub N} up to 16. To overcome this drawback we step forward performing a spectral painstaking analysis of the nodal S{sub N} equations for N up to 16 and we begin the convergence of the S{sub N} nodal equations defining an error for the angular flux and estimating the error in terms of the truncation error of the quadrature approximations of the integral term. Furthermore, we compare numerical results of this approach with those of other techniques used to solve the two-dimensional discrete approximations of the neutron transport equation. (authors)

  13. The Apelin receptor enhances Nodal/TGFβ signaling to ensure proper cardiac development

    PubMed Central

    Deshwar, Ashish R; Chng, Serene C; Ho, Lena; Reversade, Bruno; Scott, Ian C

    2016-01-01

    The Apelin receptor (Aplnr) is essential for heart development, controlling the early migration of cardiac progenitors. Here we demonstrate that in zebrafish Aplnr modulates Nodal/TGFβ signaling, a key pathway essential for mesendoderm induction and migration. Loss of Aplnr function leads to a reduction in Nodal target gene expression whereas activation of Aplnr by a non-peptide agonist increases the expression of these same targets. Furthermore, loss of Aplnr results in a delay in the expression of the cardiogenic transcription factors mespaa/ab. Elevating Nodal levels in aplnra/b morphant and double mutant embryos is sufficient to rescue cardiac differentiation defects. We demonstrate that loss of Aplnr attenuates the activity of a point source of Nodal ligands Squint and Cyclops in a non-cell autonomous manner. Our results favour a model in which Aplnr is required to fine-tune Nodal output, acting as a specific rheostat for the Nodal/TGFβ pathway during the earliest stages of cardiogenesis. DOI: http://dx.doi.org/10.7554/eLife.13758.001 PMID:27077952

  14. On the relationship between ODE solvers and iterative solvers for linear equations

    SciTech Connect

    Lorber, A.; Joubert, W.; Carey, G.F.

    1994-12-31

    The connection between the solution of linear systems of equations by both iterative methods and explicit time stepping techniques is investigated. Based on the similarities, a suite of Runge-Kutta time integration schemes with extended stability domains are developed using Chebyshev iteration polynomials. These Runge-Kutta schemes are applied to linear and non-linear systems arising from the numerical solution of PDE`s containing either physical or artificial transient terms. Specifically, the solutions of model linear convection and convection-diffusion equations are presented, as well as the solution of a representative non-linear Navier-Stokes fluid flow problem. Included are results of parallel computations.

  15. TGF-β promotes glioma cell growth via activating Nodal expression through Smad and ERK1/2 pathways

    SciTech Connect

    Sun, Jing; Liu, Su-zhi; Lin, Yan; Cao, Xiao-pan; Liu, Jia-ming

    2014-01-17

    Highlights: •TGF-β promoted Nodal expression in glioma cells. •TGF-β promoted Nodal expression via activating Smad and ERK1/2 pathways. •TGF-β promotes glioma cell growth via activating Nodal expression. -- Abstract: While there were certain studies focusing on the mechanism of TGF-β promoting the growth of glioma cells, the present work revealed another novel mechanism that TGF-β may promote glioma cell growth via enhancing Nodal expression. Our results showed that Nodal expression was significantly upregulated in glioma cells when TGF-β was added, whereas the TGF-β-induced Nodal expression was evidently inhibited by transfection Smad2 or Smad3 siRNAs, and the suppression was especially significant when the Smad3 was downregulated. Another, the attenuation of TGF-β-induced Nodal expression was observed with blockade of the ERK1/2 pathway also. Further detection of the proliferation, apoptosis, and invasion of glioma cells indicated that Nodal overexpression promoted the proliferation and invasion of tumor cells and inhibited their apoptosis, resembling the effect of TGF-β addition. Downregulation of Nodal expression via transfection Nodal-specific siRNA in the presence of TGF-β weakened the promoting effect of the latter on glioma cells growth, and transfecting Nodal siRNA alone in the absence of exogenous TGF-β more profoundly inhibited the growth of glioma cells. These results demonstrated that while both TGF-β and Nodal promoted glioma cells growth, the former might exert such effect by enhancing Nodal expression, which may form a new target for glioma therapy.

  16. Coexistent Types of Atrioventricular Nodal Re-Entrant Tachycardia

    PubMed Central

    Marine, Joseph E.; Latchamsetty, Rakesh; Zografos, Theodoros; Tanawuttiwat, Tanyanan; Sheldon, Seth H.; Buxton, Alfred E.; Calkins, Hugh; Morady, Fred; Josephson, Mark E.

    2015-01-01

    Background— There is evidence that atypical fast–slow and typical atrioventricular nodal re-entrant tachycardia (AVNRT) do not use the same limb for fast conduction, but no data exist on patients who have presented with both typical and atypical forms of this tachycardia. We compared conduction intervals during typical and atypical AVNRT that occurred in the same patient. Methods and Results— In 20 of 1299 patients with AVNRT, both typical and atypical AVNRT were induced at electrophysiology study by pacing maneuvers and autonomic stimulation or occurred spontaneously. The mean age of the patients was 47.6±10.9 years (range, 32–75 years), and 11 patients (55%) were women. Tachycardia cycle lengths were 368.0±43.1 and 365.8±41.1 ms, and earliest retrograde activation was recorded at the coronary sinus ostium in 60% and 65% of patients with typical and atypical AVNRT, respectively. Thirteen patients (65%) displayed atypical AVNRT with fast–slow characteristics. By comparing conduction intervals during slow–fast and fast–slow AVNRT in the same patient, fast pathway conduction times during the 2 types of AVNRT were calculated. The mean difference between retrograde fast pathway conduction during slow–fast AVNRT and anterograde fast pathway conduction during fast–slow AVNRT was 41.8±39.7 ms and was significantly different when compared with the estimated between-measurement error (P=0.0055). Conclusions— Our data provide further evidence that typical slow–fast and atypical fast–slow AVNRT use different anatomic pathways for fast conduction. PMID:26155802

  17. Cluster analysis of contaminated sediment data: nodal analysis.

    PubMed

    Hartwell, S Ian; Claflin, Larry W

    2005-07-01

    The objective of the present study was to explore the use of multivariate statistical methods as a means to discern relationships between contaminants and biological and/or toxicological effects in a representative data set from the National Status and Trends (NS&T) Program. Data from the National Oceanic and Atmospheric Administration, NS&T Program's Bioeffects Survey of Delaware Bay, USA, were examined using various univariate and multivariate statistical techniques, including cluster analysis. Each approach identified consistent patterns and relationships between the three types of triad data. The analyses also identified factors that bias the interpretation of the data, primarily the presence of rare and unique species and the dependence of species distributions on physical parameters. Sites and species were clustered with the unweighted pair-group method using arithmetic averages clustering with the Jaccard coefficient that clustered species and sites into mutually consistent groupings. Pearson product moment correlation coefficients, normalized for salinity, also were clustered. The most informative analysis, termed nodal analysis, was the intersection of species cluster analysis with site cluster analysis. This technique produced a visual representation of species association patterns among site clusters. Site characteristics, such as salinity and grain size, not contaminant concentrations, appeared to be the primary factors determining species distributions. This suggests the sediment-quality triad needs to use physical parameters as a distinct leg from chemical concentrations to improve sediment-quality assessments in large bodies of water. Because the Delaware Bay system has confounded gradients of contaminants and physical parameters, analyses were repeated with data from northern Chesapeake Bay, USA, with similar results. PMID:16050601

  18. Patterns of failure after the reduced volume approach for elective nodal irradiation in nasopharyngeal carcinoma

    PubMed Central

    Seol, Ki Ho

    2016-01-01

    Purpose To evaluate the patterns of nodal failure after radiotherapy (RT) with the reduced volume approach for elective neck nodal irradiation (ENI) in nasopharyngeal carcinoma (NPC). Materials and Methods Fifty-six NPC patients who underwent definitive chemoradiotherapy with the reduced volume approach for ENI were reviewed. The ENI included retropharyngeal and level II lymph nodes, and only encompassed the echelon inferior to the involved level to eliminate the entire neck irradiation. Patients received either moderate hypofractionated intensity-modulated RT for a total of 72.6 Gy (49.5 Gy to elective nodal areas) or a conventional fractionated three-dimensional conformal RT for a total of 68.4–72 Gy (39.6–45 Gy to elective nodal areas). Patterns of failure, locoregional control, and survival were analyzed. Results The median follow-up was 38 months (range, 3 to 80 months). The out-of-field nodal failure when omitting ENI was none. Three patients developed neck recurrences (one in-field recurrence in the 72.6 Gy irradiated nodal area and two in the elective irradiated region of 39.6 Gy). Overall disease failure at any site developed in 11 patients (19.6%). Among these, there were six local failures (10.7%), three regional failures (5.4%), and five distant metastases (8.9%). The 3-year locoregional control rate was 87.1%, and the distant failure-free rate was 90.4%; disease-free survival and overall survival at 3 years was 80% and 86.8%, respectively. Conclusion No patient developed nodal failure in the omitted ENI site. Our investigation has demonstrated that the reduced volume approach for ENI appears to be a safe treatment approach in NPC. PMID:27104162

  19. An extended HLLC Riemann solver for the magneto-hydrodynamics including strong internal magnetic field

    NASA Astrophysics Data System (ADS)

    Guo, Xiaocheng

    2015-06-01

    By revisiting the derivation of the previously developed HLLC Riemann solver for magneto-hydrodynamics (MHD), the paper presents an extended HLLC Riemann solver specifically designed for the MHD system in which the magnetic field can be decomposed into a strong internal magnetic field and an external component. The derived HLLC Riemann solver satisfies the conservation laws. The numerical tests show that the extended solver deals with the global MHD simulation of the Earth's magnetosphere well, and maintains high numerical resolution. It recovers the previously developed HLLC Riemann solver for the MHD as long as the internal field is set to zero. Thus, it is backward compatible with the previous HLLC solver, and suitable for the MHD simulations no matter whether a strong internal magnetic field is included or not.

  20. Application of Aeroelastic Solvers Based on Navier Stokes Equations

    NASA Technical Reports Server (NTRS)

    Keith, Theo G., Jr.; Srivastava, Rakesh

    2001-01-01

    The propulsion element of the NASA Advanced Subsonic Technology (AST) initiative is directed towards increasing the overall efficiency of current aircraft engines. This effort requires an increase in the efficiency of various components, such as fans, compressors, turbines etc. Improvement in engine efficiency can be accomplished through the use of lighter materials, larger diameter fans and/or higher-pressure ratio compressors. However, each of these has the potential to result in aeroelastic problems such as flutter or forced response. To address the aeroelastic problems, the Structural Dynamics Branch of NASA Glenn has been involved in the development of numerical capabilities for analyzing the aeroelastic stability characteristics and forced response of wide chord fans, multi-stage compressors and turbines. In order to design an engine to safely perform a set of desired tasks, accurate information of the stresses on the blade during the entire cycle of blade motion is required. This requirement in turn demands that accurate knowledge of steady and unsteady blade loading is available. To obtain the steady and unsteady aerodynamic forces for the complex flows around the engine components, for the flow regimes encountered by the rotor, an advanced compressible Navier-Stokes solver is required. A finite volume based Navier-Stokes solver has been developed at Mississippi State University (MSU) for solving the flow field around multistage rotors. The focus of the current research effort, under NASA Cooperative Agreement NCC3- 596 was on developing an aeroelastic analysis code (entitled TURBO-AE) based on the Navier-Stokes solver developed by MSU. The TURBO-AE code has been developed for flutter analysis of turbomachine components and delivered to NASA and its industry partners. The code has been verified. validated and is being applied by NASA Glenn and by aircraft engine manufacturers to analyze the aeroelastic stability characteristics of modem fans, compressors

  1. A New Robust Solver for Saturated-Unsaturated Richards' Equation

    NASA Astrophysics Data System (ADS)

    Barajas-Solano, D. A.; Tartakovsky, D. M.

    2012-12-01

    We present a novel approach for the numerical integration of the saturated-unsaturated Richards' equation, a degenerate parabolic partial differential equation that models flow in porous media. The method is based on the mixed (pore pressure-water content) form of RE, written as a set of differential algebraic equations (DAEs) of index-1 for the fully saturated case and index-2 for the partially saturated case. A DAE-based approach allows us to overcome the numerical challenges posed by the degenerate nature of the Richards' equation. The resulting set of DAEs is solved using the stiffly-accurate, single-step, 3-stage implicit Runge-Kutta method Radau IIA, chosen for its favorable accuracy and stability properties, and its ease of implementation. For each time step a nonlinear system of equations on the intermediate Runge-Kutta states of the pore pressure is solved, written so to ensure that the next step pore pressure and water content correspond to one another correctly. The implementation of our approach compares favorably to state-of-the-art DAE-based solvers in both one- and two-dimensional simulations. These solvers use multi-step backward difference formulas together with a pressure-based form of Richards' equation. To the best of our knowledge, our method is the first instance of a successful DAE-based solver that uses the mixed form of Richards' equation. We consider this a promising line of research, with future work to be done on the use of globally convergent methods for the solution of the occurring nonlinear systems of equations.

  2. A computationally efficient Multicomponent Equilibrium Solver for Aerosols (MESA)

    NASA Astrophysics Data System (ADS)

    Zaveri, Rahul A.; Easter, Richard C.; Peters, Leonard K.

    2005-12-01

    Development and application of a new Multicomponent Equilibrium Solver for Aerosols (MESA) is described for systems containing H+, NH4+, Na+, Ca2+, SO42-, HSO4-, NO3-, and Cl- ions. The equilibrium solution is obtained by integrating a set of pseudo-transient ordinary differential equations describing the precipitation and dissolution reactions for all the possible salts to steady state. A comprehensive temperature dependent mutual deliquescence relative humidity (MDRH) parameterization is developed for all the possible salt mixtures, thereby eliminating the need for a rigorous numerical solution when ambient RH is less than MDRH(T). The solver is unconditionally stable, mass conserving, and shows robust convergence. Performance of MESA was evaluated against the Web-based AIM Model III, which served as a benchmark for accuracy, and the EQUISOLV II solver for speed. Important differences in the convergence and thermodynamic errors in MESA and EQUISOLV II are discussed. The average ratios of speeds of MESA over EQUISOLV II ranged between 1.4 and 5.8, with minimum and maximum ratios of 0.6 and 17, respectively. Because MESA directly diagnoses MDRH, it is significantly more efficient when RH < MDRH. MESA's superior performance is partially due to its "hard-wired" code for the present system as opposed to EQUISOLV II, which has a more generalized structure for solving any number and type of reactions at temperatures down to 190 K. These considerations suggest that MESA is highly attractive for use in 3-D aerosol/air-quality models for lower tropospheric applications (T > 240 K) in which both accuracy and computational efficiency are critical.

  3. Diffusion MRI

    NASA Astrophysics Data System (ADS)

    Fukuyama, Hidenao

    Recent advances of magnetic resonance imaging have been described, especially stressed on the diffusion sequences. We have recently applied the diffusion sequence to functional brain imaging, and found the appropriate results. In addition to the neurosciences fields, diffusion weighted images have improved the accuracies of clinical diagnosis depending upon magnetic resonance images in stroke as well as inflammations.

  4. Reformulation of the Fourier-Bessel steady state mode solver

    NASA Astrophysics Data System (ADS)

    Gauthier, Robert C.

    2016-09-01

    The Fourier-Bessel resonator state mode solver is reformulated using Maxwell's field coupled curl equations. The matrix generating expressions are greatly simplified as well as a reduction in the number of pre-computed tables making the technique simpler to implement on a desktop computer. The reformulation maintains the theoretical equivalence of the permittivity and permeability and as such structures containing both electric and magnetic properties can be examined. Computation examples are presented for a surface nanoscale axial photonic resonator and hybrid { ε , μ } quasi-crystal resonator.

  5. Some fast elliptic solvers on parallel architectures and their complexities

    NASA Technical Reports Server (NTRS)

    Gallopoulos, E.; Saad, Y.

    1989-01-01

    The discretization of separable elliptic partial differential equations leads to linear systems with special block tridiagonal matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconstant coefficients. A method was recently proposed to parallelize and vectorize BCR. In this paper, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational compelxity lower than that of parallel BCR.

  6. Some fast elliptic solvers on parallel architectures and their complexities

    NASA Technical Reports Server (NTRS)

    Gallopoulos, E.; Saad, Youcef

    1989-01-01

    The discretization of separable elliptic partial differential equations leads to linear systems with special block triangular matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconsistant coefficients. A method was recently proposed to parallelize and vectorize BCR. Here, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches, including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational complexity lower than that of parallel BCR.

  7. Algorithms for parallel flow solvers on message passing architectures

    NASA Astrophysics Data System (ADS)

    Vanderwijngaart, Rob F.

    1995-01-01

    The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those

  8. Hierarchically parallelized constrained nonlinear solvers with automated substructuring

    NASA Technical Reports Server (NTRS)

    Padovan, J.; Kwang, A.

    1991-01-01

    This paper develops a parallelizable multilevel constrained nonlinear equation solver. The substructuring process is automated to yield appropriately balanced partitioning of each succeeding level. Due to the generality of the procedure, both sequential, partially and fully parallel environments can be handled. This includes both single and multiprocessor assignment per individual partition. Several benchmark examples are presented. These illustrate the robustness of the procedure as well as its capacity to yield significant reductions in memory utilization and calculational effort due both to updating and inversion.

  9. Hierarchically Parallelized Constrained Nonlinear Solvers with Automated Substructuring

    NASA Technical Reports Server (NTRS)

    Padovan, Joe; Kwang, Abel

    1994-01-01

    This paper develops a parallelizable multilevel multiple constrained nonlinear equation solver. The substructuring process is automated to yield appropriately balanced partitioning of each succeeding level. Due to the generality of the procedure,_sequential, as well as partially and fully parallel environments can be handled. This includes both single and multiprocessor assignment per individual partition. Several benchmark examples are presented. These illustrate the robustness of the procedure as well as its capability to yield significant reductions in memory utilization and calculational effort due both to updating and inversion.

  10. Advances in the hydrodynamics solver of CO5BOLD

    NASA Astrophysics Data System (ADS)

    Freytag, Bernd

    Many features of the Roe solver used in the hydrodynamics module of CO5BOLD have recently been added or overhauled, including the reconstruction methods (by adding the new second-order ``Frankenstein's method''), the treatment of transversal velocities, energy-flux averaging and entropy-wave treatment at small Mach numbers, the CTU scheme to combine the one-dimensional fluxes, and additional safety measures. All this results in a significantly better behavior at low Mach number flows, and an improved stability at larger Mach numbers requiring less (or no) additional tensor viscosity, which then leads to a noticeable increase in effective resolution.

  11. FDIPS: Finite Difference Iterative Potential-field Solver

    NASA Astrophysics Data System (ADS)

    Toth, Gabor; van der Holst, Bartholomeus; Huang, Zhenguang

    2016-06-01

    FDIPS is a finite difference iterative potential-field solver that can generate the 3D potential magnetic field solution based on a magnetogram. It is offered as an alternative to the spherical harmonics approach, as when the number of spherical harmonics is increased, using the raw magnetogram data given on a grid that is uniform in the sine of the latitude coordinate can result in inaccurate and unreliable results, especially in the polar regions close to the Sun. FDIPS is written in Fortran 90 and uses the MPI library for parallel execution.

  12. Object-Oriented Design for Sparse Direct Solvers

    NASA Technical Reports Server (NTRS)

    Dobrian, Florin; Kumfert, Gary; Pothen, Alex

    1999-01-01

    We discuss the object-oriented design of a software package for solving sparse, symmetric systems of equations (positive definite and indefinite) by direct methods. At the highest layers, we decouple data structure classes from algorithmic classes for flexibility. We describe the important structural and algorithmic classes in our design, and discuss the trade-offs we made for high performance. The kernels at the lower layers were optimized by hand. Our results show no performance loss from our object-oriented design, while providing flexibility, case of use, and extensibility over solvers using procedural design.

  13. Performance issues for iterative solvers in device simulation

    NASA Technical Reports Server (NTRS)

    Fan, Qing; Forsyth, P. A.; Mcmacken, J. R. F.; Tang, Wei-Pai

    1994-01-01

    Due to memory limitations, iterative methods have become the method of choice for large scale semiconductor device simulation. However, it is well known that these methods still suffer from reliability problems. The linear systems which appear in numerical simulation of semiconductor devices are notoriously ill-conditioned. In order to produce robust algorithms for practical problems, careful attention must be given to many implementation issues. This paper concentrates on strategies for developing robust preconditioners. In addition, effective data structures and convergence check issues are also discussed. These algorithms are compared with a standard direct sparse matrix solver on a variety of problems.

  14. Preconditioned CG-solvers and finite element grids

    SciTech Connect

    Bauer, R.; Selberherr, S.

    1994-12-31

    To extract parasitic capacitances in wiring structures of integrated circuits the authors developed the two- and three-dimensional finite element program SCAP (Smart Capacitance Analysis Program). The program computes the task of the electrostatic field from a solution of Poisson`s equation via finite elements and calculates the energies from which the capacitance matrix is extracted. The unknown potential vector, which has for three-dimensional applications 5000-50000 unknowns, is computed by a ICCG solver. Currently three- and six-node triangular, four- and ten-node tetrahedronal elements are supported.

  15. Novel accurate and scalable 3-D MT forward solver based on a contracting integral equation method

    NASA Astrophysics Data System (ADS)

    Kruglyakov, M.; Geraskin, A.; Kuvshinov, A.

    2016-11-01

    We present a novel, open source 3-D MT forward solver based on a method of integral equations (IE) with contracting kernel. Special attention in the solver is paid to accurate calculations of Green's functions and their integrals which are cornerstones of any IE solution. The solver supports massive parallelization and is able to deal with highly detailed and contrasting models. We report results of a 3-D numerical experiment aimed at analyzing the accuracy and scalability of the code.

  16. Converting Multi-Shell and Diffusion Spectrum Imaging to High Angular Resolution Diffusion Imaging.

    PubMed

    Yeh, Fang-Cheng; Verstynen, Timothy D

    2016-01-01

    Multi-shell and diffusion spectrum imaging (DSI) are becoming increasingly popular methods of acquiring diffusion MRI data in a research context. However, single-shell acquisitions, such as diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI), still remain the most common acquisition schemes in practice. Here we tested whether multi-shell and DSI data have conversion flexibility to be interpolated into corresponding HARDI data. We acquired multi-shell and DSI data on both a phantom and in vivo human tissue and converted them to HARDI. The correlation and difference between their diffusion signals, anisotropy values, diffusivity measurements, fiber orientations, connectivity matrices, and network measures were examined. Our analysis result showed that the diffusion signals, anisotropy, diffusivity, and connectivity matrix of the HARDI converted from multi-shell and DSI were highly correlated with those of the HARDI acquired on the MR scanner, with correlation coefficients around 0.8~0.9. The average angular error between converted and original HARDI was 20.7° at voxels with signal-to-noise ratios greater than 5. The network topology measures had less than 2% difference, whereas the average nodal measures had a percentage difference around 4~7%. In general, multi-shell and DSI acquisitions can be converted to their corresponding single-shell HARDI with high fidelity. This supports multi-shell and DSI acquisitions over HARDI acquisition as the scheme of choice for diffusion acquisitions.

  17. Converting Multi-Shell and Diffusion Spectrum Imaging to High Angular Resolution Diffusion Imaging

    PubMed Central

    Yeh, Fang-Cheng; Verstynen, Timothy D.

    2016-01-01

    Multi-shell and diffusion spectrum imaging (DSI) are becoming increasingly popular methods of acquiring diffusion MRI data in a research context. However, single-shell acquisitions, such as diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI), still remain the most common acquisition schemes in practice. Here we tested whether multi-shell and DSI data have conversion flexibility to be interpolated into corresponding HARDI data. We acquired multi-shell and DSI data on both a phantom and in vivo human tissue and converted them to HARDI. The correlation and difference between their diffusion signals, anisotropy values, diffusivity measurements, fiber orientations, connectivity matrices, and network measures were examined. Our analysis result showed that the diffusion signals, anisotropy, diffusivity, and connectivity matrix of the HARDI converted from multi-shell and DSI were highly correlated with those of the HARDI acquired on the MR scanner, with correlation coefficients around 0.8~0.9. The average angular error between converted and original HARDI was 20.7° at voxels with signal-to-noise ratios greater than 5. The network topology measures had less than 2% difference, whereas the average nodal measures had a percentage difference around 4~7%. In general, multi-shell and DSI acquisitions can be converted to their corresponding single-shell HARDI with high fidelity. This supports multi-shell and DSI acquisitions over HARDI acquisition as the scheme of choice for diffusion acquisitions. PMID:27683539

  18. Converting Multi-Shell and Diffusion Spectrum Imaging to High Angular Resolution Diffusion Imaging.

    PubMed

    Yeh, Fang-Cheng; Verstynen, Timothy D

    2016-01-01

    Multi-shell and diffusion spectrum imaging (DSI) are becoming increasingly popular methods of acquiring diffusion MRI data in a research context. However, single-shell acquisitions, such as diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI), still remain the most common acquisition schemes in practice. Here we tested whether multi-shell and DSI data have conversion flexibility to be interpolated into corresponding HARDI data. We acquired multi-shell and DSI data on both a phantom and in vivo human tissue and converted them to HARDI. The correlation and difference between their diffusion signals, anisotropy values, diffusivity measurements, fiber orientations, connectivity matrices, and network measures were examined. Our analysis result showed that the diffusion signals, anisotropy, diffusivity, and connectivity matrix of the HARDI converted from multi-shell and DSI were highly correlated with those of the HARDI acquired on the MR scanner, with correlation coefficients around 0.8~0.9. The average angular error between converted and original HARDI was 20.7° at voxels with signal-to-noise ratios greater than 5. The network topology measures had less than 2% difference, whereas the average nodal measures had a percentage difference around 4~7%. In general, multi-shell and DSI acquisitions can be converted to their corresponding single-shell HARDI with high fidelity. This supports multi-shell and DSI acquisitions over HARDI acquisition as the scheme of choice for diffusion acquisitions. PMID:27683539

  19. Converting Multi-Shell and Diffusion Spectrum Imaging to High Angular Resolution Diffusion Imaging

    PubMed Central

    Yeh, Fang-Cheng; Verstynen, Timothy D.

    2016-01-01

    Multi-shell and diffusion spectrum imaging (DSI) are becoming increasingly popular methods of acquiring diffusion MRI data in a research context. However, single-shell acquisitions, such as diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI), still remain the most common acquisition schemes in practice. Here we tested whether multi-shell and DSI data have conversion flexibility to be interpolated into corresponding HARDI data. We acquired multi-shell and DSI data on both a phantom and in vivo human tissue and converted them to HARDI. The correlation and difference between their diffusion signals, anisotropy values, diffusivity measurements, fiber orientations, connectivity matrices, and network measures were examined. Our analysis result showed that the diffusion signals, anisotropy, diffusivity, and connectivity matrix of the HARDI converted from multi-shell and DSI were highly correlated with those of the HARDI acquired on the MR scanner, with correlation coefficients around 0.8~0.9. The average angular error between converted and original HARDI was 20.7° at voxels with signal-to-noise ratios greater than 5. The network topology measures had less than 2% difference, whereas the average nodal measures had a percentage difference around 4~7%. In general, multi-shell and DSI acquisitions can be converted to their corresponding single-shell HARDI with high fidelity. This supports multi-shell and DSI acquisitions over HARDI acquisition as the scheme of choice for diffusion acquisitions.

  20. Multiply scaled constrained nonlinear equation solvers. [for nonlinear heat conduction problems

    NASA Technical Reports Server (NTRS)

    Padovan, Joe; Krishna, Lala

    1986-01-01

    To improve the numerical stability of nonlinear equation solvers, a partitioned multiply scaled constraint scheme is developed. This scheme enables hierarchical levels of control for nonlinear equation solvers. To complement the procedure, partitioned convergence checks are established along with self-adaptive partitioning schemes. Overall, such procedures greatly enhance the numerical stability of the original solvers. To demonstrate and motivate the development of the scheme, the problem of nonlinear heat conduction is considered. In this context the main emphasis is given to successive substitution-type schemes. To verify the improved numerical characteristics associated with partitioned multiply scaled solvers, results are presented for several benchmark examples.

  1. A GPU-accelerated flow solver for incompressible two-phase fluid flows

    NASA Astrophysics Data System (ADS)

    Codyer, Stephen; Raessi, Mehdi; Khanna, Gaurav

    2011-11-01

    We present a numerical solver for incompressible, immiscible, two-phase fluid flows that is accelerated by using Graphics Processing Units (GPUs). The Navier-Stokes equations are solved by the projection method, which involves solving a pressure Poisson problem at each time step. A second-order discretization of the Poisson problem leads to a sparse matrix with five and seven diagonals for two- and three-dimensional simulations, respectively. Running a serial linear algebra solver on a single CPU can take 50-99.9% of the total simulation time to solve the above system for pressure. To remove this bottleneck, we utilized the large parallelization capabilities of GPUs; we developed a linear algebra solver based on the conjugate gradient iterative method (CGIM) by using CUDA 4.0 libraries and compared its performance with CUSP, an open-source, GPU library for linear algebra. Compared to running the CGIM solver on a single CPU core, for a 2D case, our GPU solver yields speedups of up to 88x in solver time and 81x overall time on a single GPU card. In 3D cases, the speedups are up to 81x (solver) and 15x (overall). Speedup is faster at higher grid resolutions and our GPU solver outperforms CUSP. Current work examines the acceleration versus a parallel CGIM CPU solver.

  2. Topological nodal-line fermions in spin-orbit metal PbTaSe2.

    PubMed

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; Xu, Su-Yang; Zheng, Hao; Neupert, Titus; Chiu, Ching-Kai; Huang, Shin-Ming; Chang, Guoqing; Belopolski, Ilya; Sanchez, Daniel S; Neupane, Madhab; Alidoust, Nasser; Liu, Chang; Wang, BaoKai; Lee, Chi-Cheng; Jeng, Horng-Tay; Zhang, Chenglong; Yuan, Zhujun; Jia, Shuang; Bansil, Arun; Chou, Fangcheng; Lin, Hsin; Hasan, M Zahid

    2016-02-02

    Topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterized by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems.

  3. Recognizing nodal marginal zone lymphoma: recent advances and pitfalls. A systematic review

    PubMed Central

    van den Brand, Michiel; van Krieken, J. Han J.M.

    2013-01-01

    The diagnosis of nodal marginal zone lymphoma is one of the remaining problem areas in hematopathology. Because no established positive markers exist for this lymphoma, it is frequently a diagnosis of exclusion, making distinction from other low-grade B-cell lymphomas difficult or even impossible. This systematic review summarizes and discusses the current knowledge on nodal marginal zone lymphoma, including clinical features, epidemiology and etiology, histology, and cytogenetic and molecular features. In particular, recent advances in diagnostics and pathogenesis are discussed. New immunohistochemical markers have become available that could be used as positive markers for nodal marginal zone lymphoma. These markers could be used to ensure more homogeneous study groups in future research. Also, recent gene expression studies and studies describing specific gene mutations have provided clues to the pathogenesis of nodal marginal zone lymphoma, suggesting deregulation of the nuclear factor kappa B pathway. Nevertheless, nodal marginal zone lymphoma remains an enigmatic entity, requiring further study to define its pathogenesis to allow an accurate diagnosis and tailored treatment. However, recent data indicate that it is not related to splenic or extranodal lymphoma, and that it is also not related to lymphoplasmacytic lymphoma. Thus, even though the diagnosis is not always easy, it is clearly a separate entity. PMID:23813646

  4. Topological nodal-line fermions in spin-orbit metal PbTaSe2

    DOE PAGES

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; Xu, Su-Yang; Zheng, Hao; Neupert, Titus; Chiu, Ching-Kai; Huang, Shin-Ming; Chang, Guoqing; Belopolski, Ilya; et al

    2016-02-02

    Here we discuss how topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterizedmore » by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems.« less

  5. Topological nodal-line fermions in spin-orbit metal PbTaSe2.

    PubMed

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; Xu, Su-Yang; Zheng, Hao; Neupert, Titus; Chiu, Ching-Kai; Huang, Shin-Ming; Chang, Guoqing; Belopolski, Ilya; Sanchez, Daniel S; Neupane, Madhab; Alidoust, Nasser; Liu, Chang; Wang, BaoKai; Lee, Chi-Cheng; Jeng, Horng-Tay; Zhang, Chenglong; Yuan, Zhujun; Jia, Shuang; Bansil, Arun; Chou, Fangcheng; Lin, Hsin; Hasan, M Zahid

    2016-01-01

    Topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterized by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems. PMID:26829889

  6. Topological nodal-line fermions in spin-orbit metal PbTaSe2

    NASA Astrophysics Data System (ADS)

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; Xu, Su-Yang; Zheng, Hao; Neupert, Titus; Chiu, Ching-Kai; Huang, Shin-Ming; Chang, Guoqing; Belopolski, Ilya; Sanchez, Daniel S.; Neupane, Madhab; Alidoust, Nasser; Liu, Chang; Wang, Baokai; Lee, Chi-Cheng; Jeng, Horng-Tay; Zhang, Chenglong; Yuan, Zhujun; Jia, Shuang; Bansil, Arun; Chou, Fangcheng; Lin, Hsin; Hasan, M. Zahid

    2016-02-01

    Topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterized by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems.

  7. Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance.

    PubMed

    Tanaka, Mina; Takei, Kentaro; Kojima, Mikiko; Sakakibara, Hitoshi; Mori, Hitoshi

    2006-03-01

    In intact plants, the shoot apex grows predominantly and inhibits outgrowth of axillary buds. After decapitation of the shoot apex, outgrowth of axillary buds begins. This phenomenon is called an apical dominance. Although the involvement of auxin, which represses outgrowth of axillary buds, and cytokinin (CK), which promotes outgrowth of axillary buds, has been proposed, little is known about the underlying molecular mechanisms. In the present study, we demonstrated that auxin negatively regulates local CK biosynthesis in the nodal stem by controlling the expression level of the pea (Pisum sativum L.) gene adenosine phosphate-isopentenyltransferase (PsIPT), which encodes a key enzyme in CK biosynthesis. Before decapitation, PsIPT1 and PsIPT2 transcripts were undetectable; after decapitation, they were markedly induced in the nodal stem along with accumulation of CK. Expression of PsIPT was repressed by the application of indole-3-acetic acid (IAA). In excised nodal stem, PsIPT expression and CK levels also increased under IAA-free conditions. Furthermore, beta-glucuronidase expression, under the control of the PsIPT2 promoter region in transgenic Arabidopsis, was repressed by an IAA. Our results indicate that in apical dominance one role of auxin is to repress local biosynthesis of CK in the nodal stem and that, after decapitation, CKs, which are thought to be derived from the roots, are locally biosynthesized in the nodal stem rather than in the roots. PMID:16507092

  8. Temporal and spatial requirements for Nodal-induced anterior mesendoderm and mesoderm in anterior neurulation.

    PubMed

    Gonsar, Ngawang; Coughlin, Alicia; Clay-Wright, Jessica A; Borg, Bethanie R; Kindt, Lexy M; Liang, Jennifer O

    2016-01-01

    Zebrafish with defective Nodal signaling have a phenotype analogous to the fatal human birth defect anencephaly, which is caused by an open anterior neural tube. Previous work in our laboratory found that anterior open neural tube phenotypes in Nodal signaling mutants were caused by lack of mesendodermal/mesodermal tissues. Defects in these mutants are already apparent at neural plate stage, before the neuroepithelium starts to fold into a tube. Consistent with this, we found that the requirement for Nodal signaling maps to mid-late blastula stages. This timing correlates with the timing of prechordal plate mesendoderm and anterior mesoderm induction, suggesting these tissues act to promote neurulation. To further identify tissues important for neurulation, we took advantage of the variable phenotypes in Nodal signaling-deficient sqt mutant and Lefty1-overexpressing embryos. Statistical analysis indicated a strong, positive correlation between a closed neural tube and presence of several mesendoderm/mesoderm-derived tissues (hatching glands, cephalic paraxial mesoderm, notochord, and head muscles). However, the neural tube was closed in a subset of embryos that lacked any one of these tissues. This suggests that several types of Nodal-induced mesendodermal/mesodermal precursors are competent to promote neurulation. PMID:26528772

  9. Topological nodal-line fermions in spin-orbit metal PbTaSe2

    PubMed Central

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; Xu, Su-Yang; Zheng, Hao; Neupert, Titus; Chiu, Ching-Kai; Huang, Shin-Ming; Chang, Guoqing; Belopolski, Ilya; Sanchez, Daniel S.; Neupane, Madhab; Alidoust, Nasser; Liu, Chang; Wang, BaoKai; Lee, Chi-Cheng; Jeng, Horng-Tay; Zhang, Chenglong; Yuan, Zhujun; Jia, Shuang; Bansil, Arun; Chou, Fangcheng; Lin, Hsin; Hasan, M. Zahid

    2016-01-01

    Topological semimetals can support one-dimensional Fermi lines or zero-dimensional Weyl points in momentum space, where the valence and conduction bands touch. While the degeneracy points in Weyl semimetals are robust against any perturbation that preserves translational symmetry, nodal lines require protection by additional crystalline symmetries such as mirror reflection. Here we report, based on a systematic theoretical study and a detailed experimental characterization, the existence of topological nodal-line states in the non-centrosymmetric compound PbTaSe2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe2 are not only protected by the reflection symmetry but also characterized by an integer topological invariant. Our detailed angle-resolved photoemission measurements, first-principles simulations and theoretical topological analysis illustrate the physical mechanism underlying the formation of the topological nodal-line states and associated surface states for the first time, thus paving the way towards exploring the exotic properties of the topological nodal-line fermions in condensed matter systems. PMID:26829889

  10. Temporal and spatial requirements for Nodal-induced anterior mesendoderm and mesoderm in anterior neurulation.

    PubMed

    Gonsar, Ngawang; Coughlin, Alicia; Clay-Wright, Jessica A; Borg, Bethanie R; Kindt, Lexy M; Liang, Jennifer O

    2016-01-01

    Zebrafish with defective Nodal signaling have a phenotype analogous to the fatal human birth defect anencephaly, which is caused by an open anterior neural tube. Previous work in our laboratory found that anterior open neural tube phenotypes in Nodal signaling mutants were caused by lack of mesendodermal/mesodermal tissues. Defects in these mutants are already apparent at neural plate stage, before the neuroepithelium starts to fold into a tube. Consistent with this, we found that the requirement for Nodal signaling maps to mid-late blastula stages. This timing correlates with the timing of prechordal plate mesendoderm and anterior mesoderm induction, suggesting these tissues act to promote neurulation. To further identify tissues important for neurulation, we took advantage of the variable phenotypes in Nodal signaling-deficient sqt mutant and Lefty1-overexpressing embryos. Statistical analysis indicated a strong, positive correlation between a closed neural tube and presence of several mesendoderm/mesoderm-derived tissues (hatching glands, cephalic paraxial mesoderm, notochord, and head muscles). However, the neural tube was closed in a subset of embryos that lacked any one of these tissues. This suggests that several types of Nodal-induced mesendodermal/mesodermal precursors are competent to promote neurulation.

  11. Entrainment mapping in patients with sustained atrioventricular nodal reentrant tachycardia: insights into the sites of conduction slowing in the slow atrioventricular nodal pathway.

    PubMed

    Haines, D E; Nath, S; DiMarco, J P; Lobban, J H

    1997-10-01

    The inferoposterior region of the triangle of Koch is hypothesized to be the location of the atrial insertion of the slow atrioventricular (AV) nodal pathway. However, the actual site of conduction slowing in the slow AV nodal pathway is unknown. Entrainment mapping during AV nodal reentry can localize the reentrant pathway as follows: the AH interval measured from the mapping catheter = A'H (where A' is the exit site of the reentrant circuit) minus A'A (the conduction time from A' to the site of mapping); the SH interval during entrainment = SA' (the conduction time from stimulus into the reentry circuit) plus A'H. Thus, in all cases, the SH interval should be greater than or equal to the AH interval, and the deltaAH-SH should increase as distance and conduction time (SA' and A'A) from the reentry circuit increases. Fourteen patients with typical AV nodal reentry (cycle length 346 +/- 62 ms) and 1 with fast-slow (cycle length 430 ms) underwent activation and entrainment mapping from 8 to 12 sites in the triangle of Koch and coronary sinus. Pacing was performed at 2 to 3 mA above threshold, at a cycle length 10 ms shorter than tachycardia. A mapping site was defined as being in close proximity to the circuit if the deltaAH-SH was within 120% of the shortest 20th percentile deltaAH-SH value from all measured sites. In the 14 typical cases, 45 of 83 sites (54%) in the anatomic slow pathway region fulfilled criteria for close proximity to the reentry circuit compared with 13 of 50 sites (26%) outside of this region (p = 0.005). For these patients, the shortest SH interval measured from any entrainment site was 294 +/- 58 ms (89 +/- 10% of tachycardia cycle length, range 70% to 119%), indicating that the site of slow conduction in the slow pathway during AV nodal reentrant tachycardia was distal to all mapped sites. Thus, during typical AV nodal reentry, the "slow" pathway does not conduct slowly, and its insertion is located at or within the inferoposterior or

  12. Riemann solvers and Alfven waves in black hole magnetospheres

    NASA Astrophysics Data System (ADS)

    Punsly, Brian; Balsara, Dinshaw; Kim, Jinho; Garain, Sudip

    2016-09-01

    In the magnetosphere of a rotating black hole, an inner Alfven critical surface (IACS) must be crossed by inflowing plasma. Inside the IACS, Alfven waves are inward directed toward the black hole. The majority of the proper volume of the active region of spacetime (the ergosphere) is inside of the IACS. The charge and the totally transverse momentum flux (the momentum flux transverse to both the wave normal and the unperturbed magnetic field) are both determined exclusively by the Alfven polarization. Thus, it is important for numerical simulations of black hole magnetospheres to minimize the dissipation of Alfven waves. Elements of the dissipated wave emerge in adjacent cells regardless of the IACS, there is no mechanism to prevent Alfvenic information from crossing outward. Thus, numerical dissipation can affect how simulated magnetospheres attain the substantial Goldreich-Julian charge density associated with the rotating magnetic field. In order to help minimize dissipation of Alfven waves in relativistic numerical simulations we have formulated a one-dimensional Riemann solver, called HLLI, which incorporates the Alfven discontinuity and the contact discontinuity. We have also formulated a multidimensional Riemann solver, called MuSIC, that enables low dissipation propagation of Alfven waves in multiple dimensions. The importance of higher order schemes in lowering the numerical dissipation of Alfven waves is also catalogued.

  13. A massively parallel fractional step solver for incompressible flows

    SciTech Connect

    Houzeaux, G. Vazquez, M. Aubry, R. Cela, J.M.

    2009-09-20

    This paper presents a parallel implementation of fractional solvers for the incompressible Navier-Stokes equations using an algebraic approach. Under this framework, predictor-corrector and incremental projection schemes are seen as sub-classes of the same class, making apparent its differences and similarities. An additional advantage of this approach is to set a common basis for a parallelization strategy, which can be extended to other split techniques or to compressible flows. The predictor-corrector scheme consists in solving the momentum equation and a modified 'continuity' equation (namely a simple iteration for the pressure Schur complement) consecutively in order to converge to the monolithic solution, thus avoiding fractional errors. On the other hand, the incremental projection scheme solves only one iteration of the predictor-corrector per time step and adds a correction equation to fulfill the mass conservation. As shown in the paper, these two schemes are very well suited for massively parallel implementation. In fact, when compared with monolithic schemes, simpler solvers and preconditioners can be used to solve the non-symmetric momentum equations (GMRES, Bi-CGSTAB) and to solve the symmetric continuity equation (CG, Deflated CG). This gives good speedup properties of the algorithm. The implementation of the mesh partitioning technique is presented, as well as the parallel performances and speedups for thousands of processors.

  14. Using computer algebra and SMT solvers in algebraic biology

    NASA Astrophysics Data System (ADS)

    Pineda Osorio, Mateo

    2014-05-01

    Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3's great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.

  15. Matrix decomposition graphics processing unit solver for Poisson image editing

    NASA Astrophysics Data System (ADS)

    Lei, Zhao; Wei, Li

    2012-10-01

    In recent years, gradient-domain methods have been widely discussed in the image processing field, including seamless cloning and image stitching. These algorithms are commonly carried out by solving a large sparse linear system: the Poisson equation. However, solving the Poisson equation is a computational and memory intensive task which makes it not suitable for real-time image editing. A new matrix decomposition graphics processing unit (GPU) solver (MDGS) is proposed to settle the problem. A matrix decomposition method is used to distribute the work among GPU threads, so that MDGS will take full advantage of the computing power of current GPUs. Additionally, MDGS is a hybrid solver (combines both the direct and iterative techniques) and has two-level architecture. These enable MDGS to generate identical solutions with those of the common Poisson methods and achieve high convergence rate in most cases. This approach is advantageous in terms of parallelizability, enabling real-time image processing, low memory-taken and extensive applications.

  16. Agglomeration Multigrid for an Unstructured-Grid Flow Solver

    NASA Technical Reports Server (NTRS)

    Frink, Neal; Pandya, Mohagna J.

    2004-01-01

    An agglomeration multigrid scheme has been implemented into the sequential version of the NASA code USM3Dns, tetrahedral cell-centered finite volume Euler/Navier-Stokes flow solver. Efficiency and robustness of the multigrid-enhanced flow solver have been assessed for three configurations assuming an inviscid flow and one configuration assuming a viscous fully turbulent flow. The inviscid studies include a transonic flow over the ONERA M6 wing and a generic business jet with flow-through nacelles and a low subsonic flow over a high-lift trapezoidal wing. The viscous case includes a fully turbulent flow over the RAE 2822 rectangular wing. The multigrid solutions converged with 12%-33% of the Central Processing Unit (CPU) time required by the solutions obtained without multigrid. For all of the inviscid cases, multigrid in conjunction with an explicit time-stepping scheme performed the best with regard to the run time memory and CPU time requirements. However, for the viscous case multigrid had to be used with an implicit backward Euler time-stepping scheme that increased the run time memory requirement by 22% as compared to the run made without multigrid.

  17. An efficient chemical kinetics solver using high dimensional model representation

    SciTech Connect

    Shorter, J.A.; Ip, P.C.; Rabitz, H.A.

    1999-09-09

    A high dimensional model representation (HDMR) technique is introduced to capture the input-output behavior of chemical kinetic models. The HDMR expresses the output chemical species concentrations as a rapidly convergent hierarchical correlated function expansion in the input variables. In this paper, the input variables are taken as the species concentrations at time t{sub i} and the output is the concentrations at time t{sub i} + {delta}, where {delta} can be much larger than conventional integration time steps. A specially designed set of model runs is performed to determine the correlated functions making up the HDMR. The resultant HDMR can be used to (1) identify the key input variables acting independently or cooperatively on the output, and (2) create a high speed fully equivalent operational model (FEOM) serving to replace the original kinetic model and its differential equation solver. A demonstration of the HDMR technique is presented for stratospheric chemical kinetics. The FEOM proved to give accurate and stable chemical concentrations out to long times of many years. In addition, the FEOM was found to be orders of magnitude faster than a conventional stiff equation solver. This computational acceleration should have significance in many chemical kinetic applications.

  18. User documentation for PVODE, an ODE solver for parallel computers

    SciTech Connect

    Hindmarsh, A.C., LLNL

    1998-05-01

    PVODE is a general purpose ordinary differential equation (ODE) solver for stiff and nonstiff ODES It is based on CVODE [5] [6], which is written in ANSI- standard C PVODE uses MPI (Message-Passing Interface) [8] and a revised version of the vector module in CVODE to achieve parallelism and portability PVODE is intended for the SPMD (Single Program Multiple Data) environment with distributed memory, in which all vectors are identically distributed across processors In particular, the vector module is designed to help the user assign a contiguous segment of a given vector to each of the processors for parallel computation The idea is for each processor to solve a certain fixed subset of the ODES To better understand PVODE, we first need to understand CVODE and its historical background The ODE solver CVODE, which was written by Cohen and Hindmarsh, combines features of two earlier Fortran codes, VODE [l] and VODPK [3] Those two codes were written by Brown, Byrne, and Hindmarsh. Both use variable-coefficient multi-step integration methods, and address both stiff and nonstiff systems (Stiffness is defined as the presence of one or more very small damping time constants ) VODE uses direct linear algebraic techniques to solve the underlying banded or dense linear systems of equations in conjunction with a modified Newton method in the stiff ODE case On the other hand, VODPK uses a preconditioned Krylov iterative method [2] to solve the underlying linear system User-supplied preconditioners directly address the dominant source of stiffness Consequently, CVODE implements both the direct and iterative methods Currently, with regard to the nonlinear and linear system solution, PVODE has three method options available. functional iteration, Newton iteration with a diagonal approximate Jacobian, and Newton iteration with the iterative method SPGMR (Scaled Preconditioned Generalized Minimal Residual method) Both CVODE and PVODE are written in such a way that other linear

  19. Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling

    PubMed Central

    Kenyon, Emma J.; Campos, Isabel; Bull, James C.; Williams, P. Huw; Stemple, Derek L.; Clark, Matthew D.

    2015-01-01

    The RAB5 gene family is the best characterised of all human RAB families and is essential for in vitro homotypic fusion of early endosomes. In recent years, the disruption or activation of Rab5 family proteins has been used as a tool to understand growth factor signal transduction in whole animal systems such as Drosophila melanogaster and zebrafish. In this study we have examined the functions for four rab5 genes in zebrafish. Disruption of rab5ab expression by antisense morpholino oligonucleotide (MO) knockdown abolishes nodal signalling in early zebrafish embryos, whereas overexpression of rab5ab mRNA leads to ectopic expression of markers that are normally downstream of nodal signalling. By contrast MO disruption of other zebrafish rab5 genes shows little or no effect on expression of markers of dorsal organiser development. We conclude that rab5ab is essential for nodal signalling and organizer specification in the developing zebrafish embryo. PMID:25478908

  20. Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling.

    PubMed

    Kenyon, Emma J; Campos, Isabel; Bull, James C; Williams, P Huw; Stemple, Derek L; Clark, Matthew D

    2015-01-15

    The RAB5 gene family is the best characterised of all human RAB families and is essential for in vitro homotypic fusion of early endosomes. In recent years, the disruption or activation of Rab5 family proteins has been used as a tool to understand growth factor signal transduction in whole animal systems such as Drosophila melanogaster and zebrafish. In this study we have examined the functions for four rab5 genes in zebrafish. Disruption of rab5ab expression by antisense morpholino oligonucleotide (MO) knockdown abolishes nodal signalling in early zebrafish embryos, whereas overexpression of rab5ab mRNA leads to ectopic expression of markers that are normally downstream of nodal signalling. By contrast MO disruption of other zebrafish rab5 genes shows little or no effect on expression of markers of dorsal organiser development. We conclude that rab5ab is essential for nodal signalling and organizer specification in the developing zebrafish embryo.

  1. Molecular organization of the nodal region is not altered in spontaneously diabetic BB-Wistar rats.

    PubMed

    Brown, A A; Xu, T; Arroyo, E J; Levinson, S R; Brophy, P J; Peles, E; Scherer, S S

    2001-07-15

    We examined the organization of the molecular components of the nodal region in spontaneously diabetic BB-Wistar rats. Frozen sections and teased fibers from the sciatic nerves were immunostained for nodal (voltage-gated Na(+) channels, ankyrin(G), and ezrin), paranodal (contactin, Caspr, and neurofascin 155 kDa), and juxtaparanodal (Caspr2, the Shaker-type K(+) channels Kv1.1 and Kv1.2, and their associated subunit Kvbeta2) proteins. All of these proteins were properly localized in myelinated fibers from rats that had been diabetic for 15-44 days, compared to age-matched, nondiabetic animals. These results demonstrate that the axonal membrane is not reorganized, so nodal reorganization is not likely to be the cause of nerve conduction slowing in this animal model of acute diabetes. PMID:11438983

  2. Activin/Nodal signalling before implantation: setting the stage for embryo patterning

    PubMed Central

    Papanayotou, Costis; Collignon, Jérôme

    2014-01-01

    Activins and Nodal are members of the transforming growth factor beta (TGF-β) family of growth factors. Their Smad2/3-dependent signalling pathway is well known for its implication in the patterning of the embryo after implantation. Although this pathway is active early on at preimplantation stages, embryonic phenotypes for loss-of-function mutations of prominent components of the pathway are not detected before implantation. It is only fairly recently that an understanding of the role of the Activin/Nodal signalling pathway at these stages has started to emerge, notably from studies detailing how it controls the expression of target genes in embryonic stem cells. We review here what is currently known of the TGF-β-related ligands that determine the activity of Activin/Nodal signalling at preimplantation stages, and recent advances in the elucidation of the Smad2/3-dependent mechanisms underlying developmental progression. PMID:25349448

  3. Activin/Nodal signalling before implantation: setting the stage for embryo patterning.

    PubMed

    Papanayotou, Costis; Collignon, Jérôme

    2014-12-01

    Activins and Nodal are members of the transforming growth factor beta (TGF-β) family of growth factors. Their Smad2/3-dependent signalling pathway is well known for its implication in the patterning of the embryo after implantation. Although this pathway is active early on at preimplantation stages, embryonic phenotypes for loss-of-function mutations of prominent components of the pathway are not detected before implantation. It is only fairly recently that an understanding of the role of the Activin/Nodal signalling pathway at these stages has started to emerge, notably from studies detailing how it controls the expression of target genes in embryonic stem cells. We review here what is currently known of the TGF-β-related ligands that determine the activity of Activin/Nodal signalling at preimplantation stages, and recent advances in the elucidation of the Smad2/3-dependent mechanisms underlying developmental progression.

  4. Interaction of pupil offset and fifth-order nodal aberration field properties in rotationally symmetric telescopes.

    PubMed

    Hu, Haili; Liu, Jianjun; Fan, Zhigang

    2013-07-29

    In this paper we succeeded in deriving changes in the nodal positions of aberrations that belong to the fifth-order class in pupil dependence by applying a system level pupil decentration vector. Our treatment is specifically for rotationally symmetric multi-mirror optical designs that simply use an offset pupil as a means of creating an unobscured optical design. When the pupil is offset, only the vectors to determine the node locations are modified by the pupil decentration vector, while the nodal properties originally developed for titled/decentered optical systems are retained. In general, the modifications to the nodal vectors for any particular aberration type are contributed only by terms of higher order pupil dependence.

  5. Melanocytes Affect Nodal Expression and Signaling in Melanoma Cells: A Lesson from Pediatric Large Congenital Melanocytic Nevi

    PubMed Central

    Margaryan, Naira V.; Gilgur, Alina; Seftor, Elisabeth A.; Purnell, Chad; Arva, Nicoleta C.; Gosain, Arun K.; Hendrix, Mary J. C.; Strizzi, Luigi

    2016-01-01

    Expression of Nodal, a Transforming Growth Factor-beta (TGF-β) related growth factor, is associated with aggressive melanoma. Nodal expression in adult dysplastic nevi may predict the development of aggressive melanoma in some patients. A subset of pediatric patients diagnosed with giant or large congenital melanocytic nevi (LCMN) has shown increased risk for development of melanoma. Here, we investigate whether Nodal expression can help identify the rare cases of LCMN that develop melanoma and shed light on why the majority of these patients do not. Immunohistochemistry (IHC) staining results show varying degree of Nodal expression in pediatric dysplastic nevi and LCMN. Moreover, median scores from Nodal IHC expression analysis were not significantly different between these two groups. Additionally, none of the LCMN patients in this study developed melanoma, regardless of Nodal IHC levels. Co-culture experiments revealed reduced tumor growth and lower levels of Nodal and its signaling molecules P-SMAD2 and P-ERK1/2 when melanoma cells were grown in vivo or in vitro with normal melanocytes. The same was observed in melanoma cells cultured with melanocyte conditioned media containing pigmented melanocyte derived melanosomes (MDM). Since MDM contain molecules capable of inactivating radical oxygen species, to investigate potential anti-oxidant effect of MDM on Nodal expression and signaling in melanoma, melanoma cells were treated with either N-acetyl-l-cysteine (NAC), a component of the anti-oxidant glutathione or synthetic melanin, which in addition to providing pigmentation can also exert free radical scavenging activity. Melanoma cells treated with NAC or synthetic melanin showed reduced levels of Nodal, P-SMAD2 and P-ERK1/2 compared to untreated melanoma cells. Thus, the potential role for Nodal in melanoma development in LCMN is less evident than in adult dysplastic nevi possibly due to melanocyte cross-talk in LCMN capable of offsetting or delaying the pro

  6. Assessment of Ultrasound Features Predicting Axillary Nodal Metastasis in Breast Cancer: The Impact of Cortical Thickness

    PubMed Central

    Stachs, A.; Thi, A. Tra-Ha; Dieterich, M.; Stubert, J.; Hartmann, S.; Glass, Ä.; Reimer, T.; Gerber, B.

    2015-01-01

    Purpose: To evaluate the accuracy of axillary ultrasound (AUS) in detecting nodal metastasis in patients with early-stage breast cancer and to identify AUS features with high predictive power. Materials and Methods: Prospective single-center preliminary study in 105 patients with a primary diagnosis of breast cancer and clinically negative axilla. AUS was performed using a 12 MHz linear-array transducer before ultrasound-guided needle biopsy. Nodal characteristics (shape, longitudinal-transverse [LT] axis ratio, margins, cortical thickness, hyperechoic hilum) were correlated with histopathological nodal status after SLNB or axillary lymph node dissection (ALND). Results: Nodal metastases were present in 42/105 patients (40.0%). Univariate analyses showed that absence of hyperechoic hilum, round shape, LT axis ratio<2, sharp margins and cortical thickness>3 mm were associated with lymph node metastasis. Multivariate logistic regression analysis revealed cortical thickness > 3 mm as an independent predictive parameter for nodal involvement. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 66.7, 74.6, 63.6, 77.0% and 71.4% respectively when cortical thickness > 3 mm was applied as the criterion for AUS positivity. Axillary tumor volume was low in patients with pT1/2 tumors and negative AUS, since only 3.2% of patients had > 2 metastatic lymph nodes. Conclusion: Cortical thickness>3 mm is a reliable predictor of nodal metastatic involvement. Negative AUS does not exclude lymph node metastases, but extensive axillary tumor volume is rare.

  7. A predictive index of axillary nodal involvement in operable breast cancer.

    PubMed Central

    De Laurentiis, M.; Gallo, C.; De Placido, S.; Perrone, F.; Pettinato, G.; Petrella, G.; Carlomagno, C.; Panico, L.; Delrio, P.; Bianco, A. R.

    1996-01-01

    We investigated the association between pathological characteristics of primary breast cancer and degree of axillary nodal involvement and obtained a predictive index of the latter from the former. In 2076 cases, 17 histological features, including primary tumour and local invasion variables, were recorded. The whole sample was randomly split in a training (75% of cases) and a test sample. Simple and multiple correspondence analysis were used to select the variables to enter in a multinomial logit model to build an index predictive of the degree of nodal involvement. The response variable was axillary nodal status coded in four classes (N0, N1-3, N4-9, N > or = 10). The predictive index was then evaluated by testing goodness-of-fit and classification accuracy. Covariates significantly associated with nodal status were tumour size (P < 0.0001), tumour type (P < 0.0001), type of border (P = 0.048), multicentricity (P = 0.003), invasion of lymphatic and blood vessels (P < 0.0001) and nipple invasion (P = 0.006). Goodness-of-fit was validated by high concordance between observed and expected number of cases in each decile of predicted probability in both training and test samples. Classification accuracy analysis showed that true node-positive cases were well recognised (84.5%), but there was no clear distinction among the classes of node-positive cases. However, 10 year survival analysis showed a superimposible prognostic behaviour between predicted and observed nodal classes. Moreover, misclassified node-negative patients (i.e. those who are predicted positive) showed an outcome closer to patients with 1-3 metastatic nodes than to node-negative ones. In conclusion, the index cannot completely substitute for axillary node information, but it is a predictor of prognosis as accurate as nodal involvement and identifies a subgroup of node-negative patients with unfavourable prognosis. PMID:8630286

  8. Progress in development of HEDP capabilities in FLASH's Unsplit Staggered Mesh MHD solver

    NASA Astrophysics Data System (ADS)

    Lee, D.; Xia, G.; Daley, C.; Dubey, A.; Gopal, S.; Graziani, C.; Lamb, D.; Weide, K.

    2011-11-01

    FLASH is a publicly available astrophysical community code designed to solve highly compressible multi-physics reactive flows. We are adding capabilities to FLASH that will make it an open science code for the academic HEDP community. Among many important numerical requirements, we consider the following features to be important components necessary to meet our goals for FLASH as an HEDP open toolset. First, we are developing computationally efficient time-stepping integration methods that overcome the stiffness that arises in the equations describing a physical problem when there are disparate time scales. To this end, we are adding two different time-stepping schemes to FLASH that relax the time step limit when diffusive effects are present: an explicit super-time-stepping algorithm (Alexiades et al. in Com. Num. Mech. Eng. 12:31-42, 1996) and a Jacobian-Free Newton-Krylov implicit formulation. These two methods will be integrated into a robust, efficient, and high-order accurate Unsplit Staggered Mesh MHD (USM) solver (Lee and Deane in J. Comput. Phys. 227, 2009). Second, we have implemented an anisotropic Spitzer-Braginskii conductivity model to treat thermal heat conduction along magnetic field lines. Finally, we are implementing the Biermann Battery term to account for spontaneous generation of magnetic fields in the presence of non-parallel temperature and density gradients.

  9. A phase-field model coupled with lattice kinetics solver for modeling crystal growth in furnaces

    SciTech Connect

    Lin, Guang; Bao, Jie; Xu, Zhijie; Tartakovsky, Alexandre M.; Henager, Charles H.

    2014-02-02

    In this study, we present a new numerical model for crystal growth in a vertical solidification system. This model takes into account the buoyancy induced convective flow and its effect on the crystal growth process. The evolution of the crystal growth interface is simulated using the phase-field method. Two novel phase-field models are developed to model the crystal growth interface in vertical gradient furnaces with two temperature profile setups: 1) fixed wall temperature profile setup and 2) time-dependent temperature profile setup. A semi-implicit lattice kinetics solver based on the Boltzmann equation is employed to model the unsteady incompressible flow. This model is used to investigate the effect of furnace operational conditions on crystal growth interface profiles and growth velocities. For a simple case of macroscopic radial growth, the phase-field model is validated against an analytical solution. Crystal growth in vertical gradient furnaces with two temperature profile setups have been also investigated using the developed model. The numerical simulations reveal that for a certain set of temperature boundary conditions, the heat transport in the melt near the phase interface is diffusion dominant and advection is suppressed.

  10. Incidental Prophylactic Nodal Irradiation and Patterns of Nodal Relapse in Inoperable Early Stage NSCLC Patients Treated With SBRT: A Case-Matched Analysis

    SciTech Connect

    Lao, Louis; Hope, Andrew J.; Maganti, Manjula; Brade, Anthony; Bezjak, Andrea; Saibishkumar, Elantholi P.; Giuliani, Meredith; Sun, Alexander; Cho, B. C. John

    2014-09-01

    Purpose: Reported rates of non-small cell lung cancer (NSCLC) nodal failure following stereotactic body radiation therapy (SBRT) are lower than those reported in the surgical series when matched for stage. We hypothesized that this effect was due to incidental prophylactic nodal irradiation. Methods and Materials: A prospectively collected group of medically inoperable early stage NSCLC patients from 2004 to 2010 was used to identify cases with nodal relapses. Controls were matched to cases, 2:1, controlling for tumor volume (ie, same or greater) and tumor location (ie, same lobe). Reference (normalized to equivalent dose for 2-Gy fractions [EQD2]) point doses at the ipsilateral hilum and carina, demographic data, and clinical outcomes were extracted from the medical records. Univariate conditional logistical regression analyses were performed with variables of interest. Results: Cases and controls were well matched except for size. The controls, as expected, had larger gross tumor volumes (P=.02). The mean ipsilateral hilar doses were 9.6 Gy and 22.4 Gy for cases and controls, respectively (P=.014). The mean carinal doses were 7.0 Gy and 9.2 Gy, respectively (P=.13). Mediastinal nodal relapses, with and without ipsilateral hilar relapse, were associated with mean ipsilateral hilar doses of 3.6 Gy and 19.8 Gy, respectively (P=.01). The conditional density plot appears to demonstrate an inverse dose-effect relationship between ipsilateral hilar normalized total dose and risk of ipsilateral hilar relapse. Conclusions: Incidental hilar dose greater than 20 Gy is significantly associated with fewer ipsilateral hilar relapses in inoperable early stage NSCLC patients treated with SBRT.

  11. The SX Solver: A Computer Program for Analyzing Solvent-Extraction Equilibria: Version 3.0

    SciTech Connect

    Lumetta, Gregg J.

    2002-01-17

    A new computer program, the SX Solver, has been developed to analyze solvent-extraction equilibria. The program operates out of Microsoft Excel and uses the built-in Solver function to minimize the sum of the square of the residuals between measured and calculated distribution coefficients. The extraction of nitric acid by tributyl phosphate has been modeled to illustrate the programs use.

  12. A block iterative LU solver for weakly coupled linear systems. [in fluid dynamics equations

    NASA Technical Reports Server (NTRS)

    Cooke, C. H.

    1977-01-01

    A hybrid technique, called the block iterative LU solver, is proposed for solving the linear equations resulting from a finite element numerical analysis of certain fluid dynamics problems where the equations are weakly coupled between distinct sets of variables. Either the block Jacobi iterative method or the block Gauss-Seidel iterative solver is combined with LU decomposition.

  13. T2CG1, a package of preconditioned conjugate gradient solvers for TOUGH2

    SciTech Connect

    Moridis, G.; Pruess, K.; Antunez, E.

    1994-03-01

    Most of the computational work in the numerical simulation of fluid and heat flows in permeable media arises in the solution of large systems of linear equations. The simplest technique for solving such equations is by direct methods. However, because of large storage requirements and accumulation of roundoff errors, the application of direct solution techniques is limited, depending on matrix bandwidth, to systems of a few hundred to at most a few thousand simultaneous equations. T2CG1, a package of preconditioned conjugate gradient solvers, has been added to TOUGH2 to complement its direct solver and significantly increase the size of problems tractable on PCs. T2CG1 includes three different solvers: a Bi-Conjugate Gradient (BCG) solver, a Bi-Conjugate Gradient Squared (BCGS) solver, and a Generalized Minimum Residual (GMRES) solver. Results from six test problems with up to 30,000 equations show that T2CG1 (1) is significantly (and invariably) faster and requires far less memory than the MA28 direct solver, (2) it makes possible the solution of very large three-dimensional problems on PCs, and (3) that the BCGS solver is the fastest of the three in the tested problems. Sample problems are presented related to heat and fluid flow at Yucca Mountain and WIPP, environmental remediation by the Thermal Enhanced Vapor Extraction System, and geothermal resources.

  14. The DANTE Boltzmann transport solver: An unstructured mesh, 3-D, spherical harmonics algorithm compatible with parallel computer architectures

    SciTech Connect

    McGhee, J.M.; Roberts, R.M.; Morel, J.E.

    1997-06-01

    A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.

  15. Asymmetric and node-specific nodal expression patterns are controlled by two distinct cis-acting regulatory elements

    PubMed Central

    Norris, Dominic P.; Robertson, Elizabeth J.

    1999-01-01

    The TGFβ-related molecule Nodal is required for establishment of the anterior–posterior (A–P) and left–right (L-R) body axes of the vertebrate embryo. In mouse, several discrete sites of nodal activity closely correlate with its highly dynamic expression domains. nodal function in the posterior epiblast promotes primitive streak formation, whereas transient nodal expression in the extraembryonic visceral endoderm is essential for patterning the rostral central nervous system. Asymmetric nodal expression in the developing node and at later stages in left lateral plate mesoderm has been implicated as a key regulator of L-R axis determination. We have analyzed the cis-regulatory elements controlling nodal expression domains during early development. We show that the regulatory sequences conferring node-specific expression are contained in an upstream region of the locus, whereas early expression in the endoderm and epiblast and asymmetric expression at later stages on the left side of the body axis are controlled by a 600-bp intronic enhancer. Targeted deletion of a 100-bp subregion of this intronic enhancer eliminates nodal expression in the early epiblast and visceral endoderm and disrupts asymmetric expression in the node and lateral plate mesoderm. Thus, developmentally regulated nodal expression at distinct tissue sites during A–P and L-R axis formation is potentially controlled by common transcriptional activators. PMID:10385626

  16. Nodal Quasiparticle Meltdown in Ultra-High Resolution Pump-Probe Angle-Resolved Photoemission

    SciTech Connect

    Graf, Jeff; Jozwiak, Chris; Smallwood, Chris L.; Eisaki, H.; Kaindl, Robert A.; Lee, Dung-Hai; Lanzara, Alessandra

    2011-06-03

    High-T{sub c} cuprate superconductors are characterized by a strong momentum-dependent anisotropy between the low energy excitations along the Brillouin zone diagonal (nodal direction) and those along the Brillouin zone face (antinodal direction). Most obvious is the d-wave superconducting gap, with the largest magnitude found in the antinodal direction and no gap in the nodal direction. Additionally, while antin- odal quasiparticle excitations appear only below T{sub c}, superconductivity is thought to be indifferent to nodal excitations as they are regarded robust and insensitive to T{sub c}. Here we reveal an unexpected tie between nodal quasiparticles and superconductivity using high resolution time- and angle-resolved photoemission on optimally doped Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} . We observe a suppression of the nodal quasiparticle spectral weight following pump laser excitation and measure its recovery dynamics. This suppression is dramatically enhanced in the superconducting state. These results reduce the nodal-antinodal dichotomy and challenge the conventional view of nodal excitation neutrality in superconductivity. The electronic structures of high-Tc cuprates are strongly momentum-dependent. This is one reason why the momentum-resolved technique of angle-resolved photoemission spectroscopy (ARPES) has been a central tool in the field of high-temperature superconductivity. For example, coherent low energy excitations with momenta near the Brillouin zone face, or antinodal quasiparticles (QPs), are only observed below T{sub c} and have been linked to superfluid density. They have therefore been the primary focus of ARPES studies. In contrast, nodal QPs, with momenta along the Brillouin zone diagonal, have received less attention and are usually regarded as largely immune to the superconducting transition because they seem insensitive to perturbations such as disorder, doping, isotope exchange, charge ordering, and temperature. Clearly

  17. Impact of Incidental Irradiation on Clinically Uninvolved Nodal Regions in Patients With Advanced Non-Small-Cell Lung Cancer Treated With Involved-Field Radiation Therapy: Does Incidental Irradiation Contribute to the Low Incidence of Elective Nodal Failure?

    SciTech Connect

    Kimura, Tomoki; Togami, Taro; Nishiyama, Yoshihiro; Ohkawa, Motoomi; Takashima, Hitoshi

    2010-06-01

    Purpose: To evaluate the incidental irradiation dose to elective nodal regions in the treatment of advanced non-small-cell lung cancer with involved-field radiation therapy (IF-RT) and the pattern of elective nodal failure (ENF). Methods and Materials: Fifty patients with advanced non-small-cell lung cancer, who received IF-RT at Kagawa University were enrolled. To evaluate the dose of incidental irradiation, we delineated nodal regions with a Japanese map and the American Thoracic Society map (levels 1-11) in each patient retrospectively and calculated the dose parameters such as mean dose, D95, and V95 (40 Gy as the prescribed dose of elective nodal irradiation). Results: Using the Japanese map, the median mean dose was more than 40 Gy in most of the nodal regions, except at levels 1, 3, and 7. In particular, each dosimetric parameter of level 1 was significantly lower than those at other levels, and each dosimetric parameter of levels 10 to 11 ipsilateral (11I) was significantly higher than those in other nodal regions. Using the American Thoracic Society map, basically, the results were similar to those of the Japanese map. ENF was observed in 4 patients (8%), five nodal regions, and no mean dose to the nodal region exceeded 40 Gy. On the Japanese map, each parameter of these five nodal region was significantly lower than those of the other nodal regions. Conclusions: These results show that a high dose of incidental irradiation may contribute to the low incidence of ENF in patients who have received IF-RT.

  18. Experimental validation of GADRAS's coupled neutron-photon inverse radiation transport solver.

    SciTech Connect

    Mattingly, John K.; Mitchell, Dean James; Harding, Lee T.

    2010-08-01

    Sandia National Laboratories has developed an inverse radiation transport solver that applies nonlinear regression to coupled neutron-photon deterministic transport models. The inverse solver uses nonlinear regression to fit a radiation transport model to gamma spectrometry and neutron multiplicity counting measurements. The subject of this paper is the experimental validation of that solver. This paper describes a series of experiments conducted with a 4.5 kg sphere of {alpha}-phase, weapons-grade plutonium. The source was measured bare and reflected by high-density polyethylene (HDPE) spherical shells with total thicknesses between 1.27 and 15.24 cm. Neutron and photon emissions from the source were measured using three instruments: a gross neutron counter, a portable neutron multiplicity counter, and a high-resolution gamma spectrometer. These measurements were used as input to the inverse radiation transport solver to evaluate the solver's ability to correctly infer the configuration of the source from its measured radiation signatures.

  19. A High-Order Direct Solver for Helmholtz Equations with Neumann Boundary Conditions

    NASA Technical Reports Server (NTRS)

    Sun, Xian-He; Zhuang, Yu

    1997-01-01

    In this study, a compact finite-difference discretization is first developed for Helmholtz equations on rectangular domains. Special treatments are then introduced for Neumann and Neumann-Dirichlet boundary conditions to achieve accuracy and separability. Finally, a Fast Fourier Transform (FFT) based technique is used to yield a fast direct solver. Analytical and experimental results show this newly proposed solver is comparable to the conventional second-order elliptic solver when accuracy is not a primary concern, and is significantly faster than that of the conventional solver if a highly accurate solution is required. In addition, this newly proposed fourth order Helmholtz solver is parallel in nature. It is readily available for parallel and distributed computers. The compact scheme introduced in this study is likely extendible for sixth-order accurate algorithms and for more general elliptic equations.

  20. High-performance equation solvers and their impact on finite element analysis

    NASA Technical Reports Server (NTRS)

    Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. Dale, Jr.

    1990-01-01

    The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number of operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

  1. New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

    NASA Astrophysics Data System (ADS)

    Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

    2012-02-01

    Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

  2. Perturbative forward solver software for small localized fluorophores in tissue

    PubMed Central

    Martelli, F.; Bianco, S. Del; Di Ninni, P.

    2011-01-01

    In this paper a forward solver software for the time domain and the CW domain based on the Born approximation for simulating the effect of small localized fluorophores embedded in a non-fluorescent biological tissue is proposed. The fluorescence emission is treated with a mathematical model that describes the migration of photons from the source to the fluorophore and of emitted fluorescent photons from the fluorophore to the detector for all those geometries for which Green’s functions are available. Subroutines written in FORTRAN that can be used for calculating the fluorescent signal for the infinite medium and for the slab are provided with a linked file. With these subroutines, quantities such as reflectance, transmittance, and fluence rate can be calculated. PMID:22254165

  3. Blade design and analysis using a modified Euler solver

    NASA Technical Reports Server (NTRS)

    Leonard, O.; Vandenbraembussche, R. A.

    1991-01-01

    An iterative method for blade design based on Euler solver and described in an earlier paper is used to design compressor and turbine blades providing shock free transonic flows. The method shows a rapid convergence, and indicates how much the flow is sensitive to small modifications of the blade geometry, that the classical iterative use of analysis methods might not be able to define. The relationship between the required Mach number distribution and the resulting geometry is discussed. Examples show how geometrical constraints imposed upon the blade shape can be respected by using free geometrical parameters or by relaxing the required Mach number distribution. The same code is used both for the design of the required geometry and for the off-design calculations. Examples illustrate the difficulty of designing blade shapes with optimal performance also outside of the design point.

  4. AN ADAPTIVE PARTICLE-MESH GRAVITY SOLVER FOR ENZO

    SciTech Connect

    Passy, Jean-Claude; Bryan, Greg L.

    2014-11-01

    We describe and implement an adaptive particle-mesh algorithm to solve the Poisson equation for grid-based hydrodynamics codes with nested grids. The algorithm is implemented and extensively tested within the astrophysical code Enzo against the multigrid solver available by default. We find that while both algorithms show similar accuracy for smooth mass distributions, the adaptive particle-mesh algorithm is more accurate for the case of point masses, and is generally less noisy. We also demonstrate that the two-body problem can be solved accurately in a configuration with nested grids. In addition, we discuss the effect of subcycling, and demonstrate that evolving all the levels with the same timestep yields even greater precision.

  5. Workload Characterization of CFD Applications Using Partial Differential Equation Solvers

    NASA Technical Reports Server (NTRS)

    Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

    1998-01-01

    Workload characterization is used for modeling and evaluating of computing systems at different levels of detail. We present workload characterization for a class of Computational Fluid Dynamics (CFD) applications that solve Partial Differential Equations (PDEs). This workload characterization focuses on three high performance computing platforms: SGI Origin2000, EBM SP-2, a cluster of Intel Pentium Pro bases PCs. We execute extensive measurement-based experiments on these platforms to gather statistics of system resource usage, which results in workload characterization. Our workload characterization approach yields a coarse-grain resource utilization behavior that is being applied for performance modeling and evaluation of distributed high performance metacomputing systems. In addition, this study enhances our understanding of interactions between PDE solver workloads and high performance computing platforms and is useful for tuning these applications.

  6. GPU accelerated FDTD solver and its application in MRI.

    PubMed

    Chi, J; Liu, F; Jin, J; Mason, D G; Crozier, S

    2010-01-01

    The finite difference time domain (FDTD) method is a popular technique for computational electromagnetics (CEM). The large computational power often required, however, has been a limiting factor for its applications. In this paper, we will present a graphics processing unit (GPU)-based parallel FDTD solver and its successful application to the investigation of a novel B1 shimming scheme for high-field magnetic resonance imaging (MRI). The optimized shimming scheme exhibits considerably improved transmit B(1) profiles. The GPU implementation dramatically shortened the runtime of FDTD simulation of electromagnetic field compared with its CPU counterpart. The acceleration in runtime has made such investigation possible, and will pave the way for other studies of large-scale computational electromagnetic problems in modern MRI which were previously impractical.

  7. Perturbative forward solver software for small localized fluorophores in tissue.

    PubMed

    Martelli, F; Del Bianco, S; Di Ninni, P

    2012-01-01

    In this paper a forward solver software for the time domain and the CW domain based on the Born approximation for simulating the effect of small localized fluorophores embedded in a non-fluorescent biological tissue is proposed. The fluorescence emission is treated with a mathematical model that describes the migration of photons from the source to the fluorophore and of emitted fluorescent photons from the fluorophore to the detector for all those geometries for which Green's functions are available. Subroutines written in FORTRAN that can be used for calculating the fluorescent signal for the infinite medium and for the slab are provided with a linked file. With these subroutines, quantities such as reflectance, transmittance, and fluence rate can be calculated. PMID:22254165

  8. Using parallel banded linear system solvers in generalized eigenvalue problems

    NASA Technical Reports Server (NTRS)

    Zhang, Hong; Moss, William F.

    1994-01-01

    Subspace iteration is a reliable and cost effective method for solving positive definite banded symmetric generalized eigenproblems, especially in the case of large scale problems. This paper discusses an algorithm that makes use of two parallel banded solvers in subspace iteration. A shift is introduced to decompose the banded linear systems into relatively independent subsystems and to accelerate the iterations. With this shift, an eigenproblem is mapped efficiently into the memories of a multiprocessor and a high speedup is obtained for parallel implementations. An optimal shift is a shift that balances total computation and communication costs. Under certain conditions, we show how to estimate an optimal shift analytically using the decay rate for the inverse of a banded matrix, and how to improve this estimate. Computational results on iPSC/2 and iPSC/860 multiprocessors are presented.

  9. Using parallel banded linear system solvers in generalized eigenvalue problems

    NASA Technical Reports Server (NTRS)

    Zhang, Hong; Moss, William F.

    1993-01-01

    Subspace iteration is a reliable and cost effective method for solving positive definite banded symmetric generalized eigenproblems, especially in the case of large scale problems. This paper discusses an algorithm that makes use of two parallel banded solvers in subspace iteration. A shift is introduced to decompose the banded linear systems into relatively independent subsystems and to accelerate the iterations. With this shift, an eigenproblem is mapped efficiently into the memories of a multiprocessor and a high speed-up is obtained for parallel implementations. An optimal shift is a shift that balances total computation and communication costs. Under certain conditions, we show how to estimate an optimal shift analytically using the decay rate for the inverse of a banded matrix, and how to improve this estimate. Computational results on iPSC/2 and iPSC/860 multiprocessors are presented.

  10. Aeroelastic analysis of advanced propellers using an efficient Euler solver

    NASA Technical Reports Server (NTRS)

    Srivastava, R.; Reddy, T. S. R.; Mehmed, O.

    1992-01-01

    A 3D Euler solver is coupled with a 3D structural dynamics model to investigate flutter of propfans. A hybrid scheme is used to reduce computational time for the Euler equations and a normal mode analysis is used for flutter calculations. Experimental and calculated flutter results are compared for an advanced propeller propfan which experienced flutter at transonic tip relative velocities. The predicted flutter calculations are in close agreement with the experimental data. A structural damping value of 0.5 percent was required to predict the behavior observed in the experiment. Computations show that the flutter behavior is dominated by the second mode, but coupling with the first mode is required. The addition of other modes to the calculations did not affect the flutter behavior.

  11. Progress in developing Poisson-Boltzmann equation solvers

    PubMed Central

    Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil

    2013-01-01

    This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185

  12. Application of sparse matrix solvers as effective preconditioners

    SciTech Connect

    Young, D.P.; Melvin, R.G.; Johnson, F.T.; Bussoletti, J.E.; Wigton, L.B.; Samant, S.S. )

    1989-11-01

    In this paper the use of a new out-of-core sparse matrix package for the numerical solution of partial differential equations involving complex geometries arising from aerospace applications is discussed. The sparse matrix solver accepts contributions to the matrix elements in random order and assembles the matrix using fast sort/merge routines. Fill-in is reduced through the use of a physically based nested dissection ordering. For very large problems a drop tolerance is used during the matrix decomposition phase. The resulting incomplete factorization is an effective preconditioner for Krylov subspace methods, such as GMRES. Problems involving 200,000 unknowns routinely are solved on the Cray X-MP using 64MW of solid-state storage device (SSD).

  13. Extending the QUDA Library with the eigCG Solver

    SciTech Connect

    Strelchenko, Alexei; Stathopoulos, Andreas

    2014-12-12

    While the incremental eigCG algorithm [ 1 ] is included in many LQCD software packages, its realization on GPU micro-architectures was still missing. In this session we report our experi- ence of the eigCG implementation in the QUDA library. In particular, we will focus on how to employ the mixed precision technique to accelerate solutions of large sparse linear systems with multiple right-hand sides on GPUs. Although application of mixed precision techniques is a well-known optimization approach for linear solvers, its utilization for the eigenvector com- puting within eigCG requires special consideration. We will discuss implementation aspects of the mixed precision deflation and illustrate its numerical behavior on the example of the Wilson twisted mass fermion matrix inversions

  14. GPU-Accelerated Finite Element Method for Modelling Light Transport in Diffuse Optical Tomography

    PubMed Central

    Schweiger, Martin

    2011-01-01

    We introduce a GPU-accelerated finite element forward solver for the computation of light transport in scattering media. The forward model is the computationally most expensive component of iterative methods for image reconstruction in diffuse optical tomography, and performance optimisation of the forward solver is therefore crucial for improving the efficiency of the solution of the inverse problem. The GPU forward solver uses a CUDA implementation that evaluates on the graphics hardware the sparse linear system arising in the finite element formulation of the diffusion equation. We present solutions for both time-domain and frequency-domain problems. A comparison with a CPU-based implementation shows significant performance gains of the graphics accelerated solution, with improvements of approximately a factor of 10 for double-precision computations, and factors beyond 20 for single-precision computations. The gains are also shown to be dependent on the mesh complexity, where the largest gains are achieved for high mesh resolutions. PMID:22013431

  15. GPU-Accelerated Finite Element Method for Modelling Light Transport in Diffuse Optical Tomography.

    PubMed

    Schweiger, Martin

    2011-01-01

    We introduce a GPU-accelerated finite element forward solver for the computation of light transport in scattering media. The forward model is the computationally most expensive component of iterative methods for image reconstruction in diffuse optical tomography, and performance optimisation of the forward solver is therefore crucial for improving the efficiency of the solution of the inverse problem. The GPU forward solver uses a CUDA implementation that evaluates on the graphics hardware the sparse linear system arising in the finite element formulation of the diffusion equation. We present solutions for both time-domain and frequency-domain problems. A comparison with a CPU-based implementation shows significant performance gains of the graphics accelerated solution, with improvements of approximately a factor of 10 for double-precision computations, and factors beyond 20 for single-precision computations. The gains are also shown to be dependent on the mesh complexity, where the largest gains are achieved for high mesh resolutions.

  16. A three-dimensional fast solver for arbitrary vorton distributions

    SciTech Connect

    Strickland, J.H.; Baty, R.S.

    1994-05-01

    A method which is capable of an efficient calculation of the three-dimensional flow field produced by a large system of vortons (discretized regions of vorticity) is presented in this report. The system of vortons can, in turn, be used to model body surfaces, container boundaries, free-surfaces, plumes, jets, and wakes in unsteady three-dimensional flow fields. This method takes advantage of multipole and local series expansions which enables one to make calculations for interactions between groups of vortons which are in well-separated spatial domains rather than having to consider interactions between every pair of vortons. In this work, series expansions for the vector potential of the vorton system are obtained. From such expansions, the three components of velocity can be obtained explicitly. A Fortran computer code FAST3D has been written to calculate the vector potential and the velocity components at selected points in the flow field. In this code, the evaluation points do not have to coincide with the location of the vortons themselves. Test cases have been run to benchmark the truncation errors and CPU time savings associated with the method. Non-dimensional truncation errors for the magnitudes of the vector potential and velocity fields are on the order of 10{sup {minus}4}and 10{sup {minus}3} respectively. Single precision accuracy produces errors in these quantities of up to 10{sup {minus}5}. For less than 1,000 to 2,000 vortons in the field, there is virtually no CPU time savings with the fast solver. For 100,000 vortons in the flow, the fast solver obtains solutions in 1 % to 10% of the time required for the direct solution technique depending upon the configuration.

  17. Domain decomposed preconditioners with Krylov subspace methods as subdomain solvers

    SciTech Connect

    Pernice, M.

    1994-12-31

    Domain decomposed preconditioners for nonsymmetric partial differential equations typically require the solution of problems on the subdomains. Most implementations employ exact solvers to obtain these solutions. Consequently work and storage requirements for the subdomain problems grow rapidly with the size of the subdomain problems. Subdomain solves constitute the single largest computational cost of a domain decomposed preconditioner, and improving the efficiency of this phase of the computation will have a significant impact on the performance of the overall method. The small local memory available on the nodes of most message-passing multicomputers motivates consideration of the use of an iterative method for solving subdomain problems. For large-scale systems of equations that are derived from three-dimensional problems, memory considerations alone may dictate the need for using iterative methods for the subdomain problems. In addition to reduced storage requirements, use of an iterative solver on the subdomains allows flexibility in specifying the accuracy of the subdomain solutions. Substantial savings in solution time is possible if the quality of the domain decomposed preconditioner is not degraded too much by relaxing the accuracy of the subdomain solutions. While some work in this direction has been conducted for symmetric problems, similar studies for nonsymmetric problems appear not to have been pursued. This work represents a first step in this direction, and explores the effectiveness of performing subdomain solves using several transpose-free Krylov subspace methods, GMRES, transpose-free QMR, CGS, and a smoothed version of CGS. Depending on the difficulty of the subdomain problem and the convergence tolerance used, a reduction in solution time is possible in addition to the reduced memory requirements. The domain decomposed preconditioner is a Schur complement method in which the interface operators are approximated using interface probing.

  18. High Energy Boundary Conditions for a Cartesian Mesh Euler Solver

    NASA Technical Reports Server (NTRS)

    Pandya, Shishir; Murman, Scott; Aftosmis, Michael

    2003-01-01

    Inlets and exhaust nozzles are common place in the world of flight. Yet, many aerodynamic simulation packages do not provide a method of modelling such high energy boundaries in the flow field. For the purposes of aerodynamic simulation, inlets and exhausts are often fared over and it is assumed that the flow differences resulting from this assumption are minimal. While this is an adequate assumption for the prediction of lift, the lack of a plume behind the aircraft creates an evacuated base region thus effecting both drag and pitching moment values. In addition, the flow in the base region is often mis-predicted resulting in incorrect base drag. In order to accurately predict these quantities, a method for specifying inlet and exhaust conditions needs to be available in aerodynamic simulation packages. A method for a first approximation of a plume without accounting for chemical reactions is added to the Cartesian mesh based aerodynamic simulation package CART3D. The method consists of 3 steps. In the first step, a components approach where each triangle is assigned a component number is used. Here, a method for marking the inlet or exhaust plane triangles as separate components is discussed. In step two, the flow solver is modified to accept a reference state for the components marked inlet or exhaust. In the third step, the flow solver uses these separated components and the reference state to compute the correct flow condition at that triangle. The present method is implemented in the CART3D package which consists of a set of tools for generating a Cartesian volume mesh from a set of component triangulations. The Euler equations are solved on the resulting unstructured Cartesian mesh. The present methods is implemented in this package and its usefulness is demonstrated with two validation cases. A generic missile body is also presented to show the usefulness of the method on a real world geometry.

  19. Adaptive Implicit Non-Equilibrium Radiation Diffusion

    SciTech Connect

    Philip, Bobby; Wang, Zhen; Berrill, Mark A; Rodriguez Rodriguez, Manuel; Pernice, Michael

    2013-01-01

    We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  20. Multiplicity of positive and nodal solutions for scalar field equations

    NASA Astrophysics Data System (ADS)

    Cerami, Giovanna; Molle, Riccardo; Passaseo, Donato

    2014-11-01

    In this paper the question of finding infinitely many solutions to the problem -Δu+a(x)u=|u, in RN, u∈H1(RN), is considered when N≥2, p∈(2,2N/(N-2)), and the potential a(x) is a positive function which is not required to enjoy symmetry properties. Assuming that a(x) satisfies a suitable “slow decay at infinity” condition and, moreover, that its graph has some “dips”, we prove that the problem admits either infinitely many nodal solutions or infinitely many constant sign solutions. The proof method is purely variational and allows to describe the shape of the solutions. a(x)→a∞>0 as|x|→∞, a(x)≥a0>0 ∀x∈RN, a∈LlocN/2(RN), ∃ηbar∈(0,√{a∞}):lim|x|→∞ ⁡(a(x)-a∞)e=∞ be satisfied.Then there exists a positive constant,A=A(N,ηbar,a0,a∞)∈R, such that, when|a(x)-a∞|N/2,loc:=supy∈RN ⁡|a(x)-a∞|L(B1(y))The above result (see also the subsequent [3] for a different proof and more general nonlinearities) is the starting point of our work; some comments and questions come naturally looking at its statement. Indeed, assumptions (h1)-(h3) are standard and very mild, moreover, the slow decay condition (h4) is basic and it is the deep motivation for the success in obtaining “multibump” solutions. The solutions are found by a max-min argument on the action functional I restricted to special classes of multibump functions

  1. Prevalence and distribution pattern of nodal metastases in advanced ovarian cancer

    PubMed Central

    Bachmann, Cornelia; Bachmann, Robert; Kraemer, Bernhard; Brucker, Sara Yvonne; Staebler, Anette; Fend, Falko; Rothmund, Ralf; Wallwiener, Diethelm

    2016-01-01

    The objective of this study was to examine the relevance of pelvic and para-aortic lymph node involvement and the tumour characteristics affecting nodal metastases and survival in primary advanced ovarian cancer. A total of 130 consecutive patients were retrospectively investigated. All the patients received stage-related surgery with pelvic and para-aortic lymphadenectomy. The median follow-up was 53.5 months. The clinicopathological parameters and distribution pattern of nodal metastases were evaluated. Lymph node metastases were detectable in 74.62% of the cases. Overall, both pelvic and para-aortic nodes were affected in 35.9% of the patients, whereas 13.3% had metastases only in the pelvic and 13.3% only in the para-aortic lymph nodes. Histological grade 1/2 and 3, serous and endometrioid histology were independent predictors of nodal metastasis. Serous and endometrioid cancers have shown a predilection for metastasis to the pelvic lymph nodes alone, both to the pelvic and the para-aortic nodes, or the para-aortic nodes alone. Overall survival was significantly positively affected by serous histology with positive nodes (P=0.043). It is crucial to investigate the risk factors and metastatic patterns of such patients in a multicenter analysis to evaluate individual subgroups. Prospective studies are required to investigate the prognostic effect of lymphadenectomy in advanced ovarian cancer and its association with histology and distribution pattern of nodal metastasis. PMID:27703680

  2. Precision evaluation of lens systems using a nodal slide/MTF optical bench

    NASA Astrophysics Data System (ADS)

    Doherty, Victor J.; Chapnik, Philip D.

    1992-01-01

    A compact, self-contained production instrument designed to permit the rapid and precise performance characterization of a wide variety of lenses and optical systems has been developed by Eidolon Corporation. The Eidolon Production Nodal Slide/MTF Measurement System can be used to measure effective focal length (EFL), distortion, field curvature, chromatic aberration, spot size, and modulation transfer function (MTF).

  3. [The Nodal regulated dusp4 inhibits mesendoderm formation during zebrafish gastrulation].

    PubMed

    Liu, Zhao-Ting; Wei, Shi; Wang, Qiang

    2012-09-01

    MAP kinase phosphatase-2 (MKP-2/DUSP4), a dual specificity protein phosphatase with tyrosine/serine/ threonine phosphatase activity, is associated with cellular proliferation and differentiation, but its functions during embryo development are unclear. To study the developmental function of dusp4, we first examined the spatiotemporal expression pattern of this gene during zebrafish embryonic development by whole mount in situ hybridization. We found that dusp4 was maternally expressed since its transcripts were present from the one-cell to the 256-cell stages. At early gastrulation stages, dusp4 transcripts specifically distributed at margin region, where the mesendodermal cells were located. Further-more, Nodal signal was crucial for dusp4 expression. The expression of dusp4 was obviously increased in Nodal ligand overexpressed embryos, while its expression was almost lost in the Nodal signal-deficient MZoep mutants. In addition, dusp4 MO was also designed to knock down its expression in embryos. The mesendoderm formation was significantly in-creased in dusp4 morphants, but not obviously changed in dusp4 overexpressed embryos, suggesting that dusp4 is necessary, but not sufficient for the inhibitory of mesendoderm induction. Thus, our results indicate that Nodal regulated dusp4 plays a repressive role in mesendoderm induction. PMID:23017456

  4. Photoacoustic intra-operative nodal staging using clinically approved superparamagnetic iron oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Grootendorst, Diederik J.; Fratila, Raluca M.; Visscher, Martijn; Ten Haken, Bennie; van Wezel, Richard; Steenbergen, Wiendelt; Manohar, Srirang; Ruers, Theo J. M.

    2013-02-01

    Detection of tumor metastases in the lymphatic system is essential for accurate staging of various malignancies, however fast, accurate and cost-effective intra-operative evaluation of the nodal status remains difficult to perform with common available medical imaging techniques. In recent years, numerous studies have confirmed the additional value of superparamagnetic iron oxide dispersions (SPIOs) for nodal staging purposes, prompting the clearance of different SPIO dispersions for clinical practice. We evaluate whether a combination of photoacoustic (PA) imaging and a clinically approved SPIO dispersion, could be applied for intra-operative nodal staging. Metastatic adenocarcinoma was inoculated in Copenhagen rats for 5 or 8 days. After SPIO injection, the lymph nodes were photoacoustically imaged both in vivo and ex vivo whereafter imaging results were correlated with MR and histology. Results were compared to a control group without tumor inoculation. In the tumor groups clear irregularities, as small as 1 mm, were observed in the PA contrast pattern of the nodes together with an decrease of PA response. These irregularities could be correlated to the absence of contrast in the MR images and could be linked to metastatic deposits seen in the histological slides. The PA and MR images of the control animals did not show these features. We conclude that the combination of photoacoustic imaging with a clinically approved iron oxide nanoparticle dispersion is able to detect lymph node metastases in an animal model. This approach opens up new possibilities for fast intra-operative nodal staging in a clinical setting.

  5. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... authorized only as a part of an integrated communication system wherein 10.6 GHz DEMS User Stations... 47 Telecommunication 5 2013-10-01 2013-10-01 false Digital Electronic Message Service Nodal Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED)...

  6. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... authorized only as a part of an integrated communication system wherein 10.6 GHz DEMS User Stations... 47 Telecommunication 5 2012-10-01 2012-10-01 false Digital Electronic Message Service Nodal Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED)...

  7. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... authorized only as a part of an integrated communication system wherein 10.6 GHz DEMS User Stations... 47 Telecommunication 5 2014-10-01 2014-10-01 false Digital Electronic Message Service Nodal Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED)...

  8. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... authorized only as a part of an integrated communication system wherein 10.6 GHz DEMS User Stations... 47 Telecommunication 5 2011-10-01 2011-10-01 false Digital Electronic Message Service Nodal Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED)...

  9. A nodal spectral stiffness matrix for the finite-element method

    NASA Astrophysics Data System (ADS)

    Bittencourt, Marco L.; Vazquez, Thais G.

    2008-12-01

    In this paper, shape functions are proposed for the spectral finite-element method aiming to finding a nodal spectral stiffness matrix. The proposed shape functions obtain a nearly diagonal 1D stiffness matrix with better conditioning than using the Lagrange and Jacobi bases.

  10. Nodal Analysis Optimization Based on the Use of Virtual Current Sources: A Powerful New Pedagogical Method

    ERIC Educational Resources Information Center

    Chatzarakis, G. E.

    2009-01-01

    This paper presents a new pedagogical method for nodal analysis optimization based on the use of virtual current sources, applicable to any linear electric circuit (LEC), regardless of its complexity. The proposed method leads to straightforward solutions, mostly arrived at by inspection. Furthermore, the method is easily adapted to computer…

  11. Analysis of nodal aberration properties in off-axis freeform system design.

    PubMed

    Shi, Haodong; Jiang, Huilin; Zhang, Xin; Wang, Chao; Liu, Tao

    2016-08-20

    Freeform surfaces have the advantage of balancing off-axis aberration. In this paper, based on the framework of nodal aberration theory (NAT) applied to the coaxial system, the third-order astigmatism and coma wave aberration expressions of an off-axis system with Zernike polynomial surfaces are derived. The relationship between the off-axis and surface shape acting on the nodal distributions is revealed. The nodal aberration properties of the off-axis freeform system are analyzed and validated by using full-field displays (FFDs). It has been demonstrated that adding Zernike terms, up to nine, to the off-axis system modifies the nodal locations, but the field dependence of the third-order aberration does not change. On this basis, an off-axis two-mirror freeform system with 500 mm effective focal length (EFL) and 300 mm entrance pupil diameter (EPD) working in long-wave infrared is designed. The field constant aberrations induced by surface tilting are corrected by selecting specific Zernike terms. The design results show that the nodes of third-order astigmatism and coma move back into the field of view (FOV). The modulation transfer function (MTF) curves are above 0.4 at 20 line pairs per millimeter (lp/mm) which meets the infrared reconnaissance requirement. This work provides essential insight and guidance for aberration correction in off-axis freeform system design. PMID:27557003

  12. Nodal signaling regulates endodermal cell motility and actin dynamics via Rac1 and Prex1

    PubMed Central

    Housley, Michael P.; Weiner, Orion D.

    2012-01-01

    Embryo morphogenesis is driven by dynamic cell behaviors, including migration, that are coordinated with fate specification and differentiation, but how such coordination is achieved remains poorly understood. During zebrafish gastrulation, endodermal cells sequentially exhibit first random, nonpersistent migration followed by oriented, persistent migration and finally collective migration. Using a novel transgenic line that labels the endodermal actin cytoskeleton, we found that these stage-dependent changes in migratory behavior correlated with changes in actin dynamics. The dynamic actin and random motility exhibited during early gastrulation were dependent on both Nodal and Rac1 signaling. We further identified the Rac-specific guanine nucleotide exchange factor Prex1 as a Nodal target and showed that it mediated Nodal-dependent random motility. Reducing Rac1 activity in endodermal cells caused them to bypass the random migration phase and aberrantly contribute to mesodermal tissues. Together, our results reveal a novel role for Nodal signaling in regulating actin dynamics and migration behavior, which are crucial for endodermal morphogenesis and cell fate decisions. PMID:22945937

  13. Analysis of nodal aberration properties in off-axis freeform system design.

    PubMed

    Shi, Haodong; Jiang, Huilin; Zhang, Xin; Wang, Chao; Liu, Tao

    2016-08-20

    Freeform surfaces have the advantage of balancing off-axis aberration. In this paper, based on the framework of nodal aberration theory (NAT) applied to the coaxial system, the third-order astigmatism and coma wave aberration expressions of an off-axis system with Zernike polynomial surfaces are derived. The relationship between the off-axis and surface shape acting on the nodal distributions is revealed. The nodal aberration properties of the off-axis freeform system are analyzed and validated by using full-field displays (FFDs). It has been demonstrated that adding Zernike terms, up to nine, to the off-axis system modifies the nodal locations, but the field dependence of the third-order aberration does not change. On this basis, an off-axis two-mirror freeform system with 500 mm effective focal length (EFL) and 300 mm entrance pupil diameter (EPD) working in long-wave infrared is designed. The field constant aberrations induced by surface tilting are corrected by selecting specific Zernike terms. The design results show that the nodes of third-order astigmatism and coma move back into the field of view (FOV). The modulation transfer function (MTF) curves are above 0.4 at 20 line pairs per millimeter (lp/mm) which meets the infrared reconnaissance requirement. This work provides essential insight and guidance for aberration correction in off-axis freeform system design.

  14. Sensitivity derivatives and optimization of nodal point locations for vibration reduction

    NASA Technical Reports Server (NTRS)

    Pritchard, Jocelyn I.; Adelman, Howard M.; Haftka, Raphael T.

    1987-01-01

    A method is developed for sensitivity analysis and optimization of nodal point locations in connection with vibration reduction. A straightforward derivation of the expression for the derivative of nodal locations is given, and the role of the derivative in assessing design trends is demonstrated. An optimization process is developed which uses added lumped masses on the structure as design variables to move the node to a preselected location; for example, where low response amplitude is required or to a point which makes the mode shape nearly orthogonal to the force distribution, thereby minimizing the generalized force. The optimization formulation leads to values for added masses that adjust a nodal location while minimizing the total amount of added mass required to do so. As an example, the node of the second mode of a cantilever box beam is relocated to coincide with the centroid of a prescribed force distribution, thereby reducing the generalized force substantially without adding excessive mass. A comparison with an optimization formulation that directly minimizes the generalized force indicates that nodal placement gives essentially a minimum generalized force when the node is appropriately placed.

  15. Senstitivty analysis and optimization of nodal point placement for vibration reduction

    NASA Technical Reports Server (NTRS)

    Pritchard, J. I.; Adelman, H. M.; Haftka, R. T.

    1986-01-01

    A method is developed for sensitivity analysis and optimization of nodal point locations in connection with vibration reduction. A straightforward derivation of the expression for the derivative of nodal locations is given, and the role of the derivative in assessing design trends is demonstrated. An optimization process is developed which uses added lumped masses on the structure as design variables to move the node to a preselected location - for example, where low response amplitude is required or to a point which makes the mode shape nearly orthogonal to the force distribution, thereby minimizing the generalized force. The optimization formulation leads to values for added masses that adjust a nodal location while minimizing the total amount of added mass required to do so. As an example, the node of the second mode of a cantilever box beam is relocated to coincide with the centroid of a prescribed force distribution, thereby reducing the generalized force substantially without adding excessive mass. A comparison with an optimization formulation that directly minimizes the generalized force indicates that nodal placement gives essentially a minimum generalized force when the node is appropriately placed.

  16. A difference-equation formalism for the nodal domains of separable billiards

    NASA Astrophysics Data System (ADS)

    Manjunath, Naren; Samajdar, Rhine; Jain, Sudhir R.

    2016-09-01

    Recently, the nodal domain counts of planar, integrable billiards with Dirichlet boundary conditions were shown to satisfy certain difference equations in Samajdar and Jain (2014). The exact solutions of these equations give the number of domains explicitly. For complete generality, we demonstrate this novel formulation for three additional separable systems and thus extend the statement to all integrable billiards.

  17. Radiation therapy for carcinoma of the hypopharynx with special reference to nodal control

    SciTech Connect

    Teshima, T.; Chatani, M.; Inoue, T.; Miyahara, H.; Sato, T.

    1988-05-01

    From October 1977 through December 1983, 61 patients with carcinoma of the hypopharynx were treated with radiation therapy (RT) and surgery or with RT alone. Five-year survival rates by N-stage, according to the TNM classification by UICC (1978), were 52% for N0 cases, 23% for N1, and 17% for N2-3 (N1 vs. N2-3, not significant). For N1-3 cases, corresponding figures by level of cervical nodal involvement by UICC (1978) were 29% for level 3 cases, 15% for level 2, and 8% for level 4 (level 3 vs. level 4, p less than 0.04). Therefore, the level of cervical nodal involvement was a more useful prognosticator for patients with nodal metastasis than the N-stage. Effective nodal control for patients with clinically positive nodes (N1-3) was obtained with a combination of neck node dissection and RT of 50 Gy or more. For N0 cases, elective RT of 50 Gy or more, encompassing an adequate field, was required.

  18. Topological nodal-line semimetals in alkaline-earth stannides, germanides, and silicides

    NASA Astrophysics Data System (ADS)

    Huang, Huaqing; Liu, Jianpeng; Vanderbilt, David; Duan, Wenhui

    2016-05-01

    Based on first-principles calculations and an effective Hamiltonian analysis, we systematically investigate the electronic and topological properties of alkaline-earth compounds A X2 (A =Ca , Sr, Ba; X =Si , Ge, Sn). Taking BaSn2 as an example, we find that when spin-orbit coupling is ignored, these materials are three-dimensional topological nodal-line semimetals characterized by a snakelike nodal loop in three-dimensional momentum space. Drumheadlike surface states emerge either inside or outside the loop circle on the (001) surface depending on surface termination, while complicated double-drumhead-like surface states appear on the (010) surface. When spin-orbit coupling is included, the nodal line is gapped and the system becomes a topological insulator with Z2 topological invariants (1;001). Since spin-orbit coupling effects are weak in light elements, the nodal-line semimetal phase is expected to be achievable in some alkaline-earth germanides and silicides.

  19. Vaneless diffusers

    NASA Astrophysics Data System (ADS)

    Senoo, Y.

    The influence of vaneless diffusers on flow in centrifugal compressors, particularly on surge, is discussed. A vaneless diffuser can demonstrate stable operation in a wide flow range only if it is installed with a backward leaning blade impeller. The circumferential distortion of flow in the impeller disappears quickly in the vaneless diffuser. The axial distortion of flow at the diffuser inlet does not decay easily. In large specific speed compressors, flow out of the impeller is distorted axially. Pressure recovery of diffusers at distorted inlet flow is considerably improved by half guide vanes. The best height of the vanes is a little 1/2 diffuser width. In small specific speed compressors, flow out of the impeller is not much distorted and pressure recovery can be predicted with one-dimensional flow analysis. Wall friction loss is significant in narrow diffusers. The large pressure drop at a small flow rate can cause the positive gradient of the pressure-flow rate characteristic curve, which may cause surging.

  20. Mammographic Density and Prediction of Nodal Status in Breast Cancer Patients.

    PubMed

    Hack, C C; Häberle, L; Geisler, K; Schulz-Wendtland, R; Hartmann, A; Fasching, P A; Uder, M; Wachter, D L; Jud, S M; Loehberg, C R; Lux, M P; Rauh, C; Beckmann, M W; Heusinger, K

    2013-02-01

    Aim: Nodal status remains one of the most important prognostic factors in breast cancer. The cellular and molecular reasons for the spread of tumor cells to the lymph nodes are not well understood and there are only few predictors in addition to tumor size and multifocality that give an insight into additional mechanisms of lymphatic spread. Aim of our study was therefore to investigate whether breast characteristics such as mammographic density (MD) add to the predictive value of the presence of lymph node metastases in patients with primary breast cancer. Methods: In this retrospective study we analyzed primary, metastasis-free breast cancer patients from one breast center for whom data on MD and staging information were available. A total of 1831 patients were included into this study. MD was assessed as percentage MD (PMD) using a semiautomated method and two readers for every patient. Multiple logistic regression analyses with nodal status as outcome were used to investigate the predictive value of PMD in addition to age, tumor size, Ki-67, estrogen receptor (ER), progesterone receptor (PR), grading, histology, and multi-focality. Results: Multifocality, tumor size, Ki-67 and grading were relevant predictors for nodal status. Adding PMD to a prediction model which included these factors did not significantly improve the prediction of nodal status (p = 0.24, likelihood ratio test). Conclusion: Nodal status could be predicted quite well with the factors multifocality, tumor size, Ki-67 and grading. PMD does not seem to play a role in the lymphatic spread of tumor cells. It could be concluded that the amount of extracellular matrix and stromal cell content of the breast which is reflected by MD does not influence the probability of malignant breast cells spreading from the primary tumor to the lymph nodes.

  1. Concordance of studies for nodal staging is prognostic for worse survival in esophageal cancer.

    PubMed

    Dhupar, R; Correa, A M; Ajani, J; Betancourt, S; Mehran, R J; Swisher, S G; Hofstetter, W L

    2014-01-01

    Pretreatment clinical staging in esophageal cancer influences prognosis and treatment strategy. Current staging strategies utilize multiple imaging modalities, and often the results are contradictory. No studies have examined the implications of concordance of computed tomography (CT), positron emission tomography (PET), and endoscopic ultrasound (EUS) when used for the evaluation of nodal disease. The objective of this study was to determine if concordance of CT, PET, or EUS for nodal disease predicts worse overall survival. We reviewed 615 esophageal cancer patients with pretreatment CT, PET, and EUS that underwent esophagectomy for survival outcomes based on concordance of studies for nodal disease. Concordant N+ is defined as two or three studies positive for nodal disease; non-concordant N+ is defined as only one positive study. Node-positive disease by any study predicted shorter survival than node-negative disease (42% vs. 73% 5-year survival; P<0.001). Additionally, non-concordant N+ patients had shorter survival than N- patients (52% vs. 73% 5-year survival; P<0.001). Concordant N+ patients had shorter survival than non-concordant N+ patients (38- vs. 61-month median survival; P=0.017). There were no statistically significant differences in survival based on specific combinations of studies. When PET was disregarded, patients with both CT+ and EUS+ had shorter survival than patients with either CT+ or EUS+ (39- vs. 58-month median survival; P=0.029). Pretreatment CT, PET, or EUS concordance for node-positive disease predicts shorter overall survival in patients that undergo esophagectomy for esophageal cancer. Predicting survival in esophageal cancer should consider the synergistic capabilities of CT, PET, and EUS in evaluating nodal status.

  2. An approach to model reactor core nodalization for deterministic safety analysis

    NASA Astrophysics Data System (ADS)

    Salim, Mohd Faiz; Samsudin, Mohd Rafie; Mamat @ Ibrahim, Mohd Rizal; Roslan, Ridha; Sadri, Abd Aziz; Farid, Mohd Fairus Abd

    2016-01-01

    Adopting good nodalization strategy is essential to produce an accurate and high quality input model for Deterministic Safety Analysis (DSA) using System Thermal-Hydraulic (SYS-TH) computer code. The purpose of such analysis is to demonstrate the compliance against regulatory requirements and to verify the behavior of the reactor during normal and accident conditions as it was originally designed. Numerous studies in the past have been devoted to the development of the nodalization strategy for small research reactor (e.g. 250kW) up to the bigger research reactor (e.g. 30MW). As such, this paper aims to discuss the state-of-arts thermal hydraulics channel to be employed in the nodalization for RTP-TRIGA Research Reactor specifically for the reactor core. At present, the required thermal-hydraulic parameters for reactor core, such as core geometrical data (length, coolant flow area, hydraulic diameters, and axial power profile) and material properties (including the UZrH1.6, stainless steel clad, graphite reflector) have been collected, analyzed and consolidated in the Reference Database of RTP using standardized methodology, mainly derived from the available technical documentations. Based on the available information in the database, assumptions made on the nodalization approach and calculations performed will be discussed and presented. The development and identification of the thermal hydraulics channel for the reactor core will be implemented during the SYS-TH calculation using RELAP5-3D® computer code. This activity presented in this paper is part of the development of overall nodalization description for RTP-TRIGA Research Reactor under the IAEA Norwegian Extra-Budgetary Programme (NOKEBP) mentoring project on Expertise Development through the Analysis of Reactor Thermal-Hydraulics for Malaysia, denoted as EARTH-M.

  3. Radiotherapy for Esthesioneuroblastoma: Is Elective Nodal Irradiation Warranted in the Multimodality Treatment Approach?

    SciTech Connect

    Noh, O Kyu; Lee, Sang-wook; Yoon, Sang Min; Kim, Sung Bae; Kim, Sang Yoon; Kim, Chang Jin; Jo, Kyung Ja; Choi, Eun Kyung; Song, Si Yeol; Kim, Jong Hoon; Ahn, Seung Do

    2011-02-01

    Purpose: The role of elective nodal irradiation (ENI) in radiotherapy for esthesioneuroblastoma (ENB) has not been clearly defined. We analyzed treatment outcomes of patients with ENB and the frequency of cervical nodal failure in the absence of ENI. Methods and Materials: Between August 1996 and December 2007, we consulted with 19 patients with ENB regarding radiotherapy. Initial treatment consisted of surgery alone in 2 patients; surgery and postoperative radiotherapy in 4; surgery and adjuvant chemotherapy in 1; surgery, postoperative radiotherapy, and chemotherapy in 3; and chemotherapy followed by radiotherapy or concurrent chemoradiotherapy in 5. Five patients did not receive planned radiotherapy because of disease progression. Including 2 patients who received salvage radiotherapy, 14 patients were treated with radiotherapy. Elective nodal irradiation was performed in 4 patients with high-risk factors, including 3 with cervical lymph node metastasis at presentation. Results: Fourteen patients were analyzable, with a median follow-up of 27 months (range, 7-64 months). The overall 3-year survival rate was 73.4%. Local failure occurred in 3 patients (21.4%), regional cervical failure in 3 (21.4%), and distant failure in 2 (14.3%). No cervical nodal failure occurred in patients treated with combined systemic chemotherapy regardless of ENI. Three cervical failures occurred in the 4 patients treated with ENI or neck dissection (75%), none of whom received systemic chemotherapy. Conclusions: ENI during radiotherapy for ENB seems to play a limited role in preventing cervical nodal failure. Omitting ENI may be an option if patients are treated with a combination of radiotherapy and chemotherapy.

  4. Laser catheter-induced atrioventricular nodal delays and atrioventricular block in dogs: acute and chronic observations.

    PubMed

    Narula, O S; Boveja, B K; Cohen, D M; Narula, J T; Tarjan, P P

    1985-02-01

    Selective modification of atrioventricular (AV) nodal conduction, that is, induction of varying degrees of AV nodal delays or block (second or third degree), or both, was achieved with a pervenous laser catheter technique. In six adult mongrel dogs anesthetized with pentobarbital (Nembutal), 5F leads were placed through femoral and external jugular veins and placed into the right atrium and His bundle region. Through another femoral vein, a 200 micron optical fiber was inserted by way of a 7F catheter with a preformed curved tip. Guided by fluoroscopy and His bundle electrograms, the fiber's tip was positioned in the AV nodal region. After autonomic blockade was achieved with intravenous propranolol (5 mg) and atropine (1 mg), AV conduction was analyzed. An argon laser delivered 3 to 4 watts into the fiber in bursts of 10 seconds' duration until the desired degree of AV nodal delay or block (second or third degree) was manifested. Monitoring of His bundle electrograms was continued for 2 hours. Four weekly serial electrocardiograms were recorded, after which electrophysiologic studies were repeated. Acute post-lasing studies showed that: in all six dogs, the mean PR interval was prolonged from 116 ms (range 100 to 135) to 153 ms (range 120 to 185), with the prolongation being caused exclusively by AH lengthening from 68 ms (range 50 to 90) to 105 ms (range 65 to 140); the mean effective refractory period of the AV node increased from less than 185 ms (range less than 150 to less than 200) to 215 ms (range 190 to 280); and the mean atrial pacing cycle length, at which second degree AV nodal block was manifested, increased from 210 ms (range 160 to 260) to 261 ms (range 205 to 320).(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Clinical nodal staging scores for prostate cancer: a proposal for preoperative risk assessment

    PubMed Central

    Kluth, L A; Abdollah, F; Xylinas, E; Rieken, M; Fajkovic, H; Seitz, C; Sun, M; Karakiewicz, P I; Schramek, P; Herman, M P; Becker, A; Hansen, J; Ehdaie, B; Loidl, W; Pummer, K; Lee, R K; Lotan, Y; Scherr, D S; Seiler, D; Ahyai, S A; Chun, F K-H; Graefen, M; Tewari, A; Nonis, A; Bachmann, A; Montorsi, F; Gönen, M; Briganti, A; Shariat, S F

    2014-01-01

    Background: Pelvic lymph node dissection in patients undergoing radical prostatectomy for clinically localised prostate cancer is not without morbidity and its therapeutical benefit is still a matter of debate. The objective of this study was to develop a model that allows preoperative determination of the minimum number of lymph nodes needed to be removed at radical prostatectomy to ensure true nodal status. Methods: We analysed data from 4770 patients treated with radical prostatectomy and pelvic lymph node dissection between 2000 and 2011 from eight academic centres. For external validation of our model, we used data from a cohort of 3595 patients who underwent an anatomically defined extended pelvic lymph node dissection. We estimated the sensitivity of pathological nodal staging using a beta-binomial model and developed a novel clinical (preoperative) nodal staging score (cNSS), which represents the probability that a patient has lymph node metastasis as a function of the number of examined nodes. Results: In the development and validation cohorts, the probability of missing a positive lymph node decreases with increase in the number of nodes examined. A 90% cNSS can be achieved in the development and validation cohorts by examining 1–6 nodes in cT1 and 6–8 nodes in cT2 tumours. With 11 nodes examined, patients in the development and validation cohorts achieved a cNSS of 90% and 80% with cT3 tumours, respectively. Conclusions: Pelvic lymph node dissection is the only reliable technique to ensure accurate nodal staging in patients treated with radical prostatectomy for clinically localised prostate cancer. The minimum number of examined lymph nodes needed for accurate nodal staging may be predictable, being strongly dependent on prostate cancer characteristics at diagnosis. PMID:25003663

  6. GORRAM: Introducing accurate operational-speed radiative transfer Monte Carlo solvers

    NASA Astrophysics Data System (ADS)

    Buras-Schnell, Robert; Schnell, Franziska; Buras, Allan

    2016-06-01

    We present a new approach for solving the radiative transfer equation in horizontally homogeneous atmospheres. The motivation was to develop a fast yet accurate radiative transfer solver to be used in operational retrieval algorithms for next generation meteorological satellites. The core component is the program GORRAM (Generator Of Really Rapid Accurate Monte-Carlo) which generates solvers individually optimized for the intended task. These solvers consist of a Monte Carlo model capable of path recycling and a representative set of photon paths. Latter is generated using the simulated annealing technique. GORRAM automatically takes advantage of limitations on the variability of the atmosphere. Due to this optimization the number of photon paths necessary for accurate results can be reduced by several orders of magnitude. For the shown example of a forward model intended for an aerosol satellite retrieval, comparison with an exact yet slow solver shows that a precision of better than 1% can be achieved with only 36 photons. The computational time is at least an order of magnitude faster than any other type of radiative transfer solver. Merely the lookup table approach often used in satellite retrieval is faster, but on the other hand suffers from limited accuracy. This makes GORRAM-generated solvers an eligible candidate as forward model in operational-speed retrieval algorithms and data assimilation applications. GORRAM also has the potential to create fast solvers of other integrable equations.

  7. Oasis: A high-level/high-performance open source Navier-Stokes solver

    NASA Astrophysics Data System (ADS)

    Mortensen, Mikael; Valen-Sendstad, Kristian

    2015-03-01

    Oasis is a high-level/high-performance finite element Navier-Stokes solver written from scratch in Python using building blocks from the FEniCS project (fenicsproject.org). The solver is unstructured and targets large-scale applications in complex geometries on massively parallel clusters. Oasis utilizes MPI and interfaces, through FEniCS, to the linear algebra backend PETSc. Oasis advocates a high-level, programmable user interface through the creation of highly flexible Python modules for new problems. Through the high-level Python interface the user is placed in complete control of every aspect of the solver. A version of the solver, that is using piecewise linear elements for both velocity and pressure, is shown to reproduce very well the classical, spectral, turbulent channel simulations of Moser et al. (1999). The computational speed is strongly dominated by the iterative solvers provided by the linear algebra backend, which is arguably the best performance any similar implicit solver using PETSc may hope for. Higher order accuracy is also demonstrated and new solvers may be easily added within the same framework.

  8. The impact of improved sparse linear solvers on industrial engineering applications

    SciTech Connect

    Heroux, M.; Baddourah, M.; Poole, E.L.; Yang, Chao Wu

    1996-12-31

    There are usually many factors that ultimately determine the quality of computer simulation for engineering applications. Some of the most important are the quality of the analytical model and approximation scheme, the accuracy of the input data and the capability of the computing resources. However, in many engineering applications the characteristics of the sparse linear solver are the key factors in determining how complex a problem a given application code can solve. Therefore, the advent of a dramatically improved solver often brings with it dramatic improvements in our ability to do accurate and cost effective computer simulations. In this presentation we discuss the current status of sparse iterative and direct solvers in several key industrial CFD and structures codes, and show the impact that recent advances in linear solvers have made on both our ability to perform challenging simulations and the cost of those simulations. We also present some of the current challenges we have and the constraints we face in trying to improve these solvers. Finally, we discuss future requirements for sparse linear solvers on high performance architectures and try to indicate the opportunities that exist if we can develop even more improvements in linear solver capabilities.

  9. Acceleration of FDTD mode solver by high-performance computing techniques.

    PubMed

    Han, Lin; Xi, Yanping; Huang, Wei-Ping

    2010-06-21

    A two-dimensional (2D) compact finite-difference time-domain (FDTD) mode solver is developed based on wave equation formalism in combination with the matrix pencil method (MPM). The method is validated for calculation of both real guided and complex leaky modes of typical optical waveguides against the bench-mark finite-difference (FD) eigen mode solver. By taking advantage of the inherent parallel nature of the FDTD algorithm, the mode solver is implemented on graphics processing units (GPUs) using the compute unified device architecture (CUDA). It is demonstrated that the high-performance computing technique leads to significant acceleration of the FDTD mode solver with more than 30 times improvement in computational efficiency in comparison with the conventional FDTD mode solver running on CPU of a standard desktop computer. The computational efficiency of the accelerated FDTD method is in the same order of magnitude of the standard finite-difference eigen mode solver and yet require much less memory (e.g., less than 10%). Therefore, the new method may serve as an efficient, accurate and robust tool for mode calculation of optical waveguides even when the conventional eigen value mode solvers are no longer applicable due to memory limitation.

  10. The effects of advection solvers on the performance of air quality models

    SciTech Connect

    Tanrikulu, S.; Odman, M.T.

    1996-12-31

    The available numerical solvers for the advection term in the chemical species conservation equation have different properties, and consequently introduce different types of errors. These errors can affect the performance of air quality models and lead to biases in model results. In this study, a large number of advection solvers have been studied and six of them were identified as having potential for use in photochemical models. The identified solvers were evaluated extensively using various numerical tests that are relevant to air quality simulations. Among the solvers evaluated, three of them showed better performance in terms of accuracy and some other characteristics such as conservation of mass and positivity. They are the solvers by Bott, Yuamartino, and Dabdub and Seinfeld. These three solvers were incorporated into the SARMAP Air Quality Model (SAQM) and the August 3-6, 1990 ozone episode in the San Joaquin Valley of California was simulated with each. A model performance analysis was conducted for each simulation using the rich air quality database of the 1990 San Joaquin Valley Air Quality Study. The results of the simulations were compared with each other and the effects of advection solvers on the performance of the model are discussed.

  11. dftatom: A robust and general Schrödinger and Dirac solver for atomic structure calculations

    NASA Astrophysics Data System (ADS)

    Čertík, Ondřej; Pask, John E.; Vackář, Jiří

    2013-07-01

    A robust and general solver for the radial Schrödinger, Dirac, and Kohn-Sham equations is presented. The formulation admits general potentials and meshes: uniform, exponential, or other defined by nodal distribution and derivative functions. For a given mesh type, convergence can be controlled systematically by increasing the number of grid points. Radial integrations are carried out using a combination of asymptotic forms, Runge-Kutta, and implicit Adams methods. Eigenfunctions are determined by a combination of bisection and perturbation methods for robustness and speed. An outward Poisson integration is employed to increase accuracy in the core region, allowing absolute accuracies of 10-8 Hartree to be attained for total energies of heavy atoms such as uranium. Detailed convergence studies are presented and computational parameters are provided to achieve accuracies commonly required in practice. Comparisons to analytic and current-benchmark density-functional results for atomic number Z=1-92 are presented, verifying and providing a refinement to current benchmarks. An efficient, modular Fortran 95 implementation, dftatom, is provided as open source, including examples, tests, and wrappers for interface to other languages; wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines. Program summaryProgram title:dftatom Catalogue identifier: AEPA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 14122 No. of bytes in distributed program, including test data, etc.: 157453 Distribution format: tar.gz Programming language: Fortran 95 with interfaces to Python and C. Computer: Any computer with a Fortran 95 compiler. Operating system: Any OS with a Fortran 95 compiler. RAM: 500 MB

  12. Diffuse radiation

    NASA Technical Reports Server (NTRS)

    1981-01-01

    A diffuse celestial radiation which is isotropic at least on a course scale were measured from the soft X-ray region to about 150 MeV, at which energy the intensity falls below that of the galactic emission for most galactic latitudes. The spectral shape, the intensity, and the established degree of isotropy of this diffuse radiation already place severe constraints on the possible explanations for this radiation. Among the extragalactic theories, the more promising explanations of the isotropic diffuse emission appear to be radiation from exceptional galaxies from matter antimatter annihilation at the boundaries of superclusters of galaxies of matter and antimatter in baryon symmetric big bang models. Other possible sources for extragalactic diffuse gamma radiation are discussed and include normal galaxies, clusters of galaxies, primordial cosmic rays interacting with intergalactic matter, primordial black holes, and cosmic ray leakage from galaxies.

  13. Diffusion barriers

    NASA Technical Reports Server (NTRS)

    Nicolet, M. A.

    1983-01-01

    The choice of the metallic film for the contact to a semiconductor device is discussed. One way to try to stabilize a contact is by interposing a thin film of a material that has low diffusivity for the atoms in question. This thin film application is known as a diffusion barrier. Three types of barriers can be distinguished. The stuffed barrier derives its low atomic diffusivity to impurities that concentrate along the extended defects of a polycrystalline layer. Sacrificial barriers exploit the fact that some (elemental) thin films react in a laterally uniform and reproducible fashion. Sacrificial barriers have the advantage that the point of their failure is predictable. Passive barriers are those most closely approximating an ideal barrier. The most-studied case is that of sputtered TiN films. Stuffed barriers may be viewed as passive barriers whose low diffusivity material extends along the defects of the polycrystalline host.

  14. Robust large-scale parallel nonlinear solvers for simulations.

    SciTech Connect

    Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson

    2005-11-01

    This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any existing linear solver, which makes it simple to write

  15. A new set of direct and iterative solvers for the TOUGH2 family of codes

    SciTech Connect

    Moridis, G.J.

    1995-04-01

    Two new solvers are discussed. LUBAND, the first routine is a direct solver for banded systems and is based on a LU decomposition with partial pivoting and row interchange. BCGSTB, the second routine, is a Preconditioned Conjugate Gradient (PCG) solver with improved speed and convergence characteristics. Bandwidth minimization and gridblock ordering schemes are also introduced into TOUGH2 to improve speed and accuracy. TOUGH2 simulates fluid and heat flows in permeable media and is used for the evaluation of WIPP and TEVES (Thermal Enhanced Vapor Extraction System) that will be used to extract solvents from the Chemical Waste Landfill at Sandia National Laboratories.

  16. A multigrid solver for semi-implicit global shallow-water models

    NASA Technical Reports Server (NTRS)

    Barros, Saulo R. M.; Dee, Dick P.; Dickstein, Flavio

    1990-01-01

    A multigrid solver is developed for the discretized two-dimensional elliptic equation on the sphere that arises from a semiimplicit time discretization of the global shallow-water equations. Different formulations of the semiimplicit scheme result in variable-coefficient Helmholtz-type equations for which no fast direct solvers are available. The efficiency of the multigrid solver is optimal, in the sense that the total operation count is proportional to the number of unknowns. Numerical experiments using initial data derived from actual 300-mb height and wind velocity fields indicate that the present model has very good accuracy and stability properties.

  17. Application of an unstructured grid flow solver to planes, trains and automobiles

    NASA Technical Reports Server (NTRS)

    Spragle, Gregory S.; Smith, Wayne A.; Yadlin, Yoram

    1993-01-01

    Rampant, an unstructured flow solver developed at Fluent Inc., is used to compute three-dimensional, viscous, turbulent, compressible flow fields within complex solution domains. Rampant is an explicit, finite-volume flow solver capable of computing flow fields using either triangular (2d) or tetrahedral (3d) unstructured grids. Local time stepping, implicit residual smoothing, and multigrid techniques are used to accelerate the convergence of the explicit scheme. The paper describes the Rampant flow solver and presents flow field solutions about a plane, train, and automobile.

  18. Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava.

    PubMed

    Röttinger, Eric; DuBuc, Timothy Q; Amiel, Aldine R; Martindale, Mark Q

    2015-01-01

    Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms. PMID:25979707

  19. Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava.

    PubMed

    Röttinger, Eric; DuBuc, Timothy Q; Amiel, Aldine R; Martindale, Mark Q

    2015-05-15

    Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms.

  20. Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava

    PubMed Central

    Röttinger, Eric; DuBuc, Timothy Q.; Amiel, Aldine R.; Martindale, Mark Q.

    2015-01-01

    ABSTRACT Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms. PMID:25979707

  1. An optimal iterative solver for the Stokes problem

    SciTech Connect

    Wathen, A.; Silvester, D.

    1994-12-31

    Discretisations of the classical Stokes Problem for slow viscous incompressible flow gives rise to systems of equations in matrix form for the velocity u and the pressure p, where the coefficient matrix is symmetric but necessarily indefinite. The square submatrix A is symmetric and positive definite and represents a discrete (vector) Laplacian and the submatrix C may be the zero matrix or more generally will be symmetric positive semi-definite. For `stabilised` discretisations (C {ne} 0) and descretisations which are inherently `stable` (C = 0) and so do not admit spurious pressure components even as the mesh size, h approaches zero, the Schur compliment of the matrix has spectral condition number independent of h (given also that B is bounded). Here the authors will show how this property together with a multigrid preconditioner only for the Laplacian block A yields an optimal solver for the Stokes problem through use of the Minimum Residual iteration. That is, combining Minimum Residual iteration for the matrix equation with a block preconditioner which comprises a small number of multigrid V-cycles for the Laplacian block A together with a simple diagonal scaling block provides an iterative solution procedure for which the computational work grows only linearly with the problem size.

  2. Towards Batched Linear Solvers on Accelerated Hardware Platforms

    SciTech Connect

    Haidar, Azzam; Dong, Tingzing Tim; Tomov, Stanimire; Dongarra, Jack J

    2015-01-01

    As hardware evolves, an increasingly effective approach to develop energy efficient, high-performance solvers, is to design them to work on many small and independent problems. Indeed, many applications already need this functionality, especially for GPUs, which are known to be currently about four to five times more energy efficient than multicore CPUs for every floating-point operation. In this paper, we describe the development of the main one-sided factorizations: LU, QR, and Cholesky; that are needed for a set of small dense matrices to work in parallel. We refer to such algorithms as batched factorizations. Our approach is based on representing the algorithms as a sequence of batched BLAS routines for GPU-contained execution. Note that this is similar in functionality to the LAPACK and the hybrid MAGMA algorithms for large-matrix factorizations. But it is different from a straightforward approach, whereby each of GPU's symmetric multiprocessors factorizes a single problem at a time. We illustrate how our performance analysis together with the profiling and tracing tools guided the development of batched factorizations to achieve up to 2-fold speedup and 3-fold better energy efficiency compared to our highly optimized batched CPU implementations based on the MKL library on a two-sockets, Intel Sandy Bridge server. Compared to a batched LU factorization featured in the NVIDIA's CUBLAS library for GPUs, we achieves up to 2.5-fold speedup on the K40 GPU.

  3. Algorithmic Enhancements to the VULCAN Navier-Stokes Solver

    NASA Technical Reports Server (NTRS)

    Litton, D. K.; Edwards, J. R.; White, J. A.

    2003-01-01

    VULCAN (Viscous Upwind aLgorithm for Complex flow ANalysis) is a cell centered, finite volume code used to solve high speed flows related to hypersonic vehicles. Two algorithms are presented for expanding the range of applications of the current Navier-Stokes solver implemented in VULCAN. The first addition is a highly implicit approach that uses subiterations to enhance block to block connectivity between adjacent subdomains. The addition of this scheme allows more efficient solution of viscous flows on highly-stretched meshes. The second algorithm addresses the shortcomings associated with density-based schemes by the addition of a time-derivative preconditioning strategy. High speed, compressible flows are typically solved with density based schemes, which show a high level of degradation in accuracy and convergence at low Mach numbers (M less than or equal to 0.1). With the addition of preconditioning and associated modifications to the numerical discretization scheme, the eigenvalues will scale with the local velocity, and the above problems will be eliminated. With these additions, VULCAN now has improved convergence behavior for multi-block, highly-stretched meshes and also can solve the Navier-Stokes equations for very low Mach numbers.

  4. Generation of Minimum-Consistent DFA Using SAT Solver

    NASA Astrophysics Data System (ADS)

    Inui, Nobuo; Aizawa, Akiko

    The purpose of this study is to develop efficient methods for the minimum-consistent DFA (deterministic finite state automaton) problem. The graph-coloring based SAT (satisfiability) approach proposed by Heule is a state of the art method for this problem. It specially achieves high performance computing in dense problems such as in a popular benchmark problem where rich information about labels is included. In contrast, to solve sparse problems is a challenge for the minimum-consistent DFA problem. To solve sparse problems, we propose three approaches to the SAT formulation: a) the binary color representation, b) the dynamic symmetry breaking and c) the hyper-graph coloring constraint. We organized an experiment using the existing benchmark problems and sparse problems made from them. We observed that our symmetry breaking constraints made the speed up the running time of SAT solver. In addition with this, our other proposed methods were showing the possibility to improve the performance. Then we simulated the perfomance of our methods under the condition that we executed the several program set-ups in parallel. Compared with the previous research results, we finally could reduce the average relative time by 66.5% and the total relative time by 7.6% for sparse problems and by 79.7% and 38.5% for dense problems, respectively. These results showed that our proposed methods were effective for difficult problems.

  5. Approximate Riemann Solvers for the Cosmic Ray Magnetohydrodynamical Equations

    NASA Astrophysics Data System (ADS)

    Kudoh, Yuki; Hanawa, Tomoyuki

    2016-08-01

    We analyze the cosmic-ray magnetohydrodynamic (CR MHD) equations to improve the numerical simulations. We propose to solve them in the fully conservation form, which is equivalent to the conventional CR MHD equations. In the fully conservation form, the CR energy equation is replaced with the CR "number" conservation, where the CR number density is defined as the three fourths power of the CR energy density. The former contains an extra source term, while latter does not. An approximate Riemann solver is derived from the CR MHD equations in the fully conservation form. Based on the analysis, we propose a numerical scheme of which solutions satisfy the Rankine-Hugoniot relation at any shock. We demonstrate that it reproduces the Riemann solution derived by Pfrommer et al. (2006) for a 1D CR hydrodynamic shock tube problem. We compare the solution with those obtained by solving the CR energy equation. The latter solutions deviate from the Riemann solution seriously, when the CR pressure dominates over the gas pressure in the post-shocked gas. The former solutions converge to the Riemann solution and are of the second order accuracy in space and time. Our numerical examples include an expansion of high pressure sphere in an magnetized medium. Fast and slow shocks are sharply resolved in the example. We also discuss possible extension of the CR MHD equations to evaluate the average CR energy.

  6. A generalized Poisson solver for first-principles device simulations

    NASA Astrophysics Data System (ADS)

    Bani-Hashemian, Mohammad Hossein; Brück, Sascha; Luisier, Mathieu; VandeVondele, Joost

    2016-01-01

    Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.

  7. Cooperative solutions coupling a geometry engine and adaptive solver codes

    NASA Technical Reports Server (NTRS)

    Dickens, Thomas P.

    1995-01-01

    Follow-on work has progressed in using Aero Grid and Paneling System (AGPS), a geometry and visualization system, as a dynamic real time geometry monitor, manipulator, and interrogator for other codes. In particular, AGPS has been successfully coupled with adaptive flow solvers which iterate, refining the grid in areas of interest, and continuing on to a solution. With the coupling to the geometry engine, the new grids represent the actual geometry much more accurately since they are derived directly from the geometry and do not use refits to the first-cut grids. Additional work has been done with design runs where the geometric shape is modified to achieve a desired result. Various constraints are used to point the solution in a reasonable direction which also more closely satisfies the desired results. Concepts and techniques are presented, as well as examples of sample case studies. Issues such as distributed operation of the cooperative codes versus running all codes locally and pre-calculation for performance are discussed. Future directions are considered which will build on these techniques in light of changing computer environments.

  8. Approximate Riemann solvers for the cosmic ray magnetohydrodynamical equations

    NASA Astrophysics Data System (ADS)

    Kudoh, Yuki; Hanawa, Tomoyuki

    2016-11-01

    We analyse the cosmic ray magnetohydrodynamic (CR MHD) equations to improve the numerical simulations. We propose to solve them in the fully conservation form, which is equivalent to the conventional CR MHD equations. In the fully conservation form, the CR energy equation is replaced with the CR `number' conservation, where the CR number density is defined as the three-fourths power of the CR energy density. The former contains an extra source term, while latter does not. An approximate Riemann solver is derived from the CR MHD equations in the fully conservation form. Based on the analysis, we propose a numerical scheme of which solutions satisfy the Rankine-Hugoniot relation at any shock. We demonstrate that it reproduces the Riemann solution derived by Pfrommer et al. for a 1D CR hydrodynamic shock tube problem. We compare the solution with those obtained by solving the CR energy equation. The latter solutions deviate from the Riemann solution seriously, when the CR pressure dominates over the gas pressure in the post-shocked gas. The former solutions converge to the Riemann solution and are of the second-order accuracy in space and time. Our numerical examples include an expansion of high-pressure sphere in a magnetized medium. Fast and slow shocks are sharply resolved in the example. We also discuss possible extension of the CR MHD equations to evaluate the average CR energy.

  9. Development of parallel incompressible NS solver on stretched grids

    NASA Astrophysics Data System (ADS)

    Jothiprasad, G.; Caughey, D.; Pope, S. B.

    2003-11-01

    Development of a parallel NS solver for studying DNS and LES of temporal mixing layers is discussed. The equations are cast in strong conservation form on a uniform computational mesh, transformed from a stretched mesh in the physical domain. Variables are defined on a collocated grid, and the transformed equations are solved using a fractional step method. Convective and dissipative terms are treated using explicit Adams-Bashforth and implicit Crank-Nicolson, respectively. Fourth order spatial accuracy is maintained except for hyperviscous subgrid model terms, which are only 2nd order accurate. The block LU analysis of J. B. Perot, extended to fractional step methods on collocated grids, shows that an O(Δ t^2) term involving the pressure gradient must be added to the momentum equations to maintain 2nd order accuracy in time. Using a smaller stencil for the pressure gradients largely simplifies the pressure Poisson equation while still ensuring that discrete continuity is satisfied to appropriate order. Implementation on distributed-memory multiprocessors is achieved using MPI, with care taken to minimize communication overhead.

  10. Verification of continuum drift kinetic equation solvers in NIMROD

    SciTech Connect

    Held, E. D.; Ji, J.-Y.; Kruger, S. E.; Belli, E. A.; Lyons, B. C.

    2015-03-15

    Verification of continuum solutions to the electron and ion drift kinetic equations (DKEs) in NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] is demonstrated through comparison with several neoclassical transport codes, most notably NEO [E. A. Belli and J. Candy, Plasma Phys. Controlled Fusion 54, 015015 (2012)]. The DKE solutions use NIMROD's spatial representation, 2D finite-elements in the poloidal plane and a 1D Fourier expansion in toroidal angle. For 2D velocity space, a novel 1D expansion in finite elements is applied for the pitch angle dependence and a collocation grid is used for the normalized speed coordinate. The full, linearized Coulomb collision operator is kept and shown to be important for obtaining quantitative results. Bootstrap currents, parallel ion flows, and radial particle and heat fluxes show quantitative agreement between NIMROD and NEO for a variety of tokamak equilibria. In addition, velocity space distribution function contours for ions and electrons show nearly identical detailed structure and agree quantitatively. A Θ-centered, implicit time discretization and a block-preconditioned, iterative linear algebra solver provide efficient electron and ion DKE solutions that ultimately will be used to obtain closures for NIMROD's evolving fluid model.

  11. Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver

    NASA Astrophysics Data System (ADS)

    Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre

    2014-06-01

    This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.

  12. Parallelizable approximate solvers for recursions arising in preconditioning

    SciTech Connect

    Shapira, Y.

    1996-12-31

    For the recursions used in the Modified Incomplete LU (MILU) preconditioner, namely, the incomplete decomposition, forward elimination and back substitution processes, a parallelizable approximate solver is presented. The present analysis shows that the solutions of the recursions depend only weakly on their initial conditions and may be interpreted to indicate that the inexact solution is close, in some sense, to the exact one. The method is based on a domain decomposition approach, suitable for parallel implementations with message passing architectures. It requires a fixed number of communication steps per preconditioned iteration, independently of the number of subdomains or the size of the problem. The overlapping subdomains are either cubes (suitable for mesh-connected arrays of processors) or constructed by the data-flow rule of the recursions (suitable for line-connected arrays with possibly SIMD or vector processors). Numerical examples show that, in both cases, the overhead in the number of iterations required for convergence of the preconditioned iteration is small relatively to the speed-up gained.

  13. A generalized Poisson solver for first-principles device simulations.

    PubMed

    Bani-Hashemian, Mohammad Hossein; Brück, Sascha; Luisier, Mathieu; VandeVondele, Joost

    2016-01-28

    Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated. PMID:26827208

  14. Verification of continuum drift kinetic equation solvers in NIMROD

    NASA Astrophysics Data System (ADS)

    Held, E. D.; Kruger, S. E.; Ji, J.-Y.; Belli, E. A.; Lyons, B. C.

    2015-03-01

    Verification of continuum solutions to the electron and ion drift kinetic equations (DKEs) in NIMROD [C. R. Sovinec et al., J. Comp. Phys. 195, 355 (2004)] is demonstrated through comparison with several neoclassical transport codes, most notably NEO [E. A. Belli and J. Candy, Plasma Phys. Controlled Fusion 54, 015015 (2012)]. The DKE solutions use NIMROD's spatial representation, 2D finite-elements in the poloidal plane and a 1D Fourier expansion in toroidal angle. For 2D velocity space, a novel 1D expansion in finite elements is applied for the pitch angle dependence and a collocation grid is used for the normalized speed coordinate. The full, linearized Coulomb collision operator is kept and shown to be important for obtaining quantitative results. Bootstrap currents, parallel ion flows, and radial particle and heat fluxes show quantitative agreement between NIMROD and NEO for a variety of tokamak equilibria. In addition, velocity space distribution function contours for ions and electrons show nearly identical detailed structure and agree quantitatively. A Θ-centered, implicit time discretization and a block-preconditioned, iterative linear algebra solver provide efficient electron and ion DKE solutions that ultimately will be used to obtain closures for NIMROD's evolving fluid model.

  15. Two-Dimensional Ffowcs Williams/Hawkings Equation Solver

    NASA Technical Reports Server (NTRS)

    Lockard, David P.

    2005-01-01

    FWH2D is a Fortran 90 computer program that solves a two-dimensional (2D) version of the equation, derived by J. E. Ffowcs Williams and D. L. Hawkings, for sound generated by turbulent flow. FWH2D was developed especially for estimating noise generated by airflows around such approximately 2D airframe components as slats. The user provides input data on fluctuations of pressure, density, and velocity on some surface. These data are combined with information about the geometry of the surface to calculate histories of thickness and loading terms. These histories are fast-Fourier-transformed into the frequency domain. For each frequency of interest and each observer position specified by the user, kernel functions are integrated over the surface by use of the trapezoidal rule to calculate a pressure signal. The resulting frequency-domain signals are inverse-fast-Fourier-transformed back into the time domain. The output of the code consists of the time- and frequency-domain representations of the pressure signals at the observer positions. Because of its approximate nature, FWH2D overpredicts the noise from a finite-length (3D) component. The advantage of FWH2D is that it requires a fraction of the computation time of a 3D Ffowcs Williams/Hawkings solver.

  16. Incremental planning to control a blackboard-based problem solver

    NASA Technical Reports Server (NTRS)

    Durfee, E. H.; Lesser, V. R.

    1987-01-01

    To control problem solving activity, a planner must resolve uncertainty about which specific long-term goals (solutions) to pursue and about which sequences of actions will best achieve those goals. A planner is described that abstracts the problem solving state to recognize possible competing and compatible solutions and to roughly predict the importance and expense of developing these solutions. With this information, the planner plans sequences of problem solving activities that most efficiently resolve its uncertainty about which of the possible solutions to work toward. The planner only details actions for the near future because the results of these actions will influence how (and whether) a plan should be pursued. As problem solving proceeds, the planner adds new details to the plan incrementally, and monitors and repairs the plan to insure it achieves its goals whenever possible. Through experiments, researchers illustrate how these new mechanisms significantly improve problem solving decisions and reduce overall computation. They briefly discuss current research directions, including how these mechanisms can improve a problem solver's real-time response and can enhance cooperation in a distributed problem solving network.

  17. Update on Advection-Diffusion Purge Flow Model

    NASA Technical Reports Server (NTRS)

    Brieda, Lubos

    2015-01-01

    Gaseous purge is commonly used in sensitive spacecraft optical or electronic instruments to prevent infiltration of contaminants and/or water vapor. Typically, purge is sized using simplistic zero-dimensional models that do not take into account instrument geometry, surface effects, and the dependence of diffusive flux on the concentration gradient. For this reason, an axisymmetric computational fluid dynamics (CFD) simulation was recently developed to model contaminant infiltration and removal by purge. The solver uses a combined Navier-Stokes and Advection-Diffusion approach. In this talk, we report on updates in the model, namely inclusion of a particulate transport model.

  18. A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

    PubMed Central

    Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

    2012-01-01

    An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

  19. Second-order Poisson-Nernst-Planck solver for ion transport

    NASA Astrophysics Data System (ADS)

    Zheng, Qiong; Chen, Duan; Wei, Guo-Wei

    2011-06-01

    The Poisson-Nernst-Planck (PNP) theory is a simplified continuum model for a wide variety of chemical, physical and biological applications. Its ability of providing quantitative explanation and increasingly qualitative predictions of experimental measurements has earned itself much recognition in the research community. Numerous computational algorithms have been constructed for the solution of the PNP equations. However, in the realistic ion-channel context, no second-order convergent PNP algorithm has ever been reported in the literature, due to many numerical obstacles, including discontinuous coefficients, singular charges, geometric singularities, and nonlinear couplings. The present work introduces a number of numerical algorithms to overcome the abovementioned numerical challenges and constructs the first second-order convergent PNP solver in the ion-channel context. First, a Dirichlet to Neumann mapping (DNM) algorithm is designed to alleviate the charge singularity due to the protein structure. Additionally, the matched interface and boundary (MIB) method is reformulated for solving the PNP equations. The MIB method systematically enforces the interface jump conditions and achieves the second order accuracy in the presence of complex geometry and geometric singularities of molecular surfaces. Moreover, two iterative schemes are utilized to deal with the coupled nonlinear equations. Furthermore, extensive and rigorous numerical validations are carried out over a number of geometries, including a sphere, two proteins and an ion channel, to examine the numerical accuracy and convergence order of the present numerical algorithms. Finally, application is considered to a real transmembrane protein, the Gramicidin A channel protein. The performance of the proposed numerical techniques is tested against a number of factors, including mesh sizes, diffusion coefficient profiles, iterative schemes, ion concentrations, and applied voltages. Numerical predictions are

  20. Accuracy of MRI in Prediction of Tumour Thickness and Nodal Stage in Oral Tongue and Gingivobuccal Cancer With Clinical Correlation and Staging

    PubMed Central

    Parihar, Pratap Singh; Parihar, Akhilesh; Goel, Ashok Kumar; Waghwani, Kapil; Gupta, Richa; Bhutekar, Umesh

    2016-01-01

    Introduction Squamous cell carcinoma of lower gingivo-buccal complex and tongue are the most common cancer in the Indian sub-continent. The value of imaging in the staging of Oral Squamous Cell Carcinoma (OSCC) is in judging operability, assessment of the prognostic characteristics and dimensions of the primary tumour, depth of tumour invasion, the presence of cervical metastasis and detection of bone infiltration. Aim This study evaluated squamous cell carcinomas of the oral cavity (tongue and gingivo-buccal complex) on the basis of their appearance, soft tissue extent, depth of tumour invasion and staging. Further, this study assessed the accuracy of MRI in the detection of cervical lymph nodal metastasis on the basis of ADC values on diffusion weighted MR sequence. Materials and Methods T1- and T2-weighted MR, diffusion-weighted sequences and post contrast T1W sequences were performed in various planes on biopsy proven squamous cell carcinomas (61 cases) involving tongue and/or gingivo-buccal region. Depth of tumour invasion was calculated on axial images of post contrast T1W images. The Apparent Diffusion Coefficient (ADC) was measured by using two b factors (500 and 1000 s/mm2). MRI findings were compared clinically and histopathologically. Results Average depth of invasion calculated on MRI was 8.47mm and by histopathology was 6.85mm. Pearson’s correlation coefficient was 0.988. Shrinkage factor was 0.8. A 71% of patients with depth of invasion greater than 9mm showed evidence of cervical lymph nodal metastasis at one or another levels. Cut-off value to discriminate between malignant and benign lymph nodes was 1.038 x10-3 mm2/s in the present study. Conclusion Depth of tumour invasion in oral malignancies can be measured reliably on MRI which helps in predicting cervical lymph node metastasis. Benign or malignant cervical lymph nodes can be differentiated on diffusion-weighted imaging of MRI on the basis of their ADC values. PMID:27504375

  1. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

    NASA Astrophysics Data System (ADS)

    Li, Xinya; Deng, Z. Daniel; Sun, Yannan; Martinez, Jayson J.; Fu, Tao; McMichael, Geoffrey A.; Carlson, Thomas J.

    2014-11-01

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

  2. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

    PubMed Central

    Li, Xinya; Deng, Z. Daniel; Sun, Yannan; Martinez, Jayson J.; Fu, Tao; McMichael, Geoffrey A.; Carlson, Thomas J.

    2014-01-01

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature. PMID:25427517

  3. Finite difference method accelerated with sparse solvers for structural analysis of the metal-organic complexes

    NASA Astrophysics Data System (ADS)

    Guda, A. A.; Guda, S. A.; Soldatov, M. A.; Lomachenko, K. A.; Bugaev, A. L.; Lamberti, C.; Gawelda, W.; Bressler, C.; Smolentsev, G.; Soldatov, A. V.; Joly, Y.

    2016-05-01

    Finite difference method (FDM) implemented in the FDMNES software [Phys. Rev. B, 2001, 63, 125120] was revised. Thorough analysis shows, that the calculated diagonal in the FDM matrix consists of about 96% zero elements. Thus a sparse solver would be more suitable for the problem instead of traditional Gaussian elimination for the diagonal neighbourhood. We have tried several iterative sparse solvers and the direct one MUMPS solver with METIS ordering turned out to be the best. Compared to the Gaussian solver present method is up to 40 times faster and allows XANES simulations for complex systems already on personal computers. We show applicability of the software for metal-organic [Fe(bpy)3]2+ complex both for low spin and high spin states populated after laser excitation.

  4. A novel high-order, entropy stable, 3D AMR MHD solver with guaranteed positive pressure

    NASA Astrophysics Data System (ADS)

    Derigs, Dominik; Winters, Andrew R.; Gassner, Gregor J.; Walch, Stefanie

    2016-07-01

    We describe a high-order numerical magnetohydrodynamics (MHD) solver built upon a novel non-linear entropy stable numerical flux function that supports eight travelling wave solutions. By construction the solver conserves mass, momentum, and energy and is entropy stable. The method is designed to treat the divergence-free constraint on the magnetic field in a similar fashion to a hyperbolic divergence cleaning technique. The solver described herein is especially well-suited for flows involving strong discontinuities. Furthermore, we present a new formulation to guarantee positivity of the pressure. We present the underlying theory and implementation of the new solver into the multi-physics, multi-scale adaptive mesh refinement (AMR) simulation code FLASH (http://flash.uchicago.edu)

  5. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters.

    PubMed

    Li, Xinya; Deng, Z Daniel; Sun, Yannan; Martinez, Jayson J; Fu, Tao; McMichael, Geoffrey A; Carlson, Thomas J

    2014-01-01

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature. PMID:25427517

  6. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

    DOE PAGES

    Li, Xinya; Deng, Z. Daniel; USA, Richland Washington; Sun, Yannan; USA, Richland Washington; Martinez, Jayson J.; USA, Richland Washington; Fu, Tao; USA, Richland Washington; McMichael, Geoffrey A.; et al

    2014-11-27

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developedmore » using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.« less

  7. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters.

    PubMed

    Li, Xinya; Deng, Z Daniel; Sun, Yannan; Martinez, Jayson J; Fu, Tao; McMichael, Geoffrey A; Carlson, Thomas J

    2014-11-27

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

  8. A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

    SciTech Connect

    Li, Xinya; Deng, Z. Daniel; USA, Richland Washington; Sun, Yannan; USA, Richland Washington; Martinez, Jayson J.; USA, Richland Washington; Fu, Tao; USA, Richland Washington; McMichael, Geoffrey A.; USA, Richland Washington; Carlson, Thomas J.; USA, Richland Washington

    2014-11-27

    Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

  9. Efficient Implementation of Multigrid Solvers on Message-Passing Parrallel Systems

    NASA Technical Reports Server (NTRS)

    Lou, John

    1994-01-01

    We discuss our implementation strategies for finite difference multigrid partial differential equation (PDE) solvers on message-passing systems. Our target parallel architecture is Intel parallel computers: the Delta and Paragon system.

  10. Fault tolerance in an inner-outer solver: A GVR-enabled case study

    SciTech Connect

    Zhang, Ziming; Chien, Andrew A.; Teranishi, Keita

    2015-04-18

    Resilience is a major challenge for large-scale systems. It is particularly important for iterative linear solvers, since they take much of the time of many scientific applications. We show that single bit flip errors in the Flexible GMRES iterative linear solver can lead to high computational overhead or even failure to converge to the right answer. Informed by these results, we design and evaluate several strategies for fault tolerance in both inner and outer solvers appropriate across a range of error rates. We implement them, extending Trilinos’ solver library with the Global View Resilience (GVR) programming model, which provides multi-stream snapshots, multi-version data structures with portable and rich error checking/recovery. Lastly, experimental results validate correct execution with low performance overhead under varied error conditions.

  11. Fault tolerance in an inner-outer solver: A GVR-enabled case study

    DOE PAGES

    Zhang, Ziming; Chien, Andrew A.; Teranishi, Keita

    2015-04-18

    Resilience is a major challenge for large-scale systems. It is particularly important for iterative linear solvers, since they take much of the time of many scientific applications. We show that single bit flip errors in the Flexible GMRES iterative linear solver can lead to high computational overhead or even failure to converge to the right answer. Informed by these results, we design and evaluate several strategies for fault tolerance in both inner and outer solvers appropriate across a range of error rates. We implement them, extending Trilinos’ solver library with the Global View Resilience (GVR) programming model, which provides multi-streammore » snapshots, multi-version data structures with portable and rich error checking/recovery. Lastly, experimental results validate correct execution with low performance overhead under varied error conditions.« less

  12. User's Manual for PCSMS (Parallel Complex Sparse Matrix Solver). Version 1.

    NASA Technical Reports Server (NTRS)

    Reddy, C. J.

    2000-01-01

    PCSMS (Parallel Complex Sparse Matrix Solver) is a computer code written to make use of the existing real sparse direct solvers to solve complex, sparse matrix linear equations. PCSMS converts complex matrices into real matrices and use real, sparse direct matrix solvers to factor and solve the real matrices. The solution vector is reconverted to complex numbers. Though, this utility is written for Silicon Graphics (SGI) real sparse matrix solution routines, it is general in nature and can be easily modified to work with any real sparse matrix solver. The User's Manual is written to make the user acquainted with the installation and operation of the code. Driver routines are given to aid the users to integrate PCSMS routines in their own codes.

  13. An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formation

    NASA Technical Reports Server (NTRS)

    Yu, Jr-Kai; Holland, Linda Z.; Holland, Nicholas D.

    2002-01-01

    The full-length sequence and zygotic expression of an amphioxus nodal gene are described. Expression is first detected in the early gastrula just within the dorsal lip of the blastopore in a region of hypoblast that is probably comparable with the vertebrate Spemann's organizer. In the late gastrula and early neurula, expression remains bilaterally symmetrical, limited to paraxial mesoderm and immediately overlying regions of the neural plate. Later in the neurula stage, all neural expression disappears, and mesodermal expression disappears from the right side. All along the left side of the neurula, mesodermal expression spreads into the left side of the gut endoderm. Soon thereafter, all expression is down-regulated except near the anterior and posterior ends of the animal, where transcripts are still found in the mesoderm and endoderm on the left side. At this time, expression also begins in the ectoderm on the left side of the head, in the region where the mouth later forms. These results suggest that amphioxus and vertebrate nodal genes play evolutionarily conserved roles in establishing Spemann's organizer, patterning the mesoderm rostrocaudally and setting up the asymmetrical left-right axis of the body.

  14. Error estimation and adaptive order nodal method for solving multidimensional transport problems

    SciTech Connect

    Zamonsky, O.M.; Gho, C.J.; Azmy, Y.Y.

    1998-01-01

    The authors propose a modification of the Arbitrarily High Order Transport Nodal method whereby they solve each node and each direction using different expansion order. With this feature and a previously proposed a posteriori error estimator they develop an adaptive order scheme to automatically improve the accuracy of the solution of the transport equation. They implemented the modified nodal method, the error estimator and the adaptive order scheme into a discrete-ordinates code for solving monoenergetic, fixed source, isotropic scattering problems in two-dimensional Cartesian geometry. They solve two test problems with large homogeneous regions to test the adaptive order scheme. The results show that using the adaptive process the storage requirements are reduced while preserving the accuracy of the results.

  15. Self-energy of a nodal fermion in a d -wave superconductor

    NASA Astrophysics Data System (ADS)

    Chubukov, A. V.; Tsvelik, A. M.

    2006-06-01

    We reconsider the self-energy of a nodal (Dirac) fermion in a two-dimensional d -wave superconductor. A conventional belief is that ImΣ(ω,T)˜max(ω3,T3) . We show that Σ(ω,k,T) for k along the nodal direction is actually a complex function of ω,T , and the deviation from the mass shell. In particular, the second-order self-energy diverges at a finite T when either ω or k-kF vanish. We show that the full summation of infinite diagrammatic series recovers a finite result for Σ , but the full angle-resolved photoemission spectroscopy spectral function is nonmonotonic and has a kink whose location compared to the mass shell differs qualitatively for spin-and charge-mediated interactions.

  16. The effect of viscosity on steady transonic flow with a nodal solution topology

    NASA Technical Reports Server (NTRS)

    Owocki, Stanley P.; Zank, Gary P.

    1991-01-01

    The effect of viscosity on a steady, transonic flow for which the inviscid limit has a nodal solution topology near the critical point is investigated. For the accelerating case, viscous solutions tend to repel each other, so that a very delicate choice of initial conditions is required to prevent them from diverging. Only the two critical solutions extend to arbitrarily large distances into both the subsonic and supersonic flows. For the decelerating case, the solutions tend to attract, and so an entire two-parameter family of solutions now extends over large distances. The general effect of viscosity on the solution degeneracy of a nodal topology is thus to reduce or limit it for the accelerating case and to enhance it for the decelerating case. The astrophysical implications of these findings are addressed.

  17. Normal State Spectral Lineshapes of Nodal Quasiparticles in Single Layer Bi2201 Superconductor

    SciTech Connect

    Lanzara, A.

    2010-04-30

    A detailed study of the normal state photoemission lineshapes and quasiparticle dispersion for the single layer Bi{sub 2}Sr{sub 2-x}La{sub x}CuO{sub 6+{delta}}(Bi2201) superconductor is presented. We report the first experimental evidence of a double peak structure and a dip of spectral intensity in the energy distribution curves (EDCs) along the nodal direction. The double peak structure is well identified in the normal state, up to ten times the critical temperature. As a result of the same self-energy effect, a strong mass renormalization of the quasiparticle dispersion, i.e. kink, and an increase of the quasiparticle lifetime in the normal state are also observed. Our results provide unambiguous evidence on the existence of bosonic excitation in the normal state, and support a picture where nodal quasiparticles are strongly coupled to the lattice.

  18. Cryopreservation of Passiflora pohlii nodal segments and assessment of genetic stability of regenerated plants.

    PubMed

    Merhy, T S M; Vianna, M G; Garcia, R O; Pacheco, G; Mansur, E

    2014-01-01

    Passiflora pohlii is a wild species native to Brazil, with a potential agronomic interest due to its tolerance to soil-borne pathogens that cause damage to the passion fruit culture, and could be used in breeding. Because this species occurs in impacted regions, the goal of this study was the development of in vitro conservation strategies, using nodal segments from axenic plants. Encapsulation-vitrification and vitrification techniques were tested for cryopreservation of nodal segments. The highest recovery (65%) was obtained with the vitrification technique using treatment with the PVS3 vitrification solution from 30 to 120 min. Post-rewarming recovery was achieved on MSM medium supplemented with 30.8 μM BAP with incubation in the dark for 30 days before transfer in the presence of light. No differences were detected between control and cryopreserved materials as assayed by RAPD and ISSR. PMID:24997838

  19. Coherence Effects of Caroli-de Gennes-Matricon Modes in Nodal Topological Superconductors

    NASA Astrophysics Data System (ADS)

    Tsutsumi, Yasumasa; Kato, Yusuke

    2016-05-01

    Coherence effects by the impurity scattering of Caroli-de Gennes-Matricon (CdGM) modes in a vortex for nodal topological superconductors have been studied. The coherence effects reflect a topological number defined on a particular momentum space avoiding the superconducting gap nodes. First, we analytically derived the eigenvalue and eigenfunction of the CdGM modes, including the zero-energy modes, in a nodal topological superconducting state without impurities, where we focused on a possible superconducting state of UPt3 as an example. Then, we studied impurity effects on the CdGM modes by introducing the impurity self-energy, which are dominated by the coherence factor depending on the eigenfunction of the CdGM modes. For the zero-energy CdGM modes, the coherence factor vanishes in a certain momentum range, which is guaranteed by topological invariance characterized by the one-dimensional winding number.

  20. A Hybrid Nodal Method for Time-Dependent Incompressible Flow in Two-Dimensional Arbitrary Geometries

    SciTech Connect

    Toreja, A J; Uddin, R

    2002-10-21

    A hybrid nodal-integral/finite-analytic method (NI-FAM) is developed for time-dependent, incompressible flow in two-dimensional arbitrary geometries. In this hybrid approach, the computational domain is divided into parallelepiped and wedge-shaped space-time nodes (cells). The conventional nodal integral method (NIM) is applied to the interfaces between adjacent parallelepiped nodes (cells), while a finite analytic approach is applied to the interfaces between parallelepiped and wedge-shaped nodes (cells). In this paper, the hybrid method is formally developed and an application of the NI-FAM to fluid flow in an enclosed cavity is presented. Results are compared with those obtained using a commercial computational fluid dynamics code.

  1. The SX Solver: A New Computer Program for Analyzing Solvent-Extraction Equilibria.

    SciTech Connect

    Lumetta, Gregg J; McNamara, Bruce K; Rapko, Brian M

    1999-01-08

    A new computer program, the SX Solver, has been developed to analyze solvent-extraction equilibria. The program operates out of Microsoft Excel{reg_sign} and uses the built-in ''Solver'' function to minimize the sum of the square of the residuals between measured and calculated distribution coefficients. The extraction of nitric acid by tributyl phosphate has been modeled to illustrate the program's use.

  2. The SX Solver: A New Computer Program for Analyzing Solvent-Extraction Equilibria

    SciTech Connect

    McNamara, B.K.; Rapko, B.M.; Lumetta, G.J.

    1999-02-09

    A new computer program, the SX Solver, has been developed to analyze solvent-extraction equilibria. The program operates out of Microsoft Excel{reg_sign} and uses the built-in ''Solver'' function to minimize the sum of the square of the residuals between measured and calculated distribution coefficients. The extraction of nitric acid by tributylphosphate has been modeled to illustrate the program's use.

  3. The development of an intelligent interface to a computational fluid dynamics flow-solver code

    NASA Technical Reports Server (NTRS)

    Williams, Anthony D.

    1988-01-01

    Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, 3-D, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

  4. Implementation of a parallel unstructured Euler solver on the CM-5

    NASA Technical Reports Server (NTRS)

    Morano, Eric; Mavriplis, D. J.

    1995-01-01

    An efficient unstructured 3D Euler solver is parallelized on a Thinking Machine Corporation Connection Machine 5, distributed memory computer with vectoring capability. In this paper, the single instruction multiple data (SIMD) strategy is employed through the use of the CM Fortran language and the CMSSL scientific library. The performance of the CMSSL mesh partitioner is evaluated and the overall efficiency of the parallel flow solver is discussed.

  5. Maxwell solvers for the simulations of the laser-matter interaction

    NASA Astrophysics Data System (ADS)

    Nuter, Rachel; Grech, Mickael; Gonzalez de Alaiza Martinez, Pedro; Bonnaud, Guy; d'Humières, Emmanuel

    2014-06-01

    With the advent of high intensity laser beams, solving the Maxwell equations with a free-dispersive algorithm is becoming essential. Several Maxwell solvers, implemented in Particle-In-Cell codes, have been proposed. We present here some of them by describing their computational stencil in two-dimensional geometry and defining their stability area as well as their numerical dispersion relation. Numerical simulations of Backward Raman amplification and laser wake-field are presented to compare these different solvers.

  6. Diffusion Monte Carlo in internal coordinates.

    PubMed

    Petit, Andrew S; McCoy, Anne B

    2013-08-15

    An internal coordinate extension of diffusion Monte Carlo (DMC) is described as a first step toward a generalized reduced-dimensional DMC approach. The method places no constraints on the choice of internal coordinates other than the requirement that they all be independent. Using H(3)(+) and its isotopologues as model systems, the methodology is shown to be capable of successfully describing the ground state properties of molecules that undergo large amplitude, zero-point vibrational motions. Combining the approach developed here with the fixed-node approximation allows vibrationally excited states to be treated. Analysis of the ground state probability distribution is shown to provide important insights into the set of internal coordinates that are less strongly coupled and therefore more suitable for use as the nodal coordinates for the fixed-node DMC calculations. In particular, the curvilinear normal mode coordinates are found to provide reasonable nodal surfaces for the fundamentals of H(2)D(+) and D(2)H(+) despite both molecules being highly fluxional.

  7. Numerical divergence effects of equivalence theory in the nodal expansion method

    SciTech Connect

    Zika, M.R.; Downar, T.J. )

    1993-11-01

    Accurate solutions of the advanced nodal equations require the use of discontinuity factors (DFs) to account for the homogenization errors that are inherent in all coarse-mesh nodal methods. During the last several years, nodal equivalence theory (NET) has successfully been implemented for the Cartesian geometry and has received widespread acceptance in the light water reactor industry. The extension of NET to other reactor types has had limited success. Recent efforts to implement NET within the framework of the nodal expansion method have successfully been applied to the fast breeder reactor. However, attempts to apply the same methods to thermal reactors such as the Modular High-Temperature Gas Reactor (MHTGR) have led to numerical divergence problems that can be attributed directly to the magnitude of the DFs. In the work performed here, it was found that the numerical problems occur in the inner and upscatter iterations of the solution algorithm. These iterations use a Gauss-Seidel iterative technique that is always convergent for problems with unity DFs. However, for an MHTGR model that requires large DFs, both the inner and upscatter iterations were divergent. Initial investigations into methods for bounding the DFs have proven unsatisfactory as a means of remedying the convergence problems. Although the DFs could be bounded to yield a convergent solution, several cases were encountered where the resulting flux solution was less accurate than the solution without DFs. For the specific case of problems without upscattering, an alternate numerical method for the inner iteration, an LU decomposition, was identified and shown to be feasible.

  8. Nodal collocation approximation for the multidimensional PL equations applied to transport source problems

    SciTech Connect

    Verdu, G.; Capilla, M.; Talavera, C. F.; Ginestar, D.

    2012-07-01

    PL equations are classical high order approximations to the transport equations which are based on the expansion of the angular dependence of the angular neutron flux and the nuclear cross sections in terms of spherical harmonics. A nodal collocation method is used to discretize the PL equations associated with a neutron source transport problem. The performance of the method is tested solving two 1D problems with analytical solution for the transport equation and a classical 2D problem. (authors)

  9. Three-Dimensional Conformal Radiation Therapy for Esophageal Squamous Cell Carcinoma: Is Elective Nodal Irradiation Necessary?

    SciTech Connect

    Zhao Kuaile; Ma Jinbo; Liu Guang; Wu Kailiang; Shi Xuehui; Jiang Guoliang

    2010-02-01

    Purpose: To evaluate the local control, survival, and toxicity associated with three-dimensional conformal radiotherapy (3D-CRT) for squamous cell carcinoma (SCC) of the esophagus, to determine the appropriate target volumes, and to determine whether elective nodal irradiation is necessary in these patients. Methods and Materials: A prospective study of 3D-CRT was undertaken in patients with esophageal SCC without distant metastases. Patients received 68.4 Gy in 41 fractions over 44 days using late-course accelerated hyperfractionated 3D-CRT. Only the primary tumor and positive lymph nodes were irradiated. Isolated out-of-field regional nodal recurrence was defined as a recurrence in an initially uninvolved regional lymph node. Results: All 53 patients who made up the study population tolerated the irradiation well. No acute or late Grade 4 or 5 toxicity was observed. The median survival time was 30 months (95% confidence interval, 17.7-41.8). The overall survival rate at 1, 2, and 3 years was 77%, 56%, and 41%, respectively. The local control rate at 1, 2, and 3 years was 83%, 74%, and 62%, respectively. Thirty-nine of the 53 patients (74%) showed treatment failure. Seventeen of the 39 (44%) developed an in-field recurrence, 18 (46%) distant metastasis with or without regional failure, and 3 (8%) an isolated out-of-field nodal recurrence only. One patient died of disease in an unknown location. Conclusions: In patients treated with 3D-CRT for esophageal SCC, the omission of elective nodal irradiation was not associated with a significant amount of failure in lymph node regions not included in the planning target volume. Local failure and distant metastases remained the predominant problems.

  10. Salvage therapy of small volume prostate cancer nodal failures: a review of the literature.

    PubMed

    De Bari, Berardino; Alongi, Filippo; Buglione, Michela; Campostrini, Franco; Briganti, Alberto; Berardi, Genoveffa; Petralia, Giuseppe; Bellomi, Massimo; Chiti, Arturo; Fodor, Andrei; Suardi, Nazareno; Cozzarini, Cesare; Nadia, Di Muzio; Scorsetti, Marta; Orecchia, Roberto; Montorsi, Francesco; Bertoni, Filippo; Magrini, Stefano Maria; Jereczek-Fossa, Barbara Alicja

    2014-04-01

    New imaging modalities may be useful to identify prostate cancer patients with small volume, limited nodal relapse ("oligo-recurrent") potentially amenable to local treatments (radiotherapy, surgery) with the aim of long-term control of the disease, even in a condition traditionally considered prognostically unfavorable. This report reviews the new diagnostic tools and the main published data about the role of surgery and radiation therapy in this particular subgroup of patients.

  11. Sentinel Node Identification Rate and Nodal Involvement in the EORTC 10981-22023 AMAROS Trial

    PubMed Central

    Meijnen, Philip; van Tienhoven, Geertjan; van de Velde, Cornelis J. H.; Mansel, Robert E.; Bogaerts, Jan; Duez, Nicole; Cataliotti, Luigi; Klinkenbijl, Jean H. G.; Westenberg, Helen A.; van der Mijle, Huub; Snoj, Marko; Hurkmans, Coen; Rutgers, Emiel J. T.

    2010-01-01

    Background The randomized EORTC 10981-22023 AMAROS trial investigates whether breast cancer patients with a tumor-positive sentinel node biopsy (SNB) are best treated with an axillary lymph node dissection (ALND) or axillary radiotherapy (ART). The aim of the current substudy was to evaluate the identification rate and the nodal involvement. Methods The first 2,000 patients participating in the AMAROS trial were evaluated. Associations between the identification rate and technical, patient-, and tumor-related factors were evaluated. The outcome of the SNB procedure and potential further nodal involvement was assessed. Results In 65 patients, the sentinel node could not be identified. As a result, the sentinel node identification rate was 97% (1,888 of 1,953). Variables affecting the success rate were age, pathological tumor size, histology, year of accrual, and method of detection. The SNB results of 65% of the patients (n = 1,220) were negative and the patients underwent no further axillary treatment. The SNB results were positive in 34% of the patients (n = 647), including macrometastases (n = 409, 63%), micrometastases (n = 161, 25%), and isolated tumor cells (n = 77, 12%). Further nodal involvement in patients with macrometastases, micrometastases, and isolated tumor cells undergoing an ALND was 41, 18, and 18%, respectively. Conclusions With a 97% detection rate in this prospective international multicenter study, the SNB procedure is highly effective, especially when the combined method is used. Further nodal involvement in patients with micrometastases and isolated tumor cells in the sentinel node was similar—both were 18%. PMID:20300966

  12. Atrioventricular Nodal Re-entry Tachycardia in Identical Twins: A Case Report and Literature Review.

    PubMed

    Barake, Walid; Caldwell, Jane; Baranchuk, Adrian

    2013-01-01

    This report details the case of 17 year old identical twins who both presented with paroxysmal supraventricular tachycardia (PSVT). Electrophysiological studies revealed atrioventricular nodal reentry tachycardia (AVNRT) in both twins. Successful but technically challenging slow pathway ablation was performed in both twins. This is the first reported case of confirmed AVNRT in identical twins which adds strong evidence to heritability of the dual AV node physiology and AVNRT. A review of the current literature regarding PSVT in monozygotic twins is provided. PMID:23329875

  13. Nodal soliton solutions for generalized quasilinear Schrödinger equations

    SciTech Connect

    Deng, Yinbin Peng, Shuangjie; Wang, Jixiu

    2014-05-15

    This paper is concerned with constructing nodal radial solutions for generalized quasilinear Schrödinger equations in R{sup N} which arise from plasma physics, fluid mechanics, as well as high-power ultashort laser in matter. For any given integer k ⩾ 0, by using a change of variables and minimization argument, we obtain a sign-changing minimizer with k nodes of a minimization problem.

  14. Atrioventricular Nodal Re-entry Tachycardia in Identical Twins: A Case Report and Literature Review

    PubMed Central

    Barake, Walid; Caldwell, Jane; Baranchuk, Adrian

    2013-01-01

    This report details the case of 17 year old identical twins who both presented with paroxysmal supraventricular tachycardia (PSVT). Electrophysiological studies revealed atrioventricular nodal reentry tachycardia (AVNRT) in both twins. Successful but technically challenging slow pathway ablation was performed in both twins. This is the first reported case of confirmed AVNRT in identical twins which adds strong evidence to heritability of the dual AV node physiology and AVNRT. A review of the current literature regarding PSVT in monozygotic twins is provided. PMID:23329875

  15. Unidimensional Measurement May Evaluate Target Lymph Nodal Response After Induction Chemotherapy for Nasopharyngeal Carcinoma

    PubMed Central

    Chen, Chuanben; Zhang, Mingwei; Xu, Yuanji; Yue, Qiuyuan; Bai, Penggang; Zhou, Lin; Xiao, Youping; Zheng, Dechun; Lin, Kongqi; Qiu, Sufang; Chen, Yunbin; Pan, Jianji

    2016-01-01

    Abstract The aim of the study was to evaluate whether short axis and long axis on axial and coronal magnetic resonance imaging planes would reflect the tumor burden or alteration in size after induction chemotherapy in nasopharyngeal carcinoma. Patients with pathologically confirmed nasopharyngeal carcinoma (n = 37) with at least 1 positive cervical lymph node (axial short axis ≥15 mm) were consecutively enrolled in this prospective study. Lymph nodal measurements were performed along its short axis and long axis in both axial and coronal magnetic resonance imaging planes at diagnosis and after 2 cycles of induction chemotherapy. In addition, lymph nodal volumes were automatically calculated in 3D treatment-planning system, which were used as reference standard. Student's t test or nonparametric Mann–Whitney U test was used to compare the continuous quantitative variables. Meanwhile, the κ statistic and McNemar's test were used to evaluate the degree of agreement and discordance in response categorization among different measurements. Axial short axis was significantly associated with volumes at diagnosis (P < 0.001). A good agreement (κ=0.583) was found between axial short axis and volumetric criteria. However, the inconsistent lymph nodal shrinkage in 4 directions was observed. Axial short-axis shrinking was more rapid than the other 3 parameters. Interestingly, when utilizing the alternative planes for unidimensional measurements to assess tumor response, coronal short-axis showed the best concordance (κ=0.792) to the volumes. Axial short axis may effectively reflect tumor burden or change in tumor size in the assessment of target lymph nodal response after induction chemotherapy for nasopharyngeal carcinoma. However, it should be noted that axial short axis may amplify the therapeutic response. In addition, the role of coronal short axis in the assessment of tumor response needs further evaluation. PMID:26945354

  16. The finite element absolute nodal coordinate formulation incorporated with surface stress effect to model elastic bending nanowires in large deformation

    NASA Astrophysics Data System (ADS)

    He, Jin; Lilley, Carmen M.

    2009-08-01

    Surface stress was incorporated into the finite element absolute nodal coordinate formulation in order to model elastic bending of nanowires in large deformation. The absolute nodal coordinate formulation is a numerical method to model bending structures in large deformation. The generalized Young-Laplace equation was employed to model the surface stress effect on bending nanowires. Effects from surface stress and large deformation on static bending nanowires are presented and discussed. The results calculated with the absolute nodal coordinate formulation incorporated with surface stress show that the surface stress effect makes the bending nanowires behave like softer or stiffer materials depending on the boundary condition. The surface stress effect diminishes as the dimensions of the bending structures increase beyond the nanoscale. The developed algorithm is consistent with the classical absolute nodal coordinate formulation at the macroscale.

  17. Nodal: master and commander of the dorsal-ventral and left-right axes in the sea urchin embryo.

    PubMed

    Molina, M Dolores; de Crozé, Noémie; Haillot, Emmanuel; Lepage, Thierry

    2013-08-01

    Recent studies suggest that specification of the dorsal-ventral and left-right axes of the sea urchin embryo relies on Nodal-expressing signalling centres located in the ventral ectoderm and in the archenteron that share striking similarities with vertebrate organising centres. Nodal and its downstream target BMP2/4 pattern all three germ layers along the dorsal-ventral axis, repress neural fates and control morphogenesis of the larva. Moreover, Nodal establishes left-right asymmetry by repressing formation of the adult rudiment and inhibiting germline cells differentiation on the right side, while BMP2/4 promotes expression of mesodermal genes on the left side. These findings provide a framework for future studies and raise new questions regarding the events upstream and downstream of Nodal and BMP signalling during axis formation. PMID:23769944

  18. A numerically exact local solver applied to salt boundary inversion in seismic full-waveform inversion

    NASA Astrophysics Data System (ADS)

    Willemsen, Bram; Malcolm, Alison; Lewis, Winston

    2016-03-01

    In a set of problems ranging from 4-D seismic to salt boundary estimation, updates to the velocity model often have a highly localized nature. Numerical techniques for these applications such as full-waveform inversion (FWI) require an estimate of the wavefield to compute the model updates. When dealing with localized problems, it is wasteful to compute these updates in the global domain, when we only need them in our region of interest. This paper introduces a local solver that generates forward and adjoint wavefields which are, to machine precision, identical to those generated by a full-domain solver evaluated within the region of interest. This means that the local solver computes all interactions between model updates within the region of interest and the inhomogeneities in the background model outside. Because no approximations are made in the calculation of the forward and adjoint wavefields, the local solver can compute the identical gradient in the region of interest as would be computed by the more expensive full-domain solver. In this paper, the local solver is used to efficiently generate the FWI gradient at the boundary of a salt body. This gradient is then used in a level set method to automatically update the salt boundary.

  19. Fast Poisson, Fast Helmholtz and fast linear elastostatic solvers on rectangular parallelepipeds

    SciTech Connect

    Wiegmann, A.

    1999-06-01

    FFT-based fast Poisson and fast Helmholtz solvers on rectangular parallelepipeds for periodic boundary conditions in one-, two and three space dimensions can also be used to solve Dirichlet and Neumann boundary value problems. For non-zero boundary conditions, this is the special, grid-aligned case of jump corrections used in the Explicit Jump Immersed Interface method. Fast elastostatic solvers for periodic boundary conditions in two and three dimensions can also be based on the FFT. From the periodic solvers we derive fast solvers for the new 'normal' boundary conditions and essential boundary conditions on rectangular parallelepipeds. The periodic case allows a simple proof of existence and uniqueness of the solutions to the discretization of normal boundary conditions. Numerical examples demonstrate the efficiency of the fast elastostatic solvers for non-periodic boundary conditions. More importantly, the fast solvers on rectangular parallelepipeds can be used together with the Immersed Interface Method to solve problems on non-rectangular domains with general boundary conditions. Details of this are reported in the preprint The Explicit Jump Immersed Interface Method for 2D Linear Elastostatics by the author.

  20. Formin DAAM1 Organizes Actin Filaments in the Cytoplasmic Nodal Actin Network

    PubMed Central

    Luo, Weiwei; Lieu, Zi Zhao; Manser, Ed; Bershadsky, Alexander D.; Sheetz, Michael P.

    2016-01-01

    A nodal cytoplasmic actin network underlies actin cytoplasm cohesion in the absence of stress fibers. We previously described such a network that forms upon Latrunculin A (LatA) treatment, in which formin DAAM1 was localized at these nodes. Knock down of DAAM1 reduced the mobility of actin nodes but the nodes remained. Here we have investigated DAAM1 containing nodes after LatA washout. DAAM1 was found to be distributed between the cytoplasm and the plasma membrane. The membrane binding likely occurs through an interaction with lipid rafts, but is not required for F-actin assembly. Interesting the forced interaction of DAAM1 with plasma membrane through a rapamycin-dependent linkage, enhanced F-actin assembly at the cell membrane (compared to the cytoplasm) after the LatA washout. However, immediately after addition of both rapamycin and LatA, the cytoplasmic actin nodes formed transiently, before DAAM1 moved to the membrane. This was consistent with the idea that DAAM1 was initially anchored to cytoplasmic actin nodes. Further, photoactivatable tracking of DAAM1 showed DAAM1 was immobilized at these actin nodes. Thus, we suggest that DAAM1 organizes actin filaments into a nodal complex, and such nodal complexes seed actin network recovery after actin depolymerization. PMID:27760153