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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. 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)

  3. 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.

  4. 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.

  5. 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.

  6. A fast solver for systems of reaction-diffusion equations.

    SciTech Connect

    Garbey, M.; Kaper, H. G.; Romanyukha, N.

    2001-04-20

    In this paper we present a fast algorithm for the numerical solution of systems of reaction-diffusion equations, {partial_derivative}{sub t} u + a {center_dot} {del}u = {Delta}u + f(x,t,u), and x element of {Omega} contained in R{sup 3}, t > 0. Here, u is a vector-valued function, u triple bond u(x,t) element of R{sup m} is large, and the corresponding system of ODEs, {partial_derivative}{sub t}u = F(x,t,u), is stiff. Typical examples arise in air pollution studies, where a is the given wind field and the nonlinear function F models the atmospheric chemistry. The time integration of Eq. (1) is best handled by the method of characteristics. The problem is thus reduced to designing for the reaction-diffusion part a fast solver that has good stability properties for the given time step and does not require the computation of the full Jacobi matrix. An operator-splitting technique, even a high-order one, combining a fast nonlinear ODE solver with an efficient solver for the diffusion operator is less effective when the reaction term is stiff. In fact, the classical Strang splitting method may underperform a first-order source splitting method. The algorithm we propose in this paper uses an a posteriori filtering technique to stabilize the computation of the diffusion term. The algorithm parallelizes well, because the solution of the large system of ODEs is done pointwise; however, the integration of the chemistry may lead to load-balancing problems. The Tchebycheff acceleration technique proposed in offers an alternative that complements the approach presented here. To facilitate the presentation, we limit the discussion to domains {Omega} that either admit a regular discretization grid or decompose into subdomains that admit regular discretization grids. We describe the algorithm for one-dimensional domains in Section 2 and for multidimensional domains in Section 3. Section 4 briefly outlines future work.

  7. 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).

  8. 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)

  9. 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.

  10. A Monte Carlo based nodal diffusion model for criticality analysis, and, Application of high-order cross section homogenization method to two-group nodal diffusion

    NASA Astrophysics Data System (ADS)

    Ilas, Germina

    In the first part, an accurate and fast computational method is presented as an alternative to the Monte Carlo or deterministic transport theory codes currently used to determine the subcriticality of spent fuel storage lattices. The method is capable of analyzing storage configurations with simple or complex lattice cell geometry. It is developed based on two-group nodal diffusion theory, with the nodal cross sections and discontinuity factors determined from continuous-energy Monte Carlo simulations of each unique node (spent fuel assembly type). Three different approaches are developed to estimate the node-averaged diffusion coefficient. The applicability and the accuracy of the nodal method are assessed in two-dimensional geometry through several benchmark configurations typical at Savannah River Site. It is shown that the multiplication constant of the analyzed configurations is within 1% of the MCNP results. In the second part, the high-order cross section homogenization method, recently developed by McKinley and Rahnema, is implemented in the context of two-group nodal diffusion theory. The method corrects the generalized equivalence theory homogenization parameters for the effect of the core environment. The reconstructed fine-mesh (fuel pin) flux and power distributions are a natural byproduct of this method. The method was not tested for multigroup problems, where it was assumed that the multigroup flux expansion in terms of the perturbation parameter is a convergent series. Here the applicability of the method to two-group problems is studied, and it is shown that the perturbation expansion series converges for the multigroup case. A two-group nodal diffusion code with a bilinear intra-nodal flux shape is developed for the implementation of the high-order homogenization method in the context of the generalized equivalence theory. The method is tested by using as a benchmark a core configuration typical of a BWR in slab geometry, which has large

  11. Transport Corrections in Nodal Diffusion Codes for HTR Modeling

    SciTech Connect

    Abderrafi M. Ougouag; Frederick N. Gleicher

    2010-08-01

    The cores and reflectors of High Temperature Reactors (HTRs) of the Next Generation Nuclear Plant (NGNP) type are dominantly diffusive media from the point of view of behavior of the neutrons and their migration between the various structures of the reactor. This means that neutron diffusion theory is sufficient for modeling most features of such reactors and transport theory may not be needed for most applications. Of course, the above statement assumes the availability of homogenized diffusion theory data. The statement is true for most situations but not all. Two features of NGNP-type HTRs require that the diffusion theory-based solution be corrected for local transport effects. These two cases are the treatment of burnable poisons (BP) in the case of the prismatic block reactors and, for both pebble bed reactor (PBR) and prismatic block reactor (PMR) designs, that of control rods (CR) embedded in non-multiplying regions near the interface between fueled zones and said non-multiplying zones. The need for transport correction arises because diffusion theory-based solutions appear not to provide sufficient fidelity in these situations.

  12. 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.

  13. A nodal expansion method for the neutron diffusion equation in cylindrical geometry

    SciTech Connect

    Komlev, O.G.; Suslov, I.R.

    1995-12-31

    A polynomial nodal expansion method (NEM) is applied to solve multigroup diffusion equations in cylindrical R-Z geometry, Fourth-order polynomials are used to approximate one dimensional (1D) transverse integrated fluxes. The special set of the basis functions is used in R-direction. The transverse integrated leakages are approximated by both constant and quadratic polynomials. Preliminary efficiency evaluation of the NEM is carried out for a fast breeder reactor (FBR) model problem. Results indicate computational efficiency of NEM in comparison with finite-difference method (FDM).

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

    PubMed Central

    Jia, Jingfei

    2015-01-01

    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. PMID:26345531

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

    PubMed

    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.

  16. 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.

  17. Quantitative diffusion weighted MRI: a functional biomarker of nodal disease in Hodgkin lymphoma?

    PubMed

    Punwani, Shonit; Prakash, Vineet; Bainbridge, Alan; Taylor, Stuart A; Bandula, Steven; Olsen, Oystein E; Hain, Sharon F; Shankar, Ananth; Daw, Stephen; Humphries, Paul

    2010-01-01

    This study explores the relationship between MRI Apparent Diffusion Coefficient (ADC) and PET Standardized Uptake Value (SUV) measurements in pediatric Hodgkin lymphoma. Sixteen patients (mean age 15.4 yrs, 8 male) with proven Hodgkin lymphoma were recruited and staged using PET-CT, anatomical MRI and additional 1.5T diffusion weighted imaging (DWI) prior to and following chemotherapy. Pre-treatment lymph nodes and anatomically paired post-treatment residual tissue located on MRI were matched to the corresponding PET-CT. Region of interest (ROI) analysis was used to extract quantitative measurements. Mean ADC (ADC(mean)) and maximum SUV (SUV(max)) were recorded and correlation assessed using Spearman statistics. Fifty-three ROIs were sampled. Pre- and post-treatment ADC(mean) ranged from 0.77 × 10(−3) to 1.79 × 10(−3) (median 1.15 × 10(−3) mm(2)s(−1)) and 1.08 × 10(−3) to 3.18 ×10(−3) (median 1.88 × 10(−3) mm(2)s(−1)), and SUV(max) from 2.60 to 25.4 (median 8.85 mg/ml) and 1.00 to 3.50 mg/ml (median 1.90 mg/ml). Median post-treatment ADC(mean) was higher, and median SUV(max) lower than pretreatment values (p < 0.0001). There was an inverse correlation between pre-treatment ADC(mean) and SUV(max) (p = 0.005) and between fractional change ([post-treatment – pre-treatment]/pre-treatment)in ADC(mean) and SUV(max) (p =0.002). Our results confirm a strong reciprocal relationship between nodal ADC(mean) and SUV(max) in Hodgkin lymphoma;supporting the potential application of quantitative DWI as a functional biomarker of disease.

  18. Strain-based diffusion solver for realistic representation of diffusion front in physical reactions.

    PubMed

    Kim, Jong-Hyun; Lee, Jung

    2017-01-01

    When simulating fluids, such as water or fire, interacting with solids, it is a challenging problem to represent details of diffusion front in physical reaction. Previous approaches commonly use isotropic or anisotropic diffusion to model the transport of a quantity through a medium or long interface. We have identified unrealistic monotonous patterns with previous approaches and therefore, propose to extend these approaches by integrating the deformation of the material with the diffusion process. Specifically, stretching deformation represented by strain is incorporated in a divergence-constrained diffusion model. A novel diffusion model is introduced to increase the global rate at which the solid acquires relevant quantities, such as heat or saturation. This ensures that the equations describing fluid flow are linked to the change of solid geometry, and also satisfy the divergence-free condition. Experiments show that our method produces convincing results.

  19. Biological characterization of nodal versus extranodal presentation of diffuse large B-Cell lymphoma using immunohistochemistry.

    PubMed

    Kim, Min Kyoung; Bae, Sung Hwa; Bae, Young Kyung; Kum, Yoon-Seup; Ryoo, Hun Mo; Cho, Hee Soon; Lee, Kyung Hee; Koh, Sung Ae; Lee, Ha Young; Yun, So Yeon; Choi, Jun Hyeok; Hyun, Myung Soo

    2011-10-01

    Diffuse large B cell lymphoma (DLBCL) of primary nodal (PN) or primary extranodal (PEN) origin may differ immunophenotypically, in that PEN lymphoma cells may originate from activated rather than germinal center B (GCB) cells. We evaluated the relationship between DLBCL clinicopathological features, including expression of B-cell differentiation markers, and primary tumor site. Expression of CD10, Bcl-6, Bcl-2, and MUM1 was determined in paraffin-embedded tissues from 123 patients with DLBCL. Of the 123 patients with DLBCL, 40 (32.5%) had the GCB and 83 (67.5%) had the non-GCB phenotype. Fifty-one patients (42%) showed disease involvement at PEN sites, including 29 with disease in the gastrointestinal (GI) tract (14 in the stomach, 15 in the intestine). Of these 51 patients, 16 (31.4%) were classified with the GCB and 35 (68.5%) with the non-GCB subtype. There were no differences in the frequencies of GCB and non-GCB subtypes among primary sites. Of the 72 patients with PN DLBCL, 22 (31%) had the GCB and 50 (69%) had the non-GCB subtype. There were no differences in the frequencies of GCB and non-GCB subtypes between patients with PN and PEN DLBCL. Although lactate dehydrogenase (LDH) concentration > normal, stage >II, and rituximab-cyclophosphamide, doxorubicin, vincristine, and prednisone (RCHOP) treatment were independent predictors of overall survival (OS), GCB subtype, and presence of PEN disease failed to predict survival upon multivariate analysis. There was no difference in GCB and non-GCB phenotypes between patients with PN and PEN DLBCLs. Additional studies are needed to further assess molecular differences between the two groups. Copyright © 2011. Published by Elsevier Inc.

  20. Evaluation of a radiative transfer equation and diffusion approximation hybrid forward solver for fluorescence molecular imaging.

    PubMed

    Gorpas, Dimitris; Andersson-Engels, Stefan

    2012-12-01

    The solution of the forward problem in fluorescence molecular imaging strongly influences the successful convergence of the fluorophore reconstruction. The most common approach to meeting this problem has been to apply the diffusion approximation. However, this model is a first-order angular approximation of the radiative transfer equation, and thus is subject to some well-known limitations. This manuscript proposes a methodology that confronts these limitations by applying the radiative transfer equation in spatial regions in which the diffusion approximation gives decreased accuracy. The explicit integro differential equations that formulate this model were solved by applying the Galerkin finite element approximation. The required spatial discretization of the investigated domain was implemented through the Delaunay triangulation, while the azimuthal discretization scheme was used for the angular space. This model has been evaluated on two simulation geometries and the results were compared with results from an independent Monte Carlo method and the radiative transfer equation by calculating the absolute values of the relative errors between these models. The results show that the proposed forward solver can approximate the radiative transfer equation and the Monte Carlo method with better than 95% accuracy, while the accuracy of the diffusion approximation is approximately 10% lower.

  1. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations

    PubMed Central

    Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul

    2016-01-01

    Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator. Availability and implementation: BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0). Contact: paul.macklin@usc.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26656933

  2. 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.

  3. Directional Diffusion Regulator (DDR) for some numerical solvers of hyperbolic conservation laws

    NASA Astrophysics Data System (ADS)

    Jaisankar, S.; Sheshadri, T. S.

    2013-01-01

    A computational tool called "Directional Diffusion Regulator (DDR)" is proposed to bring forth real multidimensional physics into the upwind discretization in some numerical schemes of hyperbolic conservation laws. The direction based regulator when used with dimension splitting solvers, is set to moderate the excess multidimensional diffusion and hence cause genuine multidimensional upwinding like effect. The basic idea of this regulator driven method is to retain a full upwind scheme across local discontinuities, with the upwind bias decreasing smoothly to a minimum in the farthest direction. The discontinuous solutions are quantified as gradients and the regulator parameter across a typical finite volume interface or a finite difference interpolation point is formulated based on fractional local maximum gradient in any of the weak solution flow variables (say density, pressure, temperature, Mach number or even wave velocity etc.). DDR is applied to both the non-convective as well as whole unsplit dissipative flux terms of some numerical schemes, mainly of Local Lax-Friedrichs, to solve some benchmark problems describing inviscid compressible flow, shallow water dynamics and magneto-hydrodynamics. The first order solutions consistently improved depending on the extent of grid non-alignment to discontinuities, with the major influence due to regulation of non-convective diffusion. The application is also experimented on schemes such as Roe, Jameson-Schmidt-Turkel and some second order accurate methods. The consistent improvement in accuracy either at moderate or marked levels, for a variety of problems and with increasing grid size, reasonably indicate a scope for DDR as a regular tool to impart genuine multidimensional upwinding effect in a simpler framework.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Coexistent Nodal Diffuse Large B-Cell Lymphoma With Extrapulmonary Tuberculosis: A Rare Case.

    PubMed

    Sachdev, Ritesh; Duggal, Rajan; Agrawal, Krati; Goel, Shalini

    2016-02-01

    Extrapulmonary tuberculosis coexistent with lymphomas in the same organ are rare and have been reported in the literature. The most common organs that are involved are small bowel, bronchus, kidney, and lymph nodes. Interestingly, the lymphoma that is commonly present with extrapulmonary tuberculosis is Hodgkin's lymphoma followed by low-grade non-Hodgkin's lymphoma. In the present study, we report a 60-year-old man with complaints of fever, loss of appetite, and generalized weakness. On investigation, generalized lymphadenopathy was noted, and the biopsy of cervical lymph node revealed coexistence of diffuse large B-cell lymphoma with extrapulmonary tuberculosis. This case is the second reported case of diffuse large B-cell lymphoma with extrapulmonary tuberculosis in the world and the first in India.

  9. Development of a Nodal Method for the Solution of the Neutron Diffusion Equation in General Cylindrical Geometry

    SciTech Connect

    Ougouag, Abderrafi Mohammed-El-Ami; Terry, William Knox

    2002-04-01

    The usual strategy for solving the neutron diffusion equation in two or three dimensions by nodal methods is to reduce the multidimensional partial differential equation to a set of ordinary differential equations (ODEs) in the separate spatial coordinates. This reduction is accomplished by “transverse integration” of the equation.1 For example, in three-dimensional Cartesian coordinates, the three-dimensional equation is first integrated over x and y to obtain an ODE in z, then over x and z to obtain an ODE in y, and finally over y and z to obtain an ODE in x. Then the ODEs are solved to obtain onedimensional solutions for the neutron fluxes averaged over the other two dimensions. These solutions are found in regions (“nodes”) small enough for the material properties and cross sections in them to be adequately represented by average values. Because the solution in each node is an exact analytical solution, the nodes can be much larger than the mesh elements used in finite-difference solutions. Then the solutions in the different nodes are coupled by applying interface conditions, ultimately fixing the solutions to the external boundary conditions.

  10. 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.

  11. 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.

  12. 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.

  13. Tissue microarrays in diffuse large B-cell lymphomas: are they really able to identify distinct prognostic groups in lymphomas of both nodal and extranodal origin?

    PubMed

    Laszlo, D; Pruneri, G; Andreola, G; Radice, D; Calabrese, L; Rafaniello, P R; Nassi, L; Sammassimo, S; Alietti, A; Agazzi, A; Vanazzi, A; Martinelli, G

    2011-08-01

    Diffuse large B-cell lymphomas (DLBCL) can be divided into different subgroups (germinal center B-cell-like [GCB] and non-GCB) according to their gene expression profiles. Immunohistochemistry has been proposed as a surrogate for identifying these subgroups, but data about its efficacy in providing prognostic information are conflicting. This study retrospectively analyzed a series of 105 DLBCL, defined as GCB and non-GCB according to CD10, bcl-6, and MUM1 expression. All patients received a first-line anthracycline-based (CHOP-like) chemotherapy. A total of 50 patients (48%) were identified as GCB and 55 (52%) as non-GCB. The overall response rate was 89% (94/105), with 62 (59%) complete response. Disease progressions were equally distributed between the 2 subgroups and were not significantly different (P = .756) considering the primary site of involvement (nodal or extranodal). The median follow-up was 62 months (range 5-126 months). Overall survival at 5 years was not significantly different between the groups (P = .3468) and was 72.3% and 66.6% for GCB and non-GCB, respectively. The results do not support the prognostic value of GCB and non-GCB immunohistochemical categories in DLBCL of both nodal and extranodal origin. Furthermore, a limited number of antigens may be not sufficient to identify the same patterns defined by cDNA microarray. Prospective studies are warranted to address this issue.

  14. 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

  15. 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.

  16. Nodal-link semimetals

    NASA Astrophysics Data System (ADS)

    Yan, Zhongbo; Bi, Ren; Shen, Huitao; Lu, Ling; Zhang, Shou-Cheng; Wang, Zhong

    2017-07-01

    In topological semimetals, the valance band and conduction band meet at zero-dimensional nodal points or one-dimensional nodal rings, which are protected by band topology and symmetries. In this Rapid Communication, we introduce "nodal-link semimetals", which host linked nodal rings in the Brillouin zone. We put forward a general recipe based on the Hopf map for constructing models of nodal-link semimetals. The consequences of nodal ring linking in the Landau levels and Floquet properties are investigated.

  17. Facing Challenges for Monte Carlo Analysis of Full PWR Cores : Towards Optimal Detail Level for Coupled Neutronics and Proper Diffusion Data for Nodal Kinetics

    NASA Astrophysics Data System (ADS)

    Nuttin, A.; Capellan, N.; David, S.; Doligez, X.; El Mhari, C.; Méplan, O.

    2014-06-01

    Safety analysis of innovative reactor designs requires three dimensional modeling to ensure a sufficiently realistic description, starting from steady state. Actual Monte Carlo (MC) neutron transport codes are suitable candidates to simulate large complex geometries, with eventual innovative fuel. But if local values such as power densities over small regions are needed, reliable results get more difficult to obtain within an acceptable computation time. In this scope, NEA has proposed a performance test of full PWR core calculations based on Monte Carlo neutron transport, which we have used to define an optimal detail level for convergence of steady state coupled neutronics. Coupling between MCNP for neutronics and the subchannel code COBRA for thermal-hydraulics has been performed using the C++ tool MURE, developed for about ten years at LPSC and IPNO. In parallel with this study and within the same MURE framework, a simplified code of nodal kinetics based on two-group and few-point diffusion equations has been developed and validated on a typical CANDU LOCA. Methods for the computation of necessary diffusion data have been defined and applied to NU (Nat. U) and Th fuel CANDU after assembly evolutions by MURE. Simplicity of CANDU LOCA model has made possible a comparison of these two fuel behaviours during such a transient.

  18. Analysis of clinical and immunophenotypic features along with treatment outcomes of diffuse large B cell lymphoma patients, based on the involvement of nodal or extranodal primary sites.

    PubMed

    Wang, Cong; Li, Wei; Liu, Chunshui; He, Hua; Bai, Ou

    2016-03-01

    The aim of the present study was to elucidate the clinical features, immunophenotype and treatment outcomes of diffuse large B cell lymphoma (DLBCL) patients based on the involvement of the primary site i.e. lymph node or specific extranodal sites. We analyzed the clinical characteristics, immunophenotype and treatment outcomes of 207 DLBCL patients diagnosed in China between 2007 and 2014 based on the primary site of location. Based on the involvement of primary site of occurrence, DLBCL cases, were classified into different groups like, lymph node (60 cases, 28.98%), gastrointestinal tract (GI) (53 cases, 25.60%), Waldeyer's ring (WR) (31 cases, 14.97%), gland (25 cases, 12.08%), and other extranodal sites (38 cases, 18.36%). Patients with WR involvement were more frequently associated with early stage disease, favorable performance status, absence of bulky disease, normal LDH and ESR levels, and low- or low/intermediate-risk IPI than the other groups. The proportion of DLBCL patients with germinal center B cell (GCB) phenotype was 56.0% for WR, 46.5% for GI, 34.5% for lymph node, 27.8% for other extranodal sites, and 18.2% for gland (P=0.035). The 5-year overall survival (OS) of the entire patient population was 71.1%, and WR group showed a better outcome than nodal group (84.9% vs. 55.9%, P=0.015). In multivariate analysis, bulky disease, bone marrow infiltration, non-GCB phenotype, intermediate/high- or high-risk IPI and SD/PD/Death after first therapy were identified as independent factors for poor OS, while regular application of rituximab and remission after first therapy were identified as favorable prognostic factors for PFS. In this study, WR involvement was associated with more favorable clinical & pathological features along with better outcome than nodal lymphoma. The OS and PFS were largely dependent on other prognostic variables such as IPI or immunophenotype instead of the sites of involvement. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. 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.

  20. Nodal·Gdf1 Heterodimers with Bound Prodomains Enable Serum-independent Nodal Signaling and Endoderm Differentiation

    PubMed Central

    Fuerer, Christophe; Nostro, M. Cristina; Constam, Daniel B.

    2014-01-01

    The TGFβ family member Nodal is central to control pluripotent stem cell fate, but its use as a stem cell differentiation factor is limited by low specific activity. During development, Nodal depends on growth and differentiation factor (Gdf)-1 and on the shared co-receptor Cryptic to specify visceral left-right axis asymmetry. We therefore asked whether the functionality of Nodal can be augmented by Gdf1. Because Nodal and Gdf1 coimmunoprecipitate each other, they were predicted to form heterodimers, possibly to facilitate diffusion or to increase the affinity for signaling receptors. Here, we report that Gdf1 suppresses an unexpected dependence of Nodal on serum proteins and that it is critically required for non-autonomous signaling in cells expressing Cryptic. Nodal, Gdf1, and their cleaved propeptides copurified as a heterodimeric low molecular weight complex that stimulated Activin receptor (Acvr) signaling far more potently than Nodal alone. Although heterodimerization with Gdf1 did not increase binding of Nodal to Fc fusions of co-receptors or Acvr extracellular domains, it was essential for soluble Acvr2 to inhibit Nodal signaling. This implies that Gdf1 potentiates Nodal activity by stabilizing a low molecular weight fraction that is susceptible to neutralization by soluble Acvr2. Finally, in differentiating human ES cells, endodermal markers were more efficiently induced by Nodal·Gdf1 than by Nodal, suggesting that Nodal·Gdf1 is an attractive new reagent to direct stem cell differentiation. PMID:24798330

  1. 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

  2. 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

  3. 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.

  4. Inverse nodal problems

    NASA Astrophysics Data System (ADS)

    Klawonn, David

    2009-05-01

    It is shown that nodal sequences determine the underlying manifold up to scaling within classes of rectangles with Dirichlet boundary conditions, separable two-dimensional tori, two-dimensional flat Klein bottles and flat tori in two and three dimensions.

  5. Polynomial expansion nodal transport method in hexagonal geometry

    SciTech Connect

    Cho, Jin Young; Kim, Chang Hyo; Noh, Taewan

    1997-12-01

    Recently, the polynomial expansion nodal (PEN) method was developed as a new nodal diffusion scheme for hexagonal core analyses. Using the direct polynomial expansion for the node flux, the PEN method not only eliminates the complicated transverse integration procedures-especially in hexagonal geometry-which are frequently used in conventional nodal methods, but also provides a number of features such as the convenient energy group expendability and much enhanced accuracy with less computational effort. In this paper, we further develop the PEN method for the transport equation for the cases where the transport effects are important: highly heterogeneous, small (high-leakage), and fast reactors, etc. Here, we take the even-parity form of transport equation. The main reason is that the diffusion-like nature of the even-parity equation is adequate to establish the new nodal transport method (PEN-TR) using the earlier developed PEN method in diffusion theory.

  6. 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.

  7. Topological nodal line semimetals

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    We review the recent, mainly theoretical, progress in the study of topological nodal line semimetals in three dimensions. In these semimetals, the conduction and the valence bands cross each other along a one-dimensional curve in the three-dimensional Brillouin zone, and any perturbation that preserves a certain symmetry group (generated by either spatial symmetries or time-reversal symmetry) cannot remove this crossing line and open a full direct gap between the two bands. The nodal line(s) is hence topologically protected by the symmetry group, and can be associated with a topological invariant. In this review, (i) we enumerate the symmetry groups that may protect a topological nodal line; (ii) we write down the explicit form of the topological invariant for each of these symmetry groups in terms of the wave functions on the Fermi surface, establishing a topological classification; (iii) for certain classes, we review the proposals for the realization of these semimetals in real materials; (iv) we discuss different scenarios that when the protecting symmetry is broken, how a topological nodal line semimetal becomes Weyl semimetals, Dirac semimetals, and other topological phases; and (v) we discuss the possible physical effects accessible to experimental probes in these materials. Project partially supported by the National Key Research and Development Program of China (Grant Nos. 2016YFA0302400 and 2016YFA0300604), partially by the National Natural Science Foundation of China (Grant Nos. 11274359 and 11422428), the National Basic Research Program of China (Grant No. 2013CB921700), and the “Strategic Priority Research Program (B)” of the Chinese Academy of Sciences (Grant No. XDB07020100).

  8. 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

  9. 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

  10. Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units

    DTIC Science & Technology

    2011-09-22

    Physics 109, 11 (2011), 113308. [9] Klockner, A., Warburton, T., Bridge, J., and Hesthaven, J. Nodal Discontinuous Galerkin Methods on Graphics...Graphic Processing Units ( GPU ) to model reactive gas mixture with detailed chemical kinetics. The solver incorporates high-order finite volume methods...method. We explored different approaches in implementing a fast kinetics solver on the GPU . The detail of the implementation is discussed in the

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

    SciTech Connect

    ARIANI, IMELDA

    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- or 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.

  12. Nodalization study for BETHSY experiment

    SciTech Connect

    Petelin, S.; Mavko, B.; Ravnikar, I.; Cebull, P.; Hassan, Y.A.

    1996-08-01

    The BETHSY experiment 9.1.b was used to assess different versions of the RELAP5 computer code using three various detailed nodalizations. This experimental transient scenario involved a scaled 2 inch cold leg break without high pressure safety injection and with delayed operator action for a secondary system depressurization. In order to optimize details of nodalization regard to satisfactory accuracy a detailed study of different RELAP5 codes and nodalizations was performed. Qualitative evolution of RELAP5 code was also analyzed.

  13. 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 \

  14. Universal nodal Fermi velocity

    SciTech Connect

    Zhou, X.J.; Yoshida, T.; Lanzara, A.; Bogdanov, P.V.; Kellar, S.A.; Shen, K.M.; Yang, W.L.; Ronning, F.; Sasagawa, T.; Kakeshita, T.; Noda, T.; Eisaki, H.; Uchida, S.; Lin, C.T.; Zhou, F.; Xiong, J.W.; Ti, W.X.; Zhao, Z.X.; Fujimori, A.; Hussain, Z.; Shen, Z.-X.

    2003-05-27

    The physical properties of cuprate superconductors vary dramatically as a function of doping, evolving from antiferromagnetic insulator to superconductors, and to normal metal upon doping. They also vary among different families of compounds, most prominent being the superconducting transition temperature (Tc), which ranges from 38 K for optimally-doped (La2-xSrx)CuO4 (x=0.15) to 135 K for Hg2Ba2Ca2Cu3O10. Such dramatic changes with doping and material family have been observed in transport properties, optical response, magnetic excitation spectra, the superconducting condensation energy and superfluid density. All these seem to imply that the underlying microscopic quantities of cup rates are generally non-universal. This paper presents a striking exception by providing experimental evidence that the nodal Fermi velocity, a quantity that governs the low-energy quasiparticle dynamics along the (0,0)-(p,p) direction where the d-wave superconducting gap is zero in cuprate superconductors , is actually universal. This conclusion is based on extensive measurements from a wide range of doping, and from five families of hole-doped cuprates whose maximum Tc varies by a factor of three or more. The invariance of the nodal Fermi velocity all the way to the Mott insulator boundary clearly signals the breakdown of the conventional Fermi liquid theory where the metal-insulator transition is realized by the divergence of the effective mass near the insulator boundary. A possible way to understand this behavior is the nanoscale phase separation where doped holes tend to create a preferred local environment so that the behavior of the individual hole is more or less the same for low energy dynamics

  15. Parallel Multigrid Equation Solver

    SciTech Connect

    Adams, Mark

    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.

  16. 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

  17. A composite nodal finite element for hexagons

    SciTech Connect

    Hennart, J.P.; Mund, E.H. |; Valle, E. Del

    1997-10-01

    A nodal algorithm for the solution of the multigroup diffusion equations in hexagonal arrays is analyzed. Basically, the method consists of dividing each hexagon into four quarters and mapping the hexagon quarters onto squares. The resulting boundary value problem on a quadrangular domain is solved in primal weak formulation. Nodal finite element methods like the Raviart-Thomas RTk schemes provide accurate analytical expansions of the solution in the hexagons. Transverse integration cannot be performed on the equations in the quadrangular domain as simply as it is usually done on squares because these equations have essentially variable coefficients. However, by considering an auxiliary problem with constant coefficients (on the same quadrangular domain) and by using a preconditioning approach, transverse integration can be performed as for rectangular geometry. A description of the algorithm is given for a one-group diffusion equation. Numerical results are presented for a simple model problem with a known analytical solution and for k{sub eff} evaluations of some benchmark problems proposed in the literature. For the analytical problem, the results indicate that the theoretical convergence orders of RTk schemes (k = 0,1) are obtained, yielding accurate solutions at the expense of a few preconditioning iterations.

  18. 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.

  19. 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.

  20. An Open Hybrid Plasma Solver

    NASA Astrophysics Data System (ADS)

    Holmström, M.; Nilsson, H.

    2012-09-01

    We present a hybrid plasma solver (particle ions, fluid mass-less electrons). The software is built on the public available FLASH software, developed at the University of Chicago [1], that provide adaptive grids and is fully parallelized. FLASH is a general parallel solver for compressible flow problems. It is written in Fortran 90, well structured into modules, has good support, and is open source. The parallelization is done using a block-structured adaptive cartesian grid with the Message-Passing Interface (MPI) library as the underlying communication layer. The hybrid solver in FLASH uses cell centered finite differences [2] and conserves energy well [3]. Recently we have added to the hybrid solver the capability of handling vacuum regions, non-uniform resistivity, external fields, and hyperresistivity. We also present an application of the solver to the interaction between the Moon and the solar wind [4], as illustrated in Fig. 1.

  1. 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.

  2. Antiferromagnetic topological nodal line semimetals

    NASA Astrophysics Data System (ADS)

    Wang, Jing

    2017-08-01

    We study three-dimensional nodal line semimetals (NLSMs) with magnetic ordering and strong spin-orbit interaction. Two distinct classes of magnetic NLSMs are proposed. The first class is band-inversion NLSM where the accidental line node is induced by band inversion and locally protected by glide mirror plane and the combined time-reversal and inversion symmetries. This can be viewed as a trivial stacking of the two-dimensional antiferromagnetic Dirac semimetals. The second class is essential NLSM where the nodal features are filling enforced by specific magnetic symmetry group. We further provide two concrete tight-binding models for magnetic NLSMs which belong to these two different classes, respectively. We conclude with a brief discussion on the possible material venues and the experimental implications for such phases.

  3. RELATIVISTIC MAGNETOHYDRODYNAMICS: RENORMALIZED EIGENVECTORS AND FULL WAVE DECOMPOSITION RIEMANN SOLVER

    SciTech Connect

    Anton, Luis; MartI, Jose M; Ibanez, Jose M; Aloy, Miguel A.; Mimica, Petar; Miralles, Juan A.

    2010-05-01

    We obtain renormalized sets of right and left eigenvectors of the flux vector Jacobians of the relativistic MHD equations, which are regular and span a complete basis in any physical state including degenerate ones. The renormalization procedure relies on the characterization of the degeneracy types in terms of the normal and tangential components of the magnetic field to the wave front in the fluid rest frame. Proper expressions of the renormalized eigenvectors in conserved variables are obtained through the corresponding matrix transformations. Our work completes previous analysis that present different sets of right eigenvectors for non-degenerate and degenerate states, and can be seen as a relativistic generalization of earlier work performed in classical MHD. Based on the full wave decomposition (FWD) provided by the renormalized set of eigenvectors in conserved variables, we have also developed a linearized (Roe-type) Riemann solver. Extensive testing against one- and two-dimensional standard numerical problems allows us to conclude that our solver is very robust. When compared with a family of simpler solvers that avoid the knowledge of the full characteristic structure of the equations in the computation of the numerical fluxes, our solver turns out to be less diffusive than HLL and HLLC, and comparable in accuracy to the HLLD solver. The amount of operations needed by the FWD solver makes it less efficient computationally than those of the HLL family in one-dimensional problems. However, its relative efficiency increases in multidimensional simulations.

  4. Relativistic Magnetohydrodynamics: Renormalized Eigenvectors and Full Wave Decomposition Riemann Solver

    NASA Astrophysics Data System (ADS)

    Antón, Luis; Miralles, Juan A.; Martí, José M.; Ibáñez, José M.; Aloy, Miguel A.; Mimica, Petar

    2010-05-01

    We obtain renormalized sets of right and left eigenvectors of the flux vector Jacobians of the relativistic MHD equations, which are regular and span a complete basis in any physical state including degenerate ones. The renormalization procedure relies on the characterization of the degeneracy types in terms of the normal and tangential components of the magnetic field to the wave front in the fluid rest frame. Proper expressions of the renormalized eigenvectors in conserved variables are obtained through the corresponding matrix transformations. Our work completes previous analysis that present different sets of right eigenvectors for non-degenerate and degenerate states, and can be seen as a relativistic generalization of earlier work performed in classical MHD. Based on the full wave decomposition (FWD) provided by the renormalized set of eigenvectors in conserved variables, we have also developed a linearized (Roe-type) Riemann solver. Extensive testing against one- and two-dimensional standard numerical problems allows us to conclude that our solver is very robust. When compared with a family of simpler solvers that avoid the knowledge of the full characteristic structure of the equations in the computation of the numerical fluxes, our solver turns out to be less diffusive than HLL and HLLC, and comparable in accuracy to the HLLD solver. The amount of operations needed by the FWD solver makes it less efficient computationally than those of the HLL family in one-dimensional problems. However, its relative efficiency increases in multidimensional simulations.

  5. Parallel, Implicit, Finite Element Solver

    NASA Astrophysics Data System (ADS)

    Lowrie, Weston; Shumlak, Uri; Meier, Eric; Marklin, George

    2007-11-01

    A parallel, implicit, finite element solver is described for solutions to the ideal MHD equations and the Pseudo-1D Euler equations. The solver uses the conservative flux source form of the equations. This helps simplify the discretization of the finite element method by keeping the specification of the physics separate. An implicit time advance is used to allow sufficiently large time steps. The Portable Extensible Toolkit for Scientific Computation (PETSc) is implemented for parallel matrix solvers and parallel data structures. Results for several test cases are described as well as accuracy of the method.

  6. 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.

  7. 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)

  8. 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)

  9. 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.

  10. Nodal Domain Statistics for Quantum Maps, Percolation, and Stochastic Loewner Evolution

    SciTech Connect

    Keating, J. P.; Marklof, J.; Williams, I. G.

    2006-07-21

    We develop a percolation model for nodal domains in the eigenvectors of quantum chaotic torus maps. Our model follows directly from the assumption that the quantum maps are described by random matrix theory. Its accuracy in predicting statistical properties of the nodal domains is demonstrated for perturbed cat maps and supports the use of percolation theory to describe the wave functions of general Hamiltonian systems. We also demonstrate that the nodal domains of the perturbed cat maps obey the Cardy crossing formula and find evidence that the boundaries of the nodal domains are described by stochastic Loewner evolution with diffusion constant {kappa} close to the expected value of 6, suggesting that quantum chaotic wave functions may exhibit conformal invariance in the semiclassical limit.

  11. 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.

  12. Self-correcting Multigrid Solver

    SciTech Connect

    Jerome L.V. Lewandowski

    2004-06-29

    A new multigrid algorithm based on the method of self-correction for the solution of elliptic problems is described. The method exploits information contained in the residual to dynamically modify the source term (right-hand side) of the elliptic problem. It is shown that the self-correcting solver is more efficient at damping the short wavelength modes of the algebraic error than its standard equivalent. When used in conjunction with a multigrid method, the resulting solver displays an improved convergence rate with no additional computational work.

  13. Improved pressurized water reactor radial reflector modeling in nodal analysis

    SciTech Connect

    Mueller, E.Z. )

    1991-10-01

    A one-dimensional method based on a combination of the nodal equivalence theory and response matrix homogenization methods was previously described for determining environment-insensitive equivalent few-group diffusion theory parameters for homogenized radial reflector nodes of a pressurized water reactor. This reflector model, called the NGET-RM model, yields equivalent nodal parameters that do not account for the two-dimensional structure of the baffle at core corners; this can lead to significant errors in computed two-dimensional core power distributions. A semi-empirical correction procedure is proposed for reducing the two-dimensional effects associated with this particular one-dimensional reflector model. Numerical two-group experiments are performed for a given reflector configuration (and soluble boron concentration) to determine optimal values of the two empirical factors defined by this model. In this paper it is shown that the resultant factors are rather insensitive to core configuration or core conditions and that their application yields improved two-group NGET-RM reflector parameters with which accurate nodal power distributions can be obtained. The results are also compared with those obtained with another one-dimensional environment-insensitive model that has an extra degree of freedom utilized here to reduce two-dimensional effects. Some practical aspects related to the application of the proposed correction procedure are briefly discussed.

  14. 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.

  15. 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.

  16. Optical conductivity of nodal metals

    PubMed Central

    Homes, C. C.; Tu, J. J.; Li, J.; Gu, G. D.; Akrap, A.

    2013-01-01

    Fermi liquid theory is remarkably successful in describing the transport and optical properties of metals; at frequencies higher than the scattering rate, the optical conductivity adopts the well-known power law behavior σ1(ω) ∝ ω−2. We have observed an unusual non-Fermi liquid response σ1(ω) ∝ ω−1±0.2 in the ground states of several cuprate and iron-based materials which undergo electronic or magnetic phase transitions resulting in dramatically reduced or nodal Fermi surfaces. The identification of an inverse (or fractional) power-law behavior in the residual optical conductivity now permits the removal of this contribution, revealing the direct transitions across the gap and allowing the nature of the electron-boson coupling to be probed. The non-Fermi liquid behavior in these systems may be the result of a common Fermi surface topology of Dirac cone-like features in the electronic dispersion. PMID:24336241

  17. Distributions of Nodal Prices in PJM Market

    NASA Astrophysics Data System (ADS)

    Kunio, Matsumoto; Yoshio, Ichida; Michiko, Makino; Hiroaki, Tanaka

    As the deregulation of electric business proceeds, it is important to analyze the distributions of prices in the power market. In this paper, we analyze the nodal prices of the PJM market, which is representative of power markets in the US. First, we verify Weibull’s property of the distribution of nodal prices. Then we verify Poisson’s property of the interval of loss process.

  18. Nodal network generator for CAVE3

    NASA Technical Reports Server (NTRS)

    Palmieri, J. V.; Rathjen, K. A.

    1982-01-01

    A new extension of CAVE3 code was developed that automates the creation of a finite difference math model in digital form ready for input to the CAVE3 code. The new software, Nodal Network Generator, is broken into two segments. One segment generates the model geometry using a Tektronix Tablet Digitizer and the other generates the actual finite difference model and allows for graphic verification using Tektronix 4014 Graphic Scope. Use of the Nodal Network Generator is described.

  19. Nodal signalling determines biradial asymmetry in Hydra.

    PubMed

    Watanabe, Hiroshi; Schmidt, Heiko A; Kuhn, Anne; Höger, Stefanie K; Kocagöz, Yigit; Laumann-Lipp, Nico; Ozbek, Suat; Holstein, Thomas W

    2014-11-06

    In bilaterians, three orthogonal body axes define the animal form, with distinct anterior-posterior, dorsal-ventral and left-right asymmetries. The key signalling factors are Wnt family proteins for the anterior-posterior axis, Bmp family proteins for the dorsal-ventral axis and Nodal for the left-right axis. Cnidarians, the sister group to bilaterians, are characterized by one oral-aboral body axis, which exhibits a distinct biradiality of unknown molecular nature. Here we analysed the biradial growth pattern in the radially symmetrical cnidarian polyp Hydra, and we report evidence of Nodal in a pre-bilaterian clade. We identified a Nodal-related gene (Ndr) in Hydra magnipapillata, and this gene is essential for setting up an axial asymmetry along the main body axis. This asymmetry defines a lateral signalling centre, inducing a new body axis of a budding polyp orthogonal to the mother polyp's axis. Ndr is expressed exclusively in the lateral bud anlage and induces Pitx, which encodes an evolutionarily conserved transcription factor that functions downstream of Nodal. Reminiscent of its function in vertebrates, Nodal acts downstream of β-Catenin signalling. Our data support an evolutionary scenario in which a 'core-signalling cassette' consisting of β-Catenin, Nodal and Pitx pre-dated the cnidarian-bilaterian split. We presume that this cassette was co-opted for various modes of axial patterning: for example, for lateral branching in cnidarians and left-right patterning in bilaterians.

  20. Preserved nodal number effects under equal reinforcement.

    PubMed

    Wang, Ting; Dack, Charlotte; McHugh, Louise; Whelan, Robert

    2011-09-01

    The present set of experiments tested the hypothesis that the nodal number effects observed in previous studies of stimulus equivalence were due to the confounding factor of training structure that resulted in unequal reinforcement across trial types. In Experiment 1, two 5-member equivalence classes were trained across equal and unequal reinforcement conditions, both with and without a limited hold. A significant nodal effect, as measured by response speed, was found in the equal reinforcement, no-limited-hold condition. In Experiment 2, two 6-member equivalence classes were trained in equal and unequal reinforcement conditions without limited hold. In a transfer-of-function test, clear nodal effects were observed in the equal reinforcement condition. Experiment 3 replicated and extended the findings of Experiments 1 and 2 with an increased number of baseline training trials. The results of the present study suggest that the effects of nodal number are independent of differential reinforcement. Furthermore, a transfer-of-function test was most sensitive to nodal effects, response speed was the next most sensitive measure, and response accuracy was the least sensitive measure of nodal effects.

  1. A Riemann solver for single-phase and two-phase shallow flow models based on relaxation. Relations with Roe and VFRoe solvers

    SciTech Connect

    Pelanti, Marica; Bouchut, Francois; Mangeney, Anne

    2011-02-01

    We present a Riemann solver derived by a relaxation technique for classical single-phase shallow flow equations and for a two-phase shallow flow model describing a mixture of solid granular material and fluid. Our primary interest is the numerical approximation of this two-phase solid/fluid model, whose complexity poses numerical difficulties that cannot be efficiently addressed by existing solvers. In particular, we are concerned with ensuring a robust treatment of dry bed states. The relaxation system used by the proposed solver is formulated by introducing auxiliary variables that replace the momenta in the spatial gradients of the original model systems. The resulting relaxation solver is related to Roe solver in that its Riemann solution for the flow height and relaxation variables is formally computed as Roe's Riemann solution. The relaxation solver has the advantage of a certain degree of freedom in the specification of the wave structure through the choice of the relaxation parameters. This flexibility can be exploited to handle robustly vacuum states, which is a well known difficulty of standard Roe's method, while maintaining Roe's low diffusivity. For the single-phase model positivity of flow height is rigorously preserved. For the two-phase model positivity of volume fractions in general is not ensured, and a suitable restriction on the CFL number might be needed. Nonetheless, numerical experiments suggest that the proposed two-phase flow solver efficiently models wet/dry fronts and vacuum formation for a large range of flow conditions. As a corollary of our study, we show that for single-phase shallow flow equations the relaxation solver is formally equivalent to the VFRoe solver with conservative variables of Gallouet and Masella [T. Gallouet, J.-M. Masella, Un schema de Godunov approche C.R. Acad. Sci. Paris, Serie I, 323 (1996) 77-84]. The relaxation interpretation allows establishing positivity conditions for this VFRoe method.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. A survey of SAT solver

    NASA Astrophysics Data System (ADS)

    Gong, Weiwei; Zhou, Xu

    2017-06-01

    In Computer Science, the Boolean Satisfiability Problem(SAT) is the problem of determining if there exists an interpretation that satisfies a given Boolean formula. SAT is one of the first problems that was proven to be NP-complete, which is also fundamental to artificial intelligence, algorithm and hardware design. This paper reviews the main algorithms of the SAT solver in recent years, including serial SAT algorithms, parallel SAT algorithms, SAT algorithms based on GPU, and SAT algorithms based on FPGA. The development of SAT is analyzed comprehensively in this paper. Finally, several possible directions for the development of the SAT problem are proposed.

  7. Primary extra nodal Hodgkin disease: Bone presentation.

    PubMed

    Nikolica, Goran; Badnjar, Zorka; Cadjenovic, Tanja; Raceta-Masic, Dijana

    2014-01-01

    Extra nodal and extra lymphatic propagation of Hodgkin's disease is a characteristic of the fourth stage of disease when the organs are affected. Primary appearances of the disease outside the lymph node is a rare event. Therefore, it makes diagnostic problem. Skeletal system is possible localization of primary extra nodal Hodgkin's disease. Women, 42-years-old, was admitted to hospital because of swelling and pain in the right shoulder. After imaging and histological examination diagnosed Hodgkin's nodular sclerosing histological subtype disease has been established. The patient starts to receive chemotherapy. Primary extra nodal Hodgkin's disease of bone is manifested with painful swelling in geared area. Imaging method shows destruction of the affected bone, with swelling of the soft tissues. Propagation in soft tissue is not accompanied by their destruction, but rather manifested swelling of the surrounding soft tissue.

  8. MURR nodal analysis with simple interactive simulation

    NASA Astrophysics Data System (ADS)

    Enani, Mohammad Abdulsamad

    The main goal of this research is to design and produce computer codes that should do a NODAL analysis of the core of Missouri University Research Reactor 'MURR' with a simple neutron transient simulation. These codes should be executed on any of the family of the widely used modern IBM/PC (or IBM/PS) microcomputers (or compatibles). The nodal analysis code should find the power (or flux) distribution inside the reactor core and calculate fuel burnup for each of the fuel elements by using the nodal analysis technique described in chapter 3. The simulator code is a relatively simple, educational aid of MURR reactor kinetics simulation that uses one group point reactor model.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Newton Solver Stabilization for Stokes Solvers in Geodynamic Problems

    NASA Astrophysics Data System (ADS)

    Fraters, Menno; Bangerth, Wolfgang; Thieulot, Cedric; Spakman, Wim

    2017-04-01

    The most commonly used method by the geodynamical community for solving non-linear equations is the Picard fixed-point iteration. However, the Newton method has recently gained interest within this community because it formally leads to quadratic convergence close to the solution as compared to the global linear convergence of the Picard iteration. In mantle dynamics, a blend of pressure and strain-rate dependent visco-plastic rheologies is often used. While for power-law rheologies the Jacobian is guaranteed to be Symmetric Positive Definite (SPD), for more complex (compressible) rheologies, the Jacobian may become non-SPD. Here we present a new method for efficiently enforce the Jacobian to be SPD, necessary for our current highly efficient Stokes solvers, with a minimum loss in convergence rate. Furthermore, we show results for both incompressible and compressible models.

  14. Percutaneous Radiofrequency Ablation of Nodal Metastases

    SciTech Connect

    Gervais, Debra A.; Arellano, Ronald S.; Mueller, Peter R.

    2002-12-15

    We report our experience with percutaneous image-guided radiofrequency (RF) ablation to treat isolated nodal metastases. Four patients underwent image-guided percutaneous RF ablation of metastatic disease involving retrocrural nodes,retroperitoneal nodes, or pelvic nodes. Coagulation necrosis was achieved in all cases.

  15. MACSYMA's symbolic ordinary differential equation solver

    NASA Technical Reports Server (NTRS)

    Golden, J. P.

    1977-01-01

    The MACSYMA's symbolic ordinary differential equation solver ODE2 is described. The code for this routine is delineated, which is of interest because it is written in top-level MACSYMA language, and may serve as a good example of programming in that language. Other symbolic ordinary differential equation solvers are mentioned.

  16. Benchmarking transport solvers for fracture flow problems

    NASA Astrophysics Data System (ADS)

    Olkiewicz, Piotr; Dabrowski, Marcin

    2015-04-01

    Fracture flow may dominate in rocks with low porosity and it can accompany both industrial and natural processes. Typical examples of such processes are natural flows in crystalline rocks and industrial flows in geothermal systems or hydraulic fracturing. Fracture flow provides an important mechanism for transporting mass and energy. For example, geothermal energy is primarily transported by the flow of the heated water or steam rather than by the thermal diffusion. The geometry of the fracture network and the distribution of the mean apertures of individual fractures are the key parameters with regard to the fracture network transmissivity. Transport in fractures can occur through the combination of advection and diffusion processes like in the case of dissolved chemical components. The local distribution of the fracture aperture may play an important role for both flow and transport processes. In this work, we benchmark various numerical solvers for flow and transport processes in a single fracture in 2D and 3D. Fracture aperture distributions are generated by a number of synthetic methods. We examine a single-phase flow of an incompressible viscous Newtonian fluid in the low Reynolds number limit. Periodic boundary conditions are used and a pressure difference is imposed in the background. The velocity field is primarly found using the Stokes equations. We systematically compare the obtained velocity field to the results obtained by solving the Reynolds equation. This allows us to examine the impact of the aperture distribution on the permeability of the medium and the local velocity distribution for two different mathematical descriptions of the fracture flow. Furthermore, we analyse the impact of aperture distribution on the front characteristics such as the standard deviation and the fractal dimension for systems in 2D and 3D.

  17. Static benchmarking of the NESTLE advanced nodal code

    SciTech Connect

    Mosteller, R.D.

    1997-05-01

    Results from the NESTLE advanced nodal code are presented for multidimensional numerical benchmarks representing four different types of reactors, and predictions from NESTLE are compared with measured data from pressurized water reactors (PWRs). The numerical benchmarks include cases representative of PWRs, boiling water reactors (BWRs), CANDU heavy water reactors (HWRs), and high-temperature gas-cooled reactors (HTGRs). The measured PWR data include critical soluble boron concentrations and isothermal temperature coefficients of reactivity. The results demonstrate that NESTLE correctly solves the multigroup diffusion equations for both Cartesian and hexagonal geometries, that it reliably calculates k{sub eff} and reactivity coefficients for PWRs, and that--subsequent to the incorporation of additional thermal-hydraulic models--it will be able to perform accurate calculations for the corresponding parameters in BWRs, HWRs, and HTGRs as well.

  18. An immersed interface vortex particle-mesh solver

    NASA Astrophysics Data System (ADS)

    Marichal, Yves; Chatelain, Philippe; Winckelmans, Gregoire

    2014-11-01

    An immersed interface-enabled vortex particle-mesh (VPM) solver is presented for the simulation of 2-D incompressible viscous flows, in the framework of external aerodynamics. Considering the simulation of free vortical flows, such as wakes and jets, vortex particle-mesh methods already provide a valuable alternative to standard CFD methods, thanks to the interesting numerical properties arising from its Lagrangian nature. Yet, accounting for solid bodies remains challenging, despite the extensive research efforts that have been made for several decades. The present immersed interface approach aims at improving the consistency and the accuracy of one very common technique (based on Lighthill's model) for the enforcement of the no-slip condition at the wall in vortex methods. Targeting a sharp treatment of the wall calls for substantial modifications at all computational levels of the VPM solver. More specifically, the solution of the underlying Poisson equation, the computation of the diffusion term and the particle-mesh interpolation are adapted accordingly and the spatial accuracy is assessed. The immersed interface VPM solver is subsequently validated on the simulation of some challenging impulsively started flows, such as the flow past a cylinder and that past an airfoil. Research Fellow (PhD student) of the F.R.S.-FNRS of Belgium.

  19. Pathology of extra-nodal non Hodgkin lymphomas.

    PubMed

    Wright, D H

    2012-06-01

    In the management of extra-nodal lymphomas it is important to determine whether the tumour has disseminated and whether lymph nodes are involved. Some extra-nodal lymphomas may be the result of random spread of nodal lymphoma. Specific homing, however, determines the site of many extra-nodal lymphomas, as exemplified by cutaneous T-cell lymphomas, which seem to be derived from skin-homing T-cells and mucosa-associated lymphoid tissue lymphomas that show features of the mucosal immune system. Enteropathy-associated T-cell lymphoma is derived from mucosal T-cells in patients with coeliac disease. Immunological sanctuary accounts for the localisation of primary brain, eye and testicular lymphoma. Mantle cell lymphoma frequently causes tumours in the gastrointestinal tract. Random biopsies have shown that a high proportion of patients with this lymphoma have extensive occult involvement of the gastrointestinal tract at the time of first diagnosis. Follicular lymphoma occurs at both nodal and extra-nodal sites, but uncommonly at both sites at the same time. Extra-nodal follicular lymphomas frequently lack t(14;18)(q32;q21) and do not express bcl-2, which are characteristics of the nodal disease. At extra-nodal sites, follicular lymphoma is more likely to be curable than nodal follicular lymphoma. The behaviour of extra-nodal lymphomas cannot be assumed to follow that of their nodal counterparts.

  20. Development and Implementation of a Newton-BICGSTAB Iterative Solver in the FORMOSA-B BWR Core Simulator Code

    SciTech Connect

    Kastanya, Doddy Yozef Febrian; Turinsky, Paul J.

    2005-05-15

    A Newton-Krylov iterative solver has been developed to reduce the CPU execution time of boiling water reactor (BWR) core simulators implemented in the core simulator part of the Fuel Optimization for Reloads Multiple Objectives by Simulated Annealing for BWR (FORMOSA-B) code, which is an in-core fuel management optimization code for BWRs. This new solver utilizes Newton's method to explicitly treat strong nonlinearities in the problem, replacing the traditionally used nested iterative approach. Newton's method provides the solver with a higher-than-linear convergence rate, assuming that good initial estimates of the unknowns are provided. Within each Newton iteration, an appropriately preconditioned Krylov solver is utilized for solving the linearized system of equations. Taking advantage of the higher convergence rate provided by Newton's method and utilizing an efficient preconditioned Krylov solver, we have developed a Newton-Krylov solver to evaluate the three-dimensional, two-group neutron diffusion equations coupled with a two-phase flow model within a BWR core simulator. Numerical tests on the new solver have shown that speedups ranging from 1.6 to 2.1, with reference to the traditional approach of employing nested iterations to treat the nonlinear feedbacks, can be achieved. However, if a preconditioned Krylov solver is employed to complete the inner iterations of the traditional approach, negligible CPU time differences are noted between the Newton-Krylov and traditional (Krylov) approaches.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Nodal resonance in a strong standing wave

    NASA Astrophysics Data System (ADS)

    Fernández C., David J.; Mielnik, Bogdan

    1990-06-01

    The motion of charged particles in a standing electromagnetic wave is considered. For amplitudes that are not too high, the wave causes an effect of attraction of particles to the nodal points, resembling the channeling effect reported by Salomon, Dalibard, Aspect, Metcalf, and Cohen-Tannoudji [Phys. Rev. Lett. 59, 1659 (1987)] consistent with the ``high-frequency potential'' of Kapitza [Zh. Eksp. Teor. Fiz. 21, 588 (1951)]. For high-field intensities, however, the nodal points undergo a qualitative metamorphosis, converting themselves from particle attractors into resonant centers. Some chaotic phenomena arise and the description of the oscillating field in terms of an ``effective potential'' becomes inappropriate. The question of a correct Floquet Hamiltonian that could describe the standing wave within this amplitude and frequency regime is open.

  6. Multiple nodal locoregional recurrence of pheochromocytoma

    PubMed Central

    Ramírez-Plaza, César Pablo; Cárdenas, Elena Margarita Sanchiz; Humanes, Rocío Soler

    2015-01-01

    Introduction Malignancy is present in 10% of pheochromocytomas (PCC) and is defined as local/vascular infiltration of surrounding tissues or the presence of chromaffin cells deposits in distant organs. The presence of isolated nodal recurrence is very rare and only 7 cases have been reported in the medical literature. Presentation of the case The case of a 32-y male with a symptomatic recurrence of a previously operated (2-years ago) PCC is presented. Radiological and functional imaging studies confirmed the presence of multiple nodules in the surgical site. A radical left nephrectomy with extensive lymphatic clearance in order to get an R0 resection was performed. The pathologist confirmed the diagnosis of massive locoregional nodal invasion. Discussion A detailed histological report and a thorough genetic study must be considered in every operated PCC in order to identify mutations and profiles of risk for malignancy. When recurrence or metastastic disease is suspected, imaging and functional exams are done in order to obtain a proper staging. Radical surgery for the metastatic disease is the only treatment that may provide prolonged survival. If an R0 resection is not possible, then a debulking surgery is a good option when the benefit/risk ratio is acceptable. Conclusion Isolated lymph nodal recurrence is very rare in malignant PCC, with only 7 cases previously published. The role of surgery is essential to get long-term survival because provides clinical and functional control of the disease. PMID:26117450

  7. Arbitrarily high order nodal and characteristic methods

    SciTech Connect

    Azmy, Y.Y.

    1994-09-01

    The quest for higher computational efficiency initially led researchers in the neutron transport area to develop and implement high-order approximations for solving the linear Boltzmann equational. This drive aimed at achieving higher accuracy on coarse meshes, thereby resulting in a net savings of computational resources represented by execution time and memory. Many endeavors succeeded in reaching this goal, producing a variety of elegent, albeit complicated, formalisms, that proved extremely accurate and efficient in solving test, as well as practical applications, problems. The two main classes of high order transport methods that recieved the most attention are the Nodal and Characteristic methods. A de facto linear order standard for the spatial approximation (even though Quadratic Nodal Methods were also considered) was dictated by the algebraic complexity of the derivation of the discrete variable equations, the programming complexity of implementing and verifying them in codes, and limitations on computational resources available to run such codes. The significant advances in computational resources in terms of hardware capacity and speed, as well as architectural innovations such as vector and parallel processing, all but eliminated the third (above) obstacle towards the development and implementation of even higher order methods. The algebraic and programming complexities, on the other hand, were alleviated to some extent by the development of Arbitrarily High Order Transport methods of the Nodal and the Characteristic types, which are discussed in this report.

  8. 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.

  9. 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.

  10. Coexistence of four-band nodal rings and triply degenerate nodal points in centrosymmetric metal diborides

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoming; Yu, Zhi-Ming; Sheng, Xian-Lei; Yang, Hui Ying; Yang, Shengyuan A.

    2017-06-01

    Topological metals with protected band-crossing points have been attracting great interest. Here we report topological band features in a family of metal diboride materials. Using first-principles calculations, we show that these materials are metallic, and close to Fermi level, there appears coexistence of one pair of nodal rings and one pair of triply degenerate nodal points (TNPs). The nodal ring here is distinct from the previously studied ones in that its formation requires four entangled bands, not just two as in previous cases, hence it is termed as a four-band nodal ring (FNR). Remarkably, we show that FNR features Dirac-cone-like surface states, in contrast to the usual drumhead surface states for two-band nodal rings. Due to the presence of inversion symmetry, the TNP here is also different from those discussed previously in inversion-asymmetric systems. Especially, when spin-orbit coupling is included, the TNP here transforms into a novel Dirac point that is close to the borderline between the type-I and type-II Dirac point categories. We discuss their respective symmetry protections, and construct effective models for their characterization. The large linear energy range (>2 eV) in these materials should facilitate the experimental detection of the signatures of these nontrivial band crossings.

  11. 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.

  12. An advanced implicit solver for MHD

    NASA Astrophysics Data System (ADS)

    Udrea, Bogdan

    A new implicit algorithm has been developed for the solution of the time-dependent, viscous and resistive single fluid magnetohydrodynamic (MHD) equations. The algorithm is based on an approximate Riemann solver for the hyperbolic fluxes and central differencing applied on a staggered grid for the parabolic fluxes. The algorithm employs a locally aligned coordinate system that allows the solution to the Riemann problems to be solved in a natural direction, normal to cell interfaces. The result is an original scheme that is robust and reduces the complexity of the flux formulas. The evaluation of the parabolic fluxes is also implemented using a locally aligned coordinate system, this time on the staggered grid. The implicit formulation employed by WARP3 is a two level scheme that was applied for the first time to the single fluid MHD model. The flux Jacobians that appear in the implicit scheme are evaluated numerically. The linear system that results from the implicit discretization is solved using a robust symmetric Gauss-Seidel method. The code has an explicit mode capability so that implementation and test of new algorithms or new physics can be performed in this simpler mode. Last but not least the code was designed and written to run on parallel computers so that complex, high resolution runs can be per formed in hours rather than days. The code has been benchmarked against analytical and experimental gas dynamics and MHD results. The benchmarks consisted of one-dimensional Riemann problems and diffusion dominated problems, two-dimensional supersonic flow over a wedge, axisymmetric magnetoplasmadynamic (MPD) thruster simulation and three-dimensional supersonic flow over intersecting wedges and spheromak stability simulation. The code has been proven to be robust and the results of the simulations showed excellent agreement with analytical and experimental results. Parallel performance studies showed that the code performs as expected when run on parallel

  13. Parallelizing alternating direction implicit solver on GPUs

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Improved Stiff ODE Solvers for Combustion CFD

    NASA Astrophysics Data System (ADS)

    Imren, A.; Haworth, D. C.

    2016-11-01

    Increasingly large chemical mechanisms are needed to predict autoignition, heat release and pollutant emissions in computational fluid dynamics (CFD) simulations of in-cylinder processes in compression-ignition engines and other applications. Calculation of chemical source terms usually dominates the computational effort, and several strategies have been proposed to reduce the high computational cost associated with realistic chemistry in CFD. Central to most strategies is a stiff ordinary differential equation (ODE) solver to compute the change in composition due to chemical reactions over a computational time step. Most work to date on stiff ODE solvers for computational combustion has focused on backward differential formula (BDF) methods, and has not explicitly considered the implications of how the stiff ODE solver couples with the CFD algorithm. In this work, a fresh look at stiff ODE solvers is taken that includes how the solver is integrated into a turbulent combustion CFD code, and the advantages of extrapolation-based solvers in this regard are demonstrated. Benefits in CPU time and accuracy are demonstrated for homogeneous systems and compression-ignition engines, for chemical mechanisms that range in size from fewer than 50 to more than 7,000 species.

  15. 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.

  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. Development of a parallel implicit solver of fluid modeling equations for gas discharges

    NASA Astrophysics Data System (ADS)

    Hung, Chieh-Tsan; Chiu, Yuan-Ming; Hwang, Feng-Nan; Wu, Jong-Shinn

    2011-01-01

    A parallel fully implicit PETSc-based fluid modeling equations solver for simulating gas discharges is developed. Fluid modeling equations include: the neutral species continuity equation, the charged species continuity equation with drift-diffusion approximation for mass fluxes, the electron energy density equation, and Poisson's equation for electrostatic potential. Except for Poisson's equation, all model equations are discretized by the fully implicit backward Euler method as a time integrator, and finite differences with the Scharfetter-Gummel scheme for mass fluxes on the spatial domain. At each time step, the resulting large sparse algebraic nonlinear system is solved by the Newton-Krylov-Schwarz algorithm. A 2D-GEC RF discharge is used as a benchmark to validate our solver by comparing the numerical results with both the published experimental data and the theoretical prediction. The parallel performance of the solver is investigated.

  18. Plasticity underlies tumor progression: Role of Nodal signaling

    PubMed Central

    Bodenstine, Thomas M.; Chandler, Grace S.; Seftor, Richard E. B.; Seftor, Elisabeth A.; Hendrix, Mary J. C.

    2016-01-01

    The transforming growth factor beta (TGFβ) superfamily member Nodal is an established regulator of early embryonic development, with primary roles in endoderm induction, left-right asymmetry and primitive streak formation. Nodal signals through TGFβ family receptors at the plasma membrane and induces signaling cascades leading to diverse transcriptional regulation. While conceptually simple, the regulation of Nodal and its molecular effects are profoundly complex and context dependent. Pioneering work by developmental biologists has characterized the signaling pathways, regulatory components, and provided detailed insight into the mechanisms by which Nodal mediates changes at the cellular and organismal levels. Nodal is also an important factor in maintaining pluripotency of embryonic stem cells through regulation of core transcriptional programs. Collectively, this work has led to an appreciation for Nodal as a powerful morphogen capable of orchestrating multiple cellular phenotypes. Although Nodal is not active in most adult tissues, its re-expression and signaling have been linked to multiple types of human cancer, and Nodal has emerged as a driver of tumor growth and cellular plasticity. In vitro and in vivo experimental evidence has demonstrated that inhibition of Nodal signaling reduces cancer cell aggressive characteristics, while clinical data have established associations with Nodal expression and patient outcomes. As a result, there is great interest in the potential targeting of Nodal activity in a therapeutic setting for cancer patients that may provide new avenues for suppressing tumor growth and metastasis. In this review, we evaluate our current understanding of the complexities of Nodal function in cancer and highlight recent experimental evidence that sheds light on the therapeutic potential of its inhibition. PMID:26951550

  19. 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

  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. Quantitative analytical theory for disordered nodal points

    NASA Astrophysics Data System (ADS)

    Sbierski, Björn; Madsen, Kevin A.; Brouwer, Piet W.; Karrasch, Christoph

    2017-08-01

    Disorder effects are especially pronounced around nodal points in linearly dispersing band structures as present in graphene or Weyl semimetals. Despite the enormous experimental and numerical progress, even a simple quantity like the average density of states cannot be assessed quantitatively by analytical means. We demonstrate how this important problem can be solved employing the functional renormalization group method, and, for the two-dimensional case, we demonstrate excellent agreement with reference data from numerical simulations based on tight-binding models. In three dimensions our analytic results also improve drastically on existing approaches.

  2. Nodal lines and nodal loops in nonsymmorphic odd-parity superconductors

    SciTech Connect

    Micklitz, T.; Norman, M. R.

    2017-01-01

    We discuss the nodal structure of odd-parity superconductors in the presence of nonsymmorphic crystal symmetries, both with and without spin-orbit coupling, and with and without time-reversal symmetry. We comment on the relation of our work to previous work in the literature, and also the implications for unconventional superconductors such as UPt3.

  3. Nodal lines and nodal loops in nonsymmorphic odd-parity superconductors

    NASA Astrophysics Data System (ADS)

    Micklitz, T.; Norman, M. R.

    2017-01-01

    We discuss the nodal structure of odd-parity superconductors in the presence of nonsymmorphic crystal symmetries, both with and without spin-orbit coupling, and with and without time-reversal symmetry. We comment on the relation of our work to previous work in the literature, and also the implications for unconventional superconductors such as UPt3.

  4. 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.

  5. Inductive ionospheric solver for magnetospheric MHD simulations

    NASA Astrophysics Data System (ADS)

    Vanhamäki, H.

    2011-01-01

    We present a new scheme for solving the ionospheric boundary conditions required in magnetospheric MHD simulations. In contrast to the electrostatic ionospheric solvers currently in use, the new solver takes ionospheric induction into account by solving Faraday's law simultaneously with Ohm's law and current continuity. From the viewpoint of an MHD simulation, the new inductive solver is similar to the electrostatic solvers, as the same input data is used (field-aligned current [FAC] and ionospheric conductances) and similar output is produced (ionospheric electric field). The inductive solver is tested using realistic, databased models of an omega-band and westward traveling surge. Although the tests were performed with local models and MHD simulations require a global ionospheric solution, we may nevertheless conclude that the new solution scheme is feasible also in practice. In the test cases the difference between static and electrodynamic solutions is up to ~10 V km-1 in certain locations, or up to 20-40% of the total electric field. This is in agreement with previous estimates. It should also be noted that if FAC is replaced by the ground magnetic field (or ionospheric equivalent current) in the input data set, exactly the same formalism can be used to construct an inductive version of the KRM method originally developed by Kamide et al. (1981).

  6. 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.

  7. New Anti-Nodal Monoclonal Antibodies Targeting the Nodal Pre-Helix Loop Involved in Cripto-1 Binding

    PubMed Central

    Focà, Annalia; Sanguigno, Luca; Focà, Giuseppina; Strizzi, Luigi; Iannitti, Roberta; Palumbo, Rosanna; Hendrix, Mary J. C.; Leonardi, Antonio; Ruvo, Menotti; Sandomenico, Annamaria

    2015-01-01

    Nodal is a potent embryonic morphogen belonging to the TGF-β superfamily. Typically, it also binds to the ALK4/ActRIIB receptor complex in the presence of the co-receptor Cripto-1. Nodal expression is physiologically restricted to embryonic tissues and human embryonic stem cells, is absent in normal cells but re-emerges in several human cancers, including melanoma, breast, and colon cancer. Our aim was to obtain mAbs able to recognize Nodal on a major CBR (Cripto-Binding-Region) site and to block the Cripto-1-mediated signalling. To achieve this, antibodies were raised against hNodal(44–67) and mAbs generated by the hybridoma technology. We have selected one mAb, named 3D1, which strongly associates with full-length rhNodal (KD 1.4 nM) and recognizes the endogenous protein in a panel of human melanoma cell lines by western blot and FACS analyses. 3D1 inhibits the Nodal-Cripto-1 binding and blocks Smad2/3 phosphorylation. Data suggest that inhibition of the Nodal-Cripto-1 axis is a valid therapeutic approach against melanoma and 3D1 is a promising and interesting agent for blocking Nodal-Cripto mediated tumor development. These findings increase the interest for Nodal as both a diagnostic and prognostic marker and as a potential new target for therapeutic intervention. PMID:26370966

  8. An approximate Riemann solver for hypervelocity flows

    NASA Technical Reports Server (NTRS)

    Jacobs, Peter A.

    1991-01-01

    We describe an approximate Riemann solver for the computation of hypervelocity flows in which there are strong shocks and viscous interactions. The scheme has three stages, the first of which computes the intermediate states assuming isentropic waves. A second stage, based on the strong shock relations, may then be invoked if the pressure jump across either wave is large. The third stage interpolates the interface state from the two initial states and the intermediate states. The solver is used as part of a finite-volume code and is demonstrated on two test cases. The first is a high Mach number flow over a sphere while the second is a flow over a slender cone with an adiabatic boundary layer. In both cases the solver performs well.

  9. 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.

  10. 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.

  11. 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.

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

    SciTech Connect

    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 Interface (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.

  13. Nodal signaling and the evolution of deuterostome gastrulation.

    PubMed

    Chea, Helen K; Wright, Christopher V; Swalla, Billie J

    2005-10-01

    Chordates, including vertebrates, evolved within a group of animals called the deuterostomes. All holoblastic deuterostomes gastrulate at the vegetal pole and the blastopore becomes the anus, while a mouth is formed at the anterior or to the oral side. Nodal is a member of the TGF-beta superfamily of signaling molecules that are important in signaling between cells during many embryonic processes in vertebrate embryos. Nodal has also been found in other invertebrate deuterostomes, such as ascidians and sea urchins, but, so far, is missing in protostomes. Nodal has been shown to be particularly important in determining left-right asymmetries in vertebrate embryos, but less information is available for its developmental role in the invertebrate deuterostomes. We review gastrulation in the deuterostomes, then examine nodal expression early during mesoderm formation and later during the establishment of asymmetries in both vertebrates and invertebrates. Nodal is expressed asymmetrically on the left side in chordates and on the presumptive oral side of the embryo in echinoid echinoderms. The expression of nodal is in different germ layers in embryos of different phyla. Expression is in the ectoderm in most of the invertebrate deuterostomes, and in the mesoderm in vertebrates. We summarize the work that has been published to date, especially nodal expression in the invertebrate deuterostomes, and suggest future experiments to better understand the evolution of nodal signaling and deuterostome gastrulation.

  14. Market redesign and technology upgrade: a nodal implementation

    SciTech Connect

    Isemonger, Alan G.

    2009-10-15

    The California ISO and its market participants collectively cut over to a new nodal-based market on April 1, largely without incident and 11 years to the day from the initial startup in 1998. Thus far, the new nodal framework has proven robust, and the inevitable design and implementation issues that have emerged since cutover have been manageable. (author)

  15. Topological nodal line semimetals predicted from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Yu, Rui; Fang, Zhong; Dai, Xi; Weng, Hongming

    2017-06-01

    Topological semimetals are newly discovered states of quantum matter, which have extended the concept of topological states from insulators to metals and attracted great research interest in recent years. In general, there are three kinds of topological semimetals, namely Dirac semimetals, Weyl semimetals, and nodal line semimetals. Nodal line semimetals can be considered as precursor states for other topological states. For example, starting from such nodal line states, the nodal line structure might evolve into Weyl points, convert into Dirac points, or become a topological insulator by introducing the spin-orbit coupling (SOC) or mass term. In this review paper, we introduce theoretical materials that show the nodal line semimetal state, including the all-carbon Mackay-Terrones crystal (MTC), anti-perovskite Cu3PdN, pressed black phosphorus, and the CaP3 family of materials, and we present the design principles for obtaining such novel states of matter.

  16. 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.

  17. 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.

  18. 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.

  19. Effect of multiple-nodal basin drainage on cutaneous melanoma.

    PubMed

    Federico, Andrea C; Chagpar, Anees B; Ross, Merrick I; Martin, Robert C G; Noyes, R Dirk; Goydos, James S; Beitsch, Peter D; Urist, Marshall M; Ariyan, Stephan; Sussman, Jeffrey J; McMasters, Kelly M; Scoggins, Charles R

    2008-07-01

    The number of nodal basins draining a primary cutaneous melanoma is not an independent predictor of outcome. Post hoc analysis of patients entered into a randomized, prospective study. Multi-institutional academic and community medical centers. Patients aged 18 to 70 years with melanoma 1.0 mm or greater Breslow thickness. Wide local excision and sentinel lymph node biopsy were performed on all patients; patients with sentinel lymph node metastases underwent completion lymphadenectomy. Patients with multiple-nodal basin drainage were compared with those with single-nodal basin drainage. Sentinel lymph node status, locoregional recurrence-free survival, disease-free survival, and overall survival. A total of 2060 patients with single-nodal basin drainage (n = 1709 [83% of cohort]) were included in the analysis, with a median follow-up of 50 months. On univariate analysis, the group with multiple-nodal basin drainage (n = 351) was associated with female sex and primary tumor regression (P < .001). In addition, multiple-nodal basin drainage was associated with truncal primary tumor location (73.2%), while single-nodal basin drainage was more common for extremity tumors (50.9%; P < .001). On multivariate analysis, there were no differences in the rate of sentinel lymph node metastasis, disease-free survival, or overall survival between the groups. Interestingly, locoregional recurrence was significantly worse in the single-nodal basin drainage group (P = .003). Multiple-nodal basin drainage does not confer a worse prognosis for patients with cutaneous melanoma. In fact, single-nodal basin drainage appears to be associated with a greater risk of locoregional recurrence.

  20. Novel Scalable 3-D MT Inverse Solver

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    We present a new, robust and fast, three-dimensional (3-D) magnetotelluric (MT) inverse solver. As a forward modelling engine a highly-scalable solver extrEMe [1] is used. The (regularized) inversion is based on an iterative gradient-type optimization (quasi-Newton method) and exploits adjoint sources approach for fast calculation of 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 (single-site and/or inter-site) responses, and supports massive parallelization. Different parallelization strategies implemented in the code allow for optimal usage of available computational resources for a given problem set up. To parameterize an inverse domain a mask approach 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 high-performance clusters demonstrate practically linear scalability of the code up to thousands of nodes. 1. Kruglyakov, M., A. Geraskin, A. Kuvshinov, 2016. Novel accurate and scalable 3-D MT forward solver based on a contracting integral equation method, Computers and Geosciences, in press.

  1. 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.

  2. Incessant junctional reciprocating tachycardia caused by dual atrioventricular nodal pathways and atrio-nodal bypass tract.

    PubMed Central

    Santarelli, P; Sosa, E; Denes, P

    1982-01-01

    A case is described with clinical and electrocardiographic findings of incessant junctional reciprocating tachycardia. Electrophysiological study showed that longitudinal dissociation of the atrioventricular node into two pathways was responsible for the maintenance of the arrhythmia. The two intranodal pathways had different refractory periods but reciprocally related and overlapping conduction times (anterograde fast, retrograde slow, and vice versa). Induction and termination of the arrhythmia was related to the presence of a partial atrio-nodal bypass tract. Images PMID:7082510

  3. A multi-dimensional finite volume cell-centered direct ALE solver for hydrodynamics

    NASA Astrophysics Data System (ADS)

    Clair, G.; Ghidaglia, J.-M.; Perlat, J.-P.

    2016-12-01

    In this paper we describe a second order multi-dimensional scheme, belonging to the class of direct Arbitrary Lagrangian-Eulerian (ALE) methods, for the solution of non-linear hyperbolic systems of conservation law. The scheme is constructed upon a cell-centered explicit Lagrangian solver completed with an edge-based upwinded formulation of the numerical fluxes, computed from the MUSCL-Hancock method, to obtain a full ALE formulation. Numerical fluxes depend on nodal grid velocities which are either set or computed to avoid most of the mesh problems typically encountered in purely Lagrangian simulations. In order to assess the robustness of the scheme, most results proposed in this paper have been obtained by computing the grid velocities as a fraction of the Lagrangian nodal velocities, the ratio being set before running the test case. The last part of the paper describes preliminary results about the triple point test case run in the ALE framework by computing the grid velocities with the fully adaptive Large Eddy Limitation (L.E.L.) method proposed in [1]. Such a method automatically computes the grid velocities at each node defining the mesh from the local characteristics of the flow. We eventually discuss the advantages and the drawback of the coupling.

  4. Improved Solver Settings for 3D Exploding Wire Simulations in ALEGRA

    DTIC Science & Technology

    2016-08-01

    expanding plasma and shock wave resulting from the wire burst can extend to tens of cen- timeters. The elliptic nature of the magnetic diffusion...such simulations were prohibitively slow due in part to unoptimized (matrix) solver settings. In this report, we address that by varying 6 parameters...distribution is unlimited. simulation code developed by SNL for modeling high-deformation solid dynam- ics, shock -hydrodynamics, magnetohydrodynamics

  5. Disrupted Nodal and Hub Organization Account for Brain Network Abnormalities in Parkinson’s Disease

    PubMed Central

    Koshimori, Yuko; Cho, Sang-Soo; Criaud, Marion; Christopher, Leigh; Jacobs, Mark; Ghadery, Christine; Coakeley, Sarah; Harris, Madeleine; Mizrahi, Romina; Hamani, Clement; Lang, Anthony E.; Houle, Sylvain; Strafella, Antonio P.

    2016-01-01

    The recent application of graph theory to brain networks promises to shed light on complex diseases such as Parkinson’s disease (PD). This study aimed to investigate functional changes in sensorimotor and cognitive networks in Parkinsonian patients, with a focus on inter- and intra-connectivity organization in the disease-associated nodal and hub regions using the graph theoretical analyses. Resting-state functional MRI data of a total of 65 participants, including 23 healthy controls (HCs) and 42 patients, were investigated in 120 nodes for local efficiency, betweenness centrality, and degree. Hub regions were identified in the HC and patient groups. We found nodal and hub changes in patients compared with HCs, including the right pre-supplementary motor area (SMA), left anterior insula, bilateral mid-insula, bilateral dorsolateral prefrontal cortex (DLPFC), and right caudate nucleus. In general, nodal regions within the sensorimotor network (i.e., right pre-SMA and right mid-insula) displayed weakened connectivity, with the former node associated with more severe bradykinesia, and impaired integration with default mode network regions. The left mid-insula also lost its hub properties in patients. Within the executive networks, the left anterior insular cortex lost its hub properties in patients, while a new hub region was identified in the right caudate nucleus, paralleled by an increased level of inter- and intra-connectivity in the bilateral DLPFC possibly representing compensatory mechanisms. These findings highlight the diffuse changes in nodal organization and regional hub disruption accounting for the distributed abnormalities across brain networks and the clinical manifestations of PD. PMID:27891090

  6. Simulation of turbulent flows using nodal integral method

    NASA Astrophysics Data System (ADS)

    Singh, Suneet

    Nodal methods are the backbone of the production codes for neutron-diffusion and transport equations. Despite their high accuracy, use of these methods for simulation of fluid flow is relatively new. Recently, a modified nodal integral method (MNIM) has been developed for simulation of laminar flows. In view of its high accuracy and efficiency, extension of this method for the simulation of turbulent flows is a logical step forward. In this dissertation, MNIM is extended in two ways to simulate incompressible turbulent flows---a new MNIM is developed for the 2D k-epsilon equations; and 3D, parallel MNIM is developed for direct numerical simulations. Both developments are validated, and test problems are solved. In this dissertation, a new nodal numerical scheme is developed to solve the k-epsilon equations to simulate turbulent flows. The MNIM developed earlier for laminar flow equations is modified to incorporate eddy viscosity approximation and coupled with the above mentioned schemes for the k and epsilon equations, to complete the implementation of the numerical scheme for the k-epsilon model. The scheme developed is validated by comparing the results obtained by the developed method with the results available in the literature obtained using direct numerical simulations (DNS). The results of current simulations match reasonably well with the DNS results. The discrepancies in the results are mainly due to the limitations of the k-epsilon model rather than the deficiency in the developed MNIM. A parallel version of the MNIM is needed to enhance its capability, in order to carry out DNS of the turbulent flows. The parallelization of the scheme, however, presents some unique challenges as dependencies of the discrete variables are different from those that exist in other schemes (for example in finite volume based schemes). Hence, a parallel MNIM (PMNIM) is developed and implemented into a computer code with communication strategies based on the above mentioned

  7. Topological semimetals with a double-helix nodal link

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Lu, Hai-Zhou; Hou, Jing-Min

    2017-07-01

    Topological nodal line semimetals are characterized by the crossing of the conduction and valence bands along one or more closed loops in the Brillouin zone. Usually, these loops are either isolated or touch each other at some highly symmetric points. Here, we introduce a different kind of nodal line semimetal, that contains a pair of linked nodal loops. A concrete two-band model was constructed, which supports a pair of nodal lines with a double-helix structure, which can be further twisted into a Hopf link because of the periodicity of the Brillouin zone. The nodal lines are stabilized by the combined spatial inversion P and time reversal T symmetry; the individual P and T symmetries must be broken. The band exhibits nontrivial topology that each nodal loop carries a π Berry flux. Surface flatbands emerge at the open boundary and are exactly encircled by the projection of the nodal lines on the surface Brillouin zone. The experimental implementation of our model using cold atoms in optical lattices is discussed.

  8. 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

  9. VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool

    PubMed Central

    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

  10. 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/.

  11. Implicit compressible flow solvers on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Nagaoka, Makoto; Horinouchi, Nariaki

    1993-09-01

    An implicit solver for compressible flows using Bi-CGSTAB method is proposed. The Euler equations are discretized with the delta-form by the finite volume method on the cell-centered triangular unstructured meshes. The numerical flux is calculated by Roe's upwind scheme. The linearized simultaneous equations with the irregular nonsymmetric sparse matrix are solved by the Bi-CGSTAB method with the preconditioner of incomplete LU factorization. This method is also vectorized by the multi-colored ordering. Although the solver requires more computational memory, it shows faster and more robust convergence than the other conventional methods: three-stage Runge-Kutta method, point Gauss-Seidel method, and Jacobi method for two-dimensional inviscid steady flows.

  12. Implicit Riemann solvers for the Pn equations.

    SciTech Connect

    Mehlhorn, Thomas Alan; McClarren, Ryan; Brunner, Thomas A.; Holloway, James Paul

    2005-03-01

    The spherical harmonics (P{sub n}) approximation to the transport equation for time dependent problems has previously been treated using Riemann solvers and explicit time integration. Here we present an implicit time integration method for the P n equations using Riemann solvers. Both first-order and high-resolution spatial discretization schemes are detailed. One facet of the high-resolution scheme is that a system of nonlinear equations must be solved at each time step. This nonlinearity is the result of slope reconstruction techniques necessary to avoid the introduction of artifical extrema in the numerical solution. Results are presented that show auspicious agreement with analytical solutions using time steps well beyond the CFL limit.

  13. 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 modeling 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 challenging problems important to Sandia's mission that Aleph was specifically designed to address.

  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. 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)

  16. The Openpipeflow Navier-Stokes solver

    NASA Astrophysics Data System (ADS)

    Willis, Ashley P.

    Pipelines are used in a huge range of industrial processes involving fluids, and the ability to accurately predict properties of the flow through a pipe is of fundamental engineering importance. Armed with parallel MPI, Arnoldi and Newton-Krylov solvers, the Openpipeflow code can be used in a range of settings, from large-scale simulation of highly turbulent flow, to the detailed analysis of nonlinear invariant solutions (equilibria and periodic orbits) and their influence on the dynamics of the flow.

  17. Domain Decomposition for the SPN Solver MINOS

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nédélec 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® code.

  18. Gerris Flow Solver: Implementation and Application

    DTIC Science & Technology

    2013-05-12

    Zienkiewicz, 1966). It is the solver for the Imperial College Ocean Model (ICOM), which uses 3D adaptive mesh methods (Ford et al., 2004). The finite...method (Popinet, 2003). The 3D Gerris model was used to study air turbulence associated with a complex shape with good match to observations (Popinet...et al., 2004). The Ocean module of Gerris was described by Popinet and Rickard (2004) as an adaptive, finite-volume, 3D , incompressible, N-S fluid

  19. 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

  20. Primary nodal hemangiosarcoma in four dogs.

    PubMed

    Chan, Catherine M; Zwahlen, Courtney H; de Lorimier, Louis-Philippe; Yeomans, Stephen M; Hoffmann, Karon L; Moore, Antony S

    2016-11-01

    CASE DESCRIPTION 4 dogs with a slow-growing mass in the cervical region were evaluated. CLINICAL FINDINGS All dogs had no clinical signs at the time of the evaluation. There was no apparent evidence of visceral metastases or other primary tumor based on available CT or MRI data for any dog. TREATMENT AND OUTCOME For each dog, surgery to remove the mass was performed. Histologic examination of the excised tissue revealed a completely excised grade 1 or 2 lymph node hemangiosarcoma. All dogs received adjuvant chemotherapy; 2 dogs underwent curative intent chemotherapy, 1 dog underwent metronomic treatment with cyclophosphamide, and 1 dog underwent metronomic treatment with chlorambucil. The survival time was 259 days in 1 dog; 3 dogs were still alive 615, 399, and 365 days after surgery. CLINICAL RELEVANCE Primary nodal hemangiosarcoma in dogs is a rare and, to the authors' knowledge, previously undescribed disease that appears to develop in the cervical lymph nodes as a slow-growing mass or masses. Surgical excision and adjunct treatment resulted in long survival times for 3 of the 4 dogs of the present report. Given the aggressive biologic behavior of hemangiosarcomas in other body locations, adjunct chemotherapy should be considered for affected dogs, although its role in the cases described in this report was unclear. Additional clinical information is required to further characterize the biologic behavior of this tumor type and determine the expected survival times and associated risk factors in dogs.

  1. 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.

  2. 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.

  3. 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

  4. Adaptive Nodal Transport Methods for Reactor Transient Analysis

    SciTech Connect

    Thomas Downar; E. Lewis

    2005-08-31

    Develop methods for adaptively treating the angular, spatial, and time dependence of the neutron flux in reactor transient analysis. These methods were demonstrated in the DOE transport nodal code VARIANT and the US NRC spatial kinetics code, PARCS.

  5. Nodal aberration theory for wild-filed asymmetric optical systems

    NASA Astrophysics Data System (ADS)

    Chen, Yang; Cheng, Xuemin; Hao, Qun

    2016-10-01

    Nodal Aberration Theory (NAT) was used to calculate the zero field position in Full Field Display (FFD) for the given aberration term. Aiming at wide-filed non-rotational symmetric decentered optical systems, we have presented the nodal geography behavior of the family of third-order and fifth-order aberrations. Meanwhile, we have calculated the wavefront aberration expressions when one optical element in the system is tilted, which was not at the entrance pupil. By using a three-piece-cellphone lens example in optical design software CodeV, the nodal geography is testified under several situations; and the wavefront aberrations are calculated when the optical element is tilted. The properties of the nodal aberrations are analyzed by using Fringe Zernike coefficients, which are directly related with the wavefront aberration terms and usually obtained by real ray trace and wavefront surface fitting.

  6. Tightly Coupled Geodynamic Systems: Software, Implicit Solvers & Applications

    NASA Astrophysics Data System (ADS)

    May, D.; Le Pourhiet, L.; Brown, J.

    2011-12-01

    The generic term "multi-physics" is used to define physical processes which are described by a collection of partial differential equations, or "physics". Numerous processes in geodynamics fall into this category. For example, the evolution of viscous fluid flow and heat transport within the mantle (Stokes flow + energy conservation), the dynamics of melt migration (Stokes flow + Darcy flow + porosity evolution) and landscape evolution (Stokes + diffusion/advection over a surface). The development of software to numerically investigate processes that are described through the composition of different physics components are typically (a) designed for one particular set of physics and are never intended to be extended, or coupled to other processes (b) enforce that certain non-linearity's (or coupling) are explicitly removed from the system for reasons of computational efficiency, or due the lack of a robust non-linear solver (e.g. most models in the mantle convection community). We describe a software infrastructure which enables us to easily introduce new physics with minimal code modifications; tightly couple all physics without introducing splitting errors; exploit modern linear/non-linear solvers and permit the re-use of monolithic preconditioners for individual physics blocks (e.g. saddle point preconditioners for Stokes). Here we present a number of examples to illustrate the flexibility and importance of using this software infra-structure. Using the Stokes system as a prototype, we show results illustrating (i) visco-plastic shear banding experiments, (ii) how coupling Stokes flow with the evolution of the material coordinates can yield temporal stability in the free surface evolution and (iii) the discretisation error associated with decoupling Stokes equation from the heat transport equation in models of mantle convection with various rheologies.

  7. Management of nodal recurrences of endometrial cancer with IMRT

    PubMed Central

    Ho, Jennifer C.; Allen, Pamela K.; Jhingran, Anuja; Westin, Shannon N.; Lu, Karen H.; Eifel, Patricia J.; Klopp, Ann H.

    2016-01-01

    Objective Pelvic and paraortic lymph nodal regions are frequent sites of relapse in women with endometrial cancer who have not undergone adjuvant external beam radiation. We investigated outcomes after definitive management of nodal relapses of endometrial cancer with intensity modulated radiation therapy (IMRT). Methods Between 2002-2012, 38 patients with endometrial cancer who had no prior external beam radiation were treated definitively using IMRT for regionally confined pelvic or paraortic nodal recurrences. Thirteen (34%) had chemotherapy prior to radiation, and 21 (55%) received concurrent chemotherapy. The nodal basins were typically treated to 45-50 Gy, with a boost to the gross tumor to a median total of 64.7 Gy (range 59 – 73 Gy). Results The median overall survival from date of recurrence was 46.1 months and the 2-year survival was 71%. Patients who received concurrent chemotherapy had a significantly longer median survival (61.9 months versus 28.7 months, p=0.034). In-field failures were more frequent in patients who received chemotherapy prior to radiation, had a shorter recurrence-free interval, received a lower radiation dose, and had higher tumor grade. Three patients (8%) experienced grade 3-4 late gastrointestinal (GI) toxicity. Conclusions Long-term survival can be achieved in women with nodal recurrences of endometrial cancer. The use of concurrent chemotherapy and dose escalation with IMRT as feasible may improve survival for women with isolated nodal recurrences of endometrial cancer. PMID:26193429

  8. Management of nodal recurrences of endometrial cancer with IMRT.

    PubMed

    Ho, Jennifer C; Allen, Pamela K; Jhingran, Anuja; Westin, Shannon N; Lu, Karen H; Eifel, Patricia J; Klopp, Ann H

    2015-10-01

    Pelvic and paraortic lymph nodal regions are frequent sites of relapse in women with endometrial cancer who have not undergone adjuvant external beam radiation. We investigated outcomes after definitive management of nodal relapses of endometrial cancer with intensity modulated radiation therapy (IMRT). Between 2002-2012, 38 patients with endometrial cancer who had no prior external beam radiation were treated definitively using IMRT for regionally confined pelvic or paraortic nodal recurrences. Thirteen (34%) had chemotherapy prior to radiation, and 21 (55%) received concurrent chemotherapy. The nodal basins were typically treated to 45-50Gy, with a boost to the gross tumor to a median total of 64.7Gy (range 59-73Gy). The median overall survival from date of recurrence was 46.1months and the 2-year survival was 71%. Patients who received concurrent chemotherapy had a significantly longer median survival (61.9months versus 28.7months, p=0.034). In-field failures were more frequent in patients who received chemotherapy prior to radiation, had a shorter recurrence-free interval, received a lower radiation dose, and had higher tumor grade. Three patients (8%) experienced grade 3-4 late gastrointestinal (GI) toxicity. Long-term survival can be achieved in women with nodal recurrences of endometrial cancer. The use of concurrent chemotherapy and dose escalation with IMRT as feasible may improve survival for women with isolated nodal recurrences of endometrial cancer. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Nodal signalling and asymmetry of the nervous system.

    PubMed

    Signore, Iskra A; Palma, Karina; Concha, Miguel L

    2016-12-19

    The role of Nodal signalling in nervous system asymmetry is still poorly understood. Here, we review and discuss how asymmetric Nodal signalling controls the ontogeny of nervous system asymmetry using a comparative developmental perspective. A detailed analysis of asymmetry in ascidians and fishes reveals a critical context-dependency of Nodal function and emphasizes that bilaterally paired and midline-unpaired structures/organs behave as different entities. We propose a conceptual framework to dissect the developmental function of Nodal as asymmetry inducer and laterality modulator in the nervous system, which can be used to study other types of body and visceral organ asymmetries. Using insights from developmental biology, we also present novel evolutionary hypotheses on how Nodal led the evolution of directional asymmetry in the brain, with a particular focus on the epithalamus. We intend this paper to provide a synthesis on how Nodal signalling controls left-right asymmetry of the nervous system.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.

  10. Nodal discontinuous Galerkin methods on graphics processors

    NASA Astrophysics Data System (ADS)

    Klöckner, A.; Warburton, T.; Bridge, J.; Hesthaven, J. S.

    2009-11-01

    Discontinuous Galerkin (DG) methods for the numerical solution of partial differential equations have enjoyed considerable success because they are both flexible and robust: They allow arbitrary unstructured geometries and easy control of accuracy without compromising simulation stability. Lately, another property of DG has been growing in importance: The majority of a DG operator is applied in an element-local way, with weak penalty-based element-to-element coupling. The resulting locality in memory access is one of the factors that enables DG to run on off-the-shelf, massively parallel graphics processors (GPUs). In addition, DG's high-order nature lets it require fewer data points per represented wavelength and hence fewer memory accesses, in exchange for higher arithmetic intensity. Both of these factors work significantly in favor of a GPU implementation of DG. Using a single US$400 Nvidia GTX 280 GPU, we accelerate a solver for Maxwell's equations on a general 3D unstructured grid by a factor of around 50 relative to a serial computation on a current-generation CPU. In many cases, our algorithms exhibit full use of the device's available memory bandwidth. Example computations achieve and surpass 200 gigaflops/s of net application-level floating point work. In this article, we describe and derive the techniques used to reach this level of performance. In addition, we present comprehensive data on the accuracy and runtime behavior of the method.

  11. Nodal mantle cell lymphoma: a descriptive study from a tertiary care center in South India.

    PubMed

    Roy, Arun; Kar, Rakhee; Basu, Debdatta

    2013-01-01

    Mantle cell lymphoma (MCL) is a type of B-cell non-Hodgkin lymphoma (NHL) with distinctive morphologic, immunophenotypic and a characteristic cytogenetic abnormality, the t(11;14)(q13;q32) and overexpression of cyclin D1. The common histologic features include effaced lymphoid architecture by a monomorphic lymphoid population with a vaguely nodular, diffuse or mantle zone growth pattern. The classic cytomorphologic features include small to medium sized lymphoid cells with irregular nuclear contours and scanty cytoplasm, closely resembling centrocytes. This retrospective study comprises 13 cases of MCL over a period of 5½ years in our department, comprising 4% of all nodal NHL diagnosed. All cases were diagnosed on lymph node biopsy. The mean age of the presentation was 57 years. There was a male preponderance (M:F = 2.25:1). The disease was nodal in all cases. Most patients (84.5%) had generalized lymphadenopathy and/or hepatosplenomegaly. Bone marrow involvement was seen in 81.8% of cases. Three cases showed a nodular pattern on lymph node biopsy while remaining ten had a diffuse pattern. Immunophenotyping showed positivity for CD20, CD5 and cyclin D1 and CD23 negativity. Despite certain morphological similarity to other low-grade/intermediate-grade lymphomas, MCL has a characteristic appearance of its own. Since it is more aggressive than other low-grade lymphomas it needs to be accurately diagnosed.

  12. 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

    2016-09-08

    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. © 2016 by The American Society of Hematology.

  13. A study of the radiative transfer equation using a spherical harmonics-nodal collocation method

    NASA Astrophysics Data System (ADS)

    Capilla, M. T.; Talavera, C. F.; Ginestar, D.; Verdú, G.

    2017-03-01

    Optical tomography has found many medical applications that need to know how the photons interact with the different tissues. The majority of the photon transport simulations are done using the diffusion approximation, but this approximation has a limited validity when optical properties of the different tissues present large gradients, when structures near the photons source are studied or when anisotropic scattering has to be taken into account. As an alternative to the diffusion model, the PL equations for the radiative transfer problem are studied. These equations are discretized in a rectangular mesh using a nodal collocation method. The performance of this model is studied by solving different 1D and 2D benchmark problems of light propagation in tissue having media with isotropic and anisotropic scattering.

  14. Regional nodal irradiation in the conservative treatment of breast cancer

    SciTech Connect

    Haffty, B.G.; Fischer, D.; Fischer, J.J. )

    1990-10-01

    At this institution conservative treatment of breast cancer was begun in the 1960's. The following analysis represents our experience through 1984 with specific reference to the management of the regional lymph nodes. A total of 432 patients with clinical stage I and II breast cancer were treated between 1962 and 1984 with lumpectomy and radiation therapy. The breast was treated with tangential fields to a median dose of 4800 cGy and electron conedown to a total tumor bed dose of 6400 cGy. Axillary dissection was not routinely performed, particularly in the earlier years. More recently, axillary dissection has been used with increasing frequency if it was felt that the results of the dissection would influence systemic treatment. One hundred eighty-seven patients (43%) underwent axillary dissection and routinely received regional nodal irradiation to the internal mammary and supraclavicular lymph nodes. Two hundred forty-five patients (57%) did not undergo axillary dissection and routinely received regional nodal irradiation to the internal mammary, supraclavicular, and entire axillary regions to a total median dose of 4600 cGy. As of May 1989 with a median follow-up of 7.5 years, there have been a total of 12 nodal failures for an actuarial nodal control rate of 97% at 5 years and 96% at 10 years. The actuarial 5-year regional nodal control rate was the same for both the group of patients receiving regional RT alone without axillary dissection and the group of patients receiving axillary dissection and supraclavicular/internal mammary radiation. There has been minimal morbidity associated with this treatment policy. We conclude that regional nodal irradiation, with or without axillary dissection, results in a high rate of regional nodal control and minimal treatment morbidity in patients undergoing conservative treatment of early stage breast cancer.

  15. 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.

  16. 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.

  17. Some topics of Navier-Stokes solvers

    NASA Astrophysics Data System (ADS)

    Honma, H.; Nishikawa, N.

    1990-03-01

    The process of numerical simulation consists of selection of some items: a mathematical model, a numerical scheme, the level of the computer, and post processing. From this point of view, recent numerical studies of viscous flows are described especially for the fluid engineering laboratories in the Chiba University. The examples of simulations are Mach reflection on a wedge using a kinetic model equation and a cylinder-plate juncture flow using incompressible Navier Stokes equation. Some attempts at graphic monitoring of fluid mechanical calculations are also shown for some combinations of computers with Computational Fluid Dynamics (CFD) solvers.

  18. A finite different field solver for dipole modes

    SciTech Connect

    Nelson, E.M.

    1992-08-01

    A finite element field solver for dipole modes in axisymmetric structures has been written. The second-order elements used in this formulation yield accurate mode frequencies with no spurious modes. Quasi-periodic boundaries are included to allow travelling waves in periodic structures. The solver is useful in applications requiring precise frequency calculations such as detuned accelerator structures for linear colliders. Comparisons are made with measurements and with the popular but less accurate field solver URMEL.

  19. A 3D approximate maximum likelihood localization solver

    SciTech Connect

    2016-09-23

    A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with acoustic transmitters and vocalizing marine mammals to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives and support Marine Renewable Energy. 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.

  20. A novel thyroid cancer nodal map classification system to facilitate nodal localization and surgical management: The A to D map.

    PubMed

    Cunnane, Marybeth; Kyriazidis, Natalia; Kamani, Dipti; Juliano, Amy F; Kelly, Hillary R; Curtin, Hugh D; Barber, Samuel R; Randolph, Gregory W

    2017-10-01

    To evaluate the effectiveness, reproducibility, and usability of our proposed nodal nomenclature and classification system employed for several years in our high-volume thyroid cancer unit, for the adequate localization and mapping of lymph nodes in thyroid cancer patients with extensive nodal disease. Retrospective review. Thirty-three thyroid cancer patients with extensive nodal disease treated from January 2004 to May 2013 were included in our study. Preoperative ultrasound and computed tomography scans of these patients were reanalyzed by blinded radiologists to investigate the feasibility for the assignment of abnormal lymph nodes to compartments defined in our proposed nodal classification system and to identify areas of difficulty in the assignment. Analysis of nodal localization revealed a discrepancy in compartment agreement between the two radiologists in the assignment of abnormal nodes in nine patients (9/33, 27%). In six patients (6/33, 18%), discrepancy existed in labeling paratracheal and pretracheal nodes. In three patients (3/33, 9%), disagreement arose in the classification of retrocarotid nodes into lateral versus central compartment. A further refinement of the definition of key borderline regions of the pretracheal versus paratracheal and retrocarotid regions of our classification improved the agreement and demonstrated a complete concordance (100%) amongst the reviewing radiologists. The proposed nodal classification system, derived specifically for differentiated thyroid carcinoma, with readily identifiable anatomic boundaries on imaging and at surgery, facilitates communication among multidisciplinary physicians and aids in creating a uniform and reproducible radiographic nodal map to guide surgical therapy. 4 Laryngoscope, 127:2429-2436, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  1. Type-II nodal loops: Theory and material realization

    NASA Astrophysics Data System (ADS)

    Li, Si; Yu, Zhi-Ming; Liu, Ying; Guan, Shan; Wang, Shan-Shan; Zhang, Xiaoming; Yao, Yugui; Yang, Shengyuan A.

    2017-08-01

    A nodal loop appears when two bands, typically one electronlike and one holelike, are crossing each other linearly along a one-dimensional manifold in reciprocal space. Here, we propose a type of nodal loop which emerges from the crossing between two bands which are both electronlike (or holelike) along a certain direction. Close to any point on such a loop (dubbed as a type-II nodal loop), the linear spectrum is strongly tilted and tipped over along one transverse direction, leading to marked differences in magnetic, optical, and transport responses compared with conventional (type-I) nodal loops. We show that the compound K4P3 is an example that hosts a pair of type-II nodal loops close to the Fermi level. Each loop traverses the whole Brillouin zone, and hence can only be annihilated in a pair when symmetry is preserved. The symmetry and topological protections of the loops as well as the associated surface states are discussed.

  2. AV nodal dual pathway electrophysiology and Wenckebach periodicity.

    PubMed

    Zhang, Youhua; Mazgalev, Todor N

    2011-11-01

    The precise mechanism(s) governing the phenomenon of AV nodal Wenckebach periodicity is not fully elucidated. Currently 2 hypotheses, the decremental conduction and the Rosenbluethian step-delay, are most frequently used. We have provided new evidence that, in addition, dual pathway (DPW) electrophysiology is directly involved in the manifestation of AV nodal Wenckebach phenomenon. AV nodal cellular action potentials (APs) were recorded from 6 rabbit AV node preparations during standard A1A2 and incremental pacing protocols. His electrogram alternans, a validated index of DPW electrophysiology, was used to monitor fast (FP) and slow (SP) pathway conduction. The data were collected in intact AV nodes, as well as after SP ablation. In all studied hearts the Wenckebach cycle started with FP propagation, followed by transition to SP until its ultimate block. During this process complex cellular APs were observed, with decremental foot formations reflecting the fading FP and second depolarizations produced by the SP. In addition, the AV node cells exhibited a progressive loss in maximal diastolic membrane potential (MDP) due to incomplete repolarization. The pause created with the blocked Wenckebach beat was associated with restoration of MDP and reinitiation of the conduction cycle via the FP wavefront. DPW electrophysiology is dynamically involved in the development of AV nodal Wenckebach periodicity. In the intact AV node, the cycle starts with FP that is progressively weakened and then replaced by SP propagation, until block occurs. AV nodal SP modification did not eliminate Wenckebach periodicity but strongly affected its paradigm. © 2011 Wiley Periodicals, Inc.

  3. 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.

  4. Explicit solvers in an implicit code

    NASA Astrophysics Data System (ADS)

    Martinez Montesinos, Beatriz; Kaus, Boris J. P.; Popov, Anton

    2017-04-01

    Many geodynamic processes occur over long timescales (millions of years), and are best solved with implicit solvers. Yet, some processes, such as hydrofracking, or wave propagation, occur over smaller timescales. In those cases, it might be advantageous to use an explicit rather than an implicit approach as it requires significantly less memory and computational costs. Here, we discuss our ongoing work to include explicit solvers in the parallel software package LaMEM (Lithosphere and Mantle Evolution Model). As a first step, we focus on modelling seismic wave propagation in heterogeneous 3D poro-elasto-plastic models. To do that, we add inertial terms to the momentum equations as well as elastic compressibility to the mass conservation equations in an explicit way using the staggered grid finite difference discretization method. Results are similar to that of existing wave propagation codes and are capable to simulate wave propagation in heterogeneous media. To simulate geomechanical problems, timestep restrictions posed by the seismic wave speed are usually too severe to allow simulating deformation on a timescale of months-years. The classical (FLAC) method introduces a mass-density scaling in which a non-physical (larger) density is employed in the momentum equations. We will discuss how this method fits simple benchmarks for elastic and elastoplastic deformation. As an application, we use the code to model different complex media subject to compression and we investigate how mass scaling influence in our results.

  5. 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.)

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Jakobson, Dmitry; Naud, Frédéric

    2017-04-01

    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.

  8. Spin-Orbit Nodal Semimetals in the Layer Groups

    NASA Astrophysics Data System (ADS)

    Wieder, Benjamin; Kim, Youngkuk; Kane, Charles

    Recent interest in point and line node semimetals has lead to the proposal and discovery of these phenomena in numerous systems. Frequently, though, these nodal systems are described in terms of individual properties reliant on specific space group intricacies or band-tuning conditions. Restricting ourselves to cases with strong spin-orbit interaction, we develop a more general framework which captures existing systems and predicts new examples of nodal materials. In many previously proposed systems, the three-dimensional nature of the space group has obscured key generalities. Therefore, we show how within our framework one can predict and characterize a diverse set of nodal phenomena even in two-dimensional systems constructed of three-dimensional sites, known as the ``Layer Groups''. Introducing a set of simple models, we characterize the allowed semimetallic structures in the layer groups and draw connections to analogous three-dimensional systems.

  9. Distant nodal metastasis: is it always an unresectable disease?

    PubMed Central

    Celotti, Andrea; Molfino, Sarah; Baggi, Paolo; Tarasconi, Antonio; Baronio, Gianluca; Arru, Luca; Gheza, Federico; Tiberio, Guido; Portolani, Nazario

    2017-01-01

    This article aims at analyzing the published literature concerning the treatment of patients with gastric cancer and distant nodal metastases, actually considered metastatic disease. A systematic search was undertaken using Medline, Embase, Cochrane and Web-of-Science libraries. No specific restriction on year of publication was used; preference was given to English papers. Both clinical series and literature reviews were selected. Only 11 papers address the issue of surgery for nodal basins outside the D2 dissection area. From these papers, in selected cases extended surgery may prove useful in prolonging survival, when a comprehensive therapeutic pathway including chemotherapy is scheduled. In conclusion, in presence of nodal metastases outside the loco-regional nodes, surgery may be considered for metastatic nodes in stations 13 and 16, in selected cases. PMID:28217751

  10. 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.

  11. 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.

  12. Nodal Structure and the Partitioning of Equivalence Classes

    PubMed Central

    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 A→B→C→D→E→F were produced by training AB, BC, CD, DE, and EF. Then, unique responses were trained to the C and D stimuli in each class. The responses trained to C generalized to B and A, while the responses trained to D generalized to E and F. Thus, each 4-node 6-member equivalence class was bifurcated into two 3-member functional classes: A→B→C and D→E→F, with class membership precisely predicted by nodal structure. A final emergent relations test documented the intactness of the underlying 4-node 6-member equivalence classes. The coexistence of the interchangeability of stimuli in an equivalence class and the bifurcation of such a class in terms of nodal structure was explained in the following manner. The conditional discriminations that are used to establish a class also imposes a nodal structure on the stimuli in the class. Thus, the stimuli in the class acquire two sets of relational properties. If the format of a test trial allows only one response option per class, responding on those trials will be in accordance with class membership and will not express the effects of nodal distance. If the format of a test trial allows more than one response option per class, responding on those trials will be determined by the nodal structure of the class. Thus, the relational properties expressed by the stimuli in an equivalence class are determined by the discriminative function served by the format of a test trial. PMID:18540220

  13. A parallel explicit solver for unsteady compressible flows

    NASA Astrophysics Data System (ADS)

    Akay, H. U.; Ecer, A.; Kemle, W. B.

    A previously developed sequential solver for unsteady compressible Euler equations is implemented on INTEL iPSC/860 parallel computer. An explicit finite element formulation using Clebsch variable form of the Euler equations is presented. A streamwise upwinding technique is employed for introducing artificial diffusion to convective terms. Applications are presented for the solution of transonic potential equations. For parallel implementation of the method, the three-dimensional solution domain is partitioned into a number of subdomains requiring each subdomain to reside on a separate processor for parallel computations. The exchange of information between the solution blocks is due to overlapped boundaries at the block interfaces. The same algorithm can also be applied to steady flows by continuing the time integrations until the steady flow conditions are reached. It has been observed that the convergence rate to steady state is affected little with increased number of solution blocks. Efficiency curves for nearly-balanced loads are obtained for different partitioning algorithms. The partition efficiency is shown to affect the central processing unit (CPU) efficiency of the algorithm directly.

  14. 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.

  15. Regional Nodal Irradiation in Early-Stage Breast Cancer.

    PubMed

    Whelan, Timothy J; Olivotto, Ivo A; Parulekar, Wendy R; Ackerman, Ida; Chua, Boon H; Nabid, Abdenour; Vallis, Katherine A; White, Julia R; Rousseau, Pierre; Fortin, Andre; Pierce, Lori J; Manchul, Lee; Chafe, Susan; Nolan, Maureen C; Craighead, Peter; Bowen, Julie; McCready, David R; Pritchard, Kathleen I; Gelmon, Karen; Murray, Yvonne; Chapman, Judy-Anne W; Chen, Bingshu E; Levine, Mark N

    2015-07-23

    Most women with breast cancer who undergo breast-conserving surgery receive whole-breast irradiation. We examined whether the addition of regional nodal irradiation to whole-breast irradiation improved outcomes. We randomly assigned women with node-positive or high-risk node-negative breast cancer who were treated with breast-conserving surgery and adjuvant systemic therapy to undergo either whole-breast irradiation plus regional nodal irradiation (including internal mammary, supraclavicular, and axillary lymph nodes) (nodal-irradiation group) or whole-breast irradiation alone (control group). The primary outcome was overall survival. Secondary outcomes were disease-free survival, isolated locoregional disease-free survival, and distant disease-free survival. Between March 2000 and February 2007, a total of 1832 women were assigned to the nodal-irradiation group or the control group (916 women in each group). The median follow-up was 9.5 years. At the 10-year follow-up, there was no significant between-group difference in survival, with a rate of 82.8% in the nodal-irradiation group and 81.8% in the control group (hazard ratio, 0.91; 95% confidence interval [CI], 0.72 to 1.13; P=0.38). The rates of disease-free survival were 82.0% in the nodal-irradiation group and 77.0% in the control group (hazard ratio, 0.76; 95% CI, 0.61 to 0.94; P=0.01). Patients in the nodal-irradiation group had higher rates of grade 2 or greater acute pneumonitis (1.2% vs. 0.2%, P=0.01) and lymphedema (8.4% vs. 4.5%, P=0.001). Among women with node-positive or high-risk node-negative breast cancer, the addition of regional nodal irradiation to whole-breast irradiation did not improve overall survival but reduced the rate of breast-cancer recurrence. (Funded by the Canadian Cancer Society Research Institute and others; MA.20 ClinicalTrials.gov number, NCT00005957.).

  16. Preoperative staging of nodal status in gastric cancer

    PubMed Central

    Berlth, Felix; Chon, Seung-Hun; Chevallay, Mickael; Jung, Minoa Karin

    2017-01-01

    An accurate preoperative staging of nodal status is crucial in gastric cancer, because it has a great impact on prognosis and therapeutic decision-making. Different staging methods have been evaluated for gastric cancer in order to predict nodal involvement. So far, no technique could meet the necessary requirements, which include a high detection rate of infiltrated lymph nodes and a low frequency of false-positive results. This article summarizes different staging methods used to assess lymph node status in patients with gastric cancer, evaluates the evidence, and proposes to establish new methods. PMID:28217758

  17. Regional Nodal Irradiation in Early-Stage Breast Cancer

    PubMed Central

    Whelan, Timothy J.; Olivotto, Ivo A.; Parulekar, Wendy R.; Ackerman, Ida; Chua, Boon H.; Nabid, Abdenour; Vallis, Katherine A.; White, Julia R.; Rousseau, Pierre; Fortin, Andre; Pierce, Lori J.; Manchul, Lee; Chafe, Susan; Nolan, Maureen C.; Craighead, Peter; Bowen, Julie; McCready, David R.; Pritchard, Kathleen I.; Gelmon, Karen; Murray, Yvonne; Chapman, Judy-Anne W.; Chen, Bingshu E.; Levine, Mark N.

    2015-01-01

    BACKGROUND Most women with breast cancer who undergo breast-conserving surgery receive whole-breast irradiation. We examined whether the addition of regional nodal irradiation to whole-breast irradiation improved outcomes. METHODS We randomly assigned women with node-positive or high-risk node-negative breast cancer who were treated with breast-conserving surgery and adjuvant systemic therapy to undergo either whole-breast irradiation plus regional nodal irradiation (including internal mammary, supraclavicular, and axillary lymph nodes) (nodal-irradiation group) or whole-breast irradiation alone (control group). The primary outcome was overall survival. Secondary outcomes were disease-free survival, isolated locoregional disease-free survival, and distant disease-free survival. RESULTS Between March 2000 and February 2007, a total of 1832 women were assigned to the nodal-irradiation group or the control group (916 women in each group). The median follow-up was 9.5 years. At the 10-year follow-up, there was no significant between-group difference in survival, with a rate of 82.8% in the nodal-irradiation group and 81.8% in the control group (hazard ratio, 0.91; 95% confidence interval [CI], 0.72 to 1.13; P = 0.38). The rates of disease-free survival were 82.0% in the nodal-irradiation group and 77.0% in the control group (hazard ratio, 0.76; 95% CI, 0.61 to 0.94; P = 0.01). Patients in the nodal-irradiation group had higher rates of grade 2 or greater acute pneumonitis (1.2% vs. 0.2%, P = 0.01) and lymphedema (8.4% vs. 4.5%, P = 0.001). CONCLUSIONS Among women with node-positive or high-risk node-negative breast cancer, the addition of regional nodal irradiation to whole-breast irradiation did not improve overall survival but reduced the rate of breast-cancer recurrence. PMID:26200977

  18. Nodal metastases in thyroid cancer: prognostic implications and management.

    PubMed

    Wang, Laura Y; Ganly, Ian

    2016-04-01

    The significance of cervical lymph node metastases in differentiated thyroid cancer has been controversial and continues to evolve. Current staging systems consider nodal metastases to confer a poorer prognosis, particularly in older patients. Increasingly, the literature suggests that characteristics of the metastatic lymph nodes such as size and number are also prognostic. There is a growing trend toward less aggressive treatment of low-volume nodal disease. The aim of this review is to summarize the current literature and discuss prognostic and management implications of lymph node metastases in differentiated thyroid cancer.

  19. 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.

  20. Nodal metastases in thyroid cancer: prognostic implications and management

    PubMed Central

    Wang, Laura Y; Ganly, Ian

    2016-01-01

    The significance of cervical lymph node metastases in differentiated thyroid cancer has been controversial and continues to evolve. Current staging systems consider nodal metastases to confer a poorer prognosis, particularly in older patients. Increasingly, the literature suggests that characteristics of the metastatic lymph nodes such as size and number are also prognostic. There is a growing trend toward less aggressive treatment of low-volume nodal disease. The aim of this review is to summarize the current literature and discuss prognostic and management implications of lymph node metastases in differentiated thyroid cancer. PMID:26948758

  1. Working towards a numerical solver for seismic wave propagation in unsaturated porous media

    NASA Astrophysics Data System (ADS)

    Boxberg, Marc S.; Friederich, Wolfgang

    2017-04-01

    Modeling the propagation of seismic waves in porous media gets more and more popular in the seismological community. However, it is still a challenging task in the field of computational seismology. Nevertheless, it is important to account for the fluid content of, e.g., reservoir rocks or soils, and the interaction between the fluid and the rock or between different immiscible fluids to accurately describe seismic wave propagation through such porous media. Often, numerical models are based on the elastic wave equation and some might include artificially introduced attenuation. This simplifies the computation, because it only approximates the physics behind that problem. However, the results are also simplified and could miss phenomena and lack accuracy in some applications. We present a numerical solver for wave propagation in porous media saturated by two immiscible fluids. It is based on Biot's theory of poroelasticity and accounts for macroscopic flow that occurs on the same scale as the wavelength of the seismic waves. Fluid flow is described by a Darcy type flow law and interactions between the fluids by means of capillary pressure curve models. In addition, consistent boundary conditions on interfaces between poroelastic media and elastic or acoustic media are derived from this poroelastic theory itself. The poroelastic solver is integrated into the larger software package NEXD that uses the nodal discontinuous Galerkin method to solve wave equations in 1D, 2D, and 3D on a mesh of linear (1D), triangular (2D), or tetrahedral (3D) elements. Triangular and tetrahedral elements have great advantages as soon as the model has a complex structure, like it is often the case for geologic models. We illustrate the capabilities of the codes by numerical examples. This work can be applied to various scientific questions in, e.g., exploration and monitoring of hydrocarbon or geothermal reservoirs as well as CO2 storage sites.

  2. 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)

  3. 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.

  4. Cosmic-ray propagation with DRAGON2: I. numerical solver and astrophysical ingredients

    NASA Astrophysics Data System (ADS)

    Evoli, Carmelo; Gaggero, Daniele; Vittino, Andrea; Di Bernardo, Giuseppe; Di Mauro, Mattia; Ligorini, Arianna; Ullio, Piero; Grasso, Dario

    2017-02-01

    We present version 2 of the DRAGON code designed for computing realistic predictions of the CR densities in the Galaxy. The code numerically solves the interstellar CR transport equation (including inhomogeneous and anisotropic diffusion, either in space and momentum, advective transport and energy losses), under realistic conditions. The new version includes an updated numerical solver and several models for the astrophysical ingredients involved in the transport equation. Improvements in the accuracy of the numerical solution are proved against analytical solutions and in reference diffusion scenarios. The novel features implemented in the code allow to simulate the diverse scenarios proposed to reproduce the most recent measurements of local and diffuse CR fluxes, going beyond the limitations of the homogeneous galactic transport paradigm. To this end, several applications using DRAGON2 are presented as well. This new version facilitates the users to include their own physical models by means of a modular C++ structure.

  5. 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.

  6. 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.

  7. 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].

  8. 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.

  9. Linear iterative solvers for implicit ODE methods

    NASA Technical Reports Server (NTRS)

    Saylor, Paul E.; Skeel, Robert D.

    1990-01-01

    The numerical solution of stiff initial value problems, which lead to the problem of solving large systems of mildly nonlinear equations are considered. For many problems derived from engineering and science, a solution is possible only with methods derived from iterative linear equation solvers. A common approach to solving the nonlinear equations is to employ an approximate solution obtained from an explicit method. The error is examined to determine how it is distributed among the stiff and non-stiff components, which bears on the choice of an iterative method. The conclusion is that error is (roughly) uniformly distributed, a fact that suggests the Chebyshev method (and the accompanying Manteuffel adaptive parameter algorithm). This method is described, also commenting on Richardson's method and its advantages for large problems. Richardson's method and the Chebyshev method with the Mantueffel algorithm are applied to the solution of the nonlinear equations by Newton's method.

  10. 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.

  11. Neutrino transport in type II supernovae: Boltzmann solver vs. Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Yamada, Shoichi; Janka, Hans-Thomas; Suzuki, Hideyuki

    1999-04-01

    We have coded a Boltzmann solver based on a finite difference scheme (S_N method) aiming at calculations of neutrino transport in type II supernovae. Close comparison between the Boltzmann solver and a Monte Carlo transport code has been made for realistic atmospheres of post bounce core models under the assumption of a static background. We have also investigated in detail the dependence of the results on the numbers of radial, angular, and energy grid points and the way to discretize the spatial advection term which is used in the Boltzmann solver. A general relativistic calculation has been done for one of the models. We find good overall agreement between the two methods. This gives credibility to both methods which are based on completely different formulations. In particular, the number and energy fluxes and the mean energies of the neutrinos show remarkably good agreement, because these quantities are determined in a region where the angular distribution of the neutrinos is nearly isotropic and they are essentially frozen in later on. On the other hand, because of a relatively small number of angular grid points (which is inevitable due to limitations of the computation time) the Boltzmann solver tends to slightly underestimate the flux factor and the Eddington factor outside the (mean) ``neutrinosphere'' where the angular distribution of the neutrinos becomes highly anisotropic. As a result, the neutrino number (and energy) density is somewhat overestimated in this region. This fact suggests that the Boltzmann solver should be applied to calculations of the neutrino heating in the hot-bubble region with some caution because there might be a tendency to overestimate the energy deposition rate in disadvantageous situations. A comparison shows that this trend is opposite to the results obtained with a multi-group flux-limited diffusion approximation of neutrino transport. Employing three different flux limiters, we find that all of them lead to a significant

  12. Lattice Boltzmann solver of Rossler equation

    NASA Astrophysics Data System (ADS)

    Yan, Guangwu; Ruan, Li

    2000-06-01

    We proposed a lattice Boltzmann model for the Rossler equation. Using a method of multiscales in the lattice Boltzmann model, we get the diffusion reaction as a special case. If the diffusion effect disappeared, we can obtain the lattice Boltzmann solution of the Rossler equation on the mesescopic scale. The numerical results show the method can be used to simulate Rossler equation.

  13. Scalable Iterative Solvers Applied to 3D Parallel Simulation of Advanced Semiconductor Devices

    NASA Astrophysics Data System (ADS)

    García-Loureiro, A. J.; Aldegunde, M.; Seoane, N.

    2009-08-01

    We have studied the performance of a preconditioned iterative solver to speed up a 3D semiconductor device simulator. Since 3D simulations necessitate large computing resources, the choice of algorithms and their parameters become of utmost importance. This code uses a density gradient drift-diffusion semiconductor transport model based on the finite element method which is one of the most general and complex discretisation techniques. It has been implemented for a distributed memory multiprocessor environment using the Message Passing Interface (MPI) library. We have applied this simulator to a 67 nm effective gate length Si MOSFET.

  14. Universal phase transition and band structures for spinless nodal-line and Weyl semimetals

    NASA Astrophysics Data System (ADS)

    Okugawa, Ryo; Murakami, Shuichi

    2017-09-01

    We study a general phase transition between spinless topological nodal-line semimetal and Weyl semimetal phases. We classify topological nodal lines into two types based on their positions and shapes, and their phase transitions depend on their types. We show that a topological nodal-line semimetal becomes a Weyl semimetal by breaking time-reversal symmetry when the nodal lines enclose time-reversal-invariant momenta (type-A nodal lines). We also discuss an effect of crystallographic symmetries determining the band structure of the topological nodal-line semimetals. Thanks to protection by the symmetries, the topological nodal-line semimetals can transition into spinless Weyl semimetals or maintain the nodal lines in many crystals after inversion symmetry is broken.

  15. 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…

  16. PoroTomo Subtask 6.3 Nodal Seismometers Metadata

    SciTech Connect

    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.

  17. Polymorphic nodal elements and their application in discontinuous Galerkin methods

    NASA Astrophysics Data System (ADS)

    Gassner, Gregor J.; Lörcher, Frieder; Munz, Claus-Dieter; Hesthaven, Jan S.

    2009-03-01

    In this work, we discuss two different but related aspects of the development of efficient discontinuous Galerkin methods on hybrid element grids for the computational modeling of gas dynamics in complex geometries or with adapted grids. In the first part, a recursive construction of different nodal sets for hp finite elements is presented. They share the property that the nodes along the sides of the two-dimensional elements and along the edges of the three-dimensional elements are the Legendre-Gauss-Lobatto points. The different nodal elements are evaluated by computing the Lebesgue constants of the corresponding Vandermonde matrix. In the second part, these nodal elements are applied within the modal discontinuous Galerkin framework. We still use a modal based formulation, but introduce a nodal based integration technique to reduce computational cost in the spirit of pseudospectral methods. We illustrate the performance of the scheme on several large scale applications and discuss its use in a recently developed space-time expansion discontinuous Galerkin scheme.

  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. The Penn State Nodal Expansion Transient Analysis Technique with thermal-hydraulic feedback

    SciTech Connect

    Borkowski, J.; Bandini, B.; Baratta, A. )

    1989-11-01

    The nuclear engineering department of the Pennsylvania State University has under development a nodal neutron kinetics code. The PEnn State Nodal Expansion TRansient Analysis TEchnique (PENETRATE) performs two-group, three-dimensional nodal kinetics calculations using the nodal expansion method (NEM). The focus of this discussion is its performance in the solution of the Langenbuch-Maurer-Werner light water rector (LMW LWR) problem. This transient requires an accurate model of both control rod motion and coupled thermal-hydraulic feedback.

  20. Orbital nodal surfaces: Topological challenges for density functionals

    NASA Astrophysics Data System (ADS)

    Aschebrock, Thilo; Armiento, Rickard; Kümmel, Stephan

    2017-06-01

    Nodal surfaces of orbitals, in particular of the highest occupied one, play a special role in Kohn-Sham density-functional theory. The exact Kohn-Sham exchange potential, for example, shows a protruding ridge along such nodal surfaces, leading to the counterintuitive feature of a potential that goes to different asymptotic limits in different directions. We show here that nodal surfaces can heavily affect the potential of semilocal density-functional approximations. For the functional derivatives of the Armiento-Kümmel (AK13) [Phys. Rev. Lett. 111, 036402 (2013), 10.1103/PhysRevLett.111.036402] and Becke88 [Phys. Rev. A 38, 3098 (1988), 10.1103/PhysRevA.38.3098] energy functionals, i.e., the corresponding semilocal exchange potentials, as well as the Becke-Johnson [J. Chem. Phys. 124, 221101 (2006), 10.1063/1.2213970] and van Leeuwen-Baerends (LB94) [Phys. Rev. A 49, 2421 (1994), 10.1103/PhysRevA.49.2421] model potentials, we explicitly demonstrate exponential divergences in the vicinity of nodal surfaces. We further point out that many other semilocal potentials have similar features. Such divergences pose a challenge for the convergence of numerical solutions of the Kohn-Sham equations. We prove that for exchange functionals of the generalized gradient approximation (GGA) form, enforcing correct asymptotic behavior of the potential or energy density necessarily leads to irregular behavior on or near orbital nodal surfaces. We formulate constraints on the GGA exchange enhancement factor for avoiding such divergences.

  1. Functional mathematical model of dual pathway AV nodal conduction.

    PubMed

    Climent, A M; Guillem, M S; Zhang, Y; Millet, J; Mazgalev, T N

    2011-04-01

    Dual atrioventricular (AV) nodal pathway physiology is described as two different wave fronts that propagate from the atria to the His bundle: one with a longer effective refractory period [fast pathway (FP)] and a second with a shorter effective refractory period [slow pathway (SP)]. By using His electrogram alternance, we have developed a mathematical model of AV conduction that incorporates dual AV nodal pathway physiology. Experiments were performed on five rabbit atrial-AV nodal preparations to develop and test the presented model. His electrogram alternances from the inferior margin of the His bundle were used to identify fast and slow wave front propagations. The ability to predict AV conduction time and the interaction between FP and SP wave fronts have been analyzed during regular and irregular atrial rhythms (e.g., atrial fibrillation). In addition, the role of dual AV nodal pathway wave fronts in the generation of Wenckebach periodicities has been illustrated. Finally, AV node ablative modifications have been evaluated. The model accurately reproduced interactions between FP and SP during regular and irregular atrial pacing protocols. In all experiments, specificity and sensitivity higher than 85% were obtained in the prediction of the pathway responsible for conduction. It has been shown that, during atrial fibrillation, the SP ablation significantly increased the mean HH interval (204 ± 39 vs. 274 ± 50 ms, P < 0.05), whereas FP ablation did not produce significant slowing of ventricular rate. The presented mathematical model can help in understanding some of the intriguing AV node mechanisms and should be considered as a step forward in the studies of AV nodal conduction.

  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 be...

  3. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 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 be...

  4. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 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 be...

  5. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 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 be...

  6. 47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 5 2013-10-01 2013-10-01 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 be...

  7. 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.

  8. Numerical Solution of Poroelastic Wave Equation Using Nodal Discontinuous Galerkin Finite Element Method

    NASA Astrophysics Data System (ADS)

    Shukla, K.; Wang, Y.; Jaiswal, P.

    2014-12-01

    In a porous medium the seismic energy not only propagates through matrix but also through pore-fluids. The differential movement between sediment grains of the matrix and interstitial fluid generates a diffusive wave which is commonly referred to as the slow P-wave. A combined system of equation which includes both elastic and diffusive phases is known as the poroelasticity. Analyzing seismic data through poroelastic modeling results in accurate interpretation of amplitude and separation of wave modes, leading to more accurate estimation of geomehanical properties of rocks. Despite its obvious multi-scale application, from sedimentary reservoir characterization to deep-earth fractured crust, poroelasticity remains under-developed primarily due to the complex nature of its constituent equations. We present a detail formulation of poroleastic wave equations for isotropic media by combining the Biot's and Newtonian mechanics. System of poroelastic wave equation constitutes for eight time dependent hyperbolic PDEs in 2D whereas in case of 3D number goes up to thirteen. Eigen decomposition of Jacobian of these systems confirms the presence of an additional slow-P wave phase with velocity lower than shear wave, posing stability issues on numerical scheme. To circumvent the issue, we derived a numerical scheme using nodal discontinuous Galerkin approach by adopting the triangular meshes in 2D which is extended to tetrahedral for 3D problems. In our nodal DG approach the basis function over a triangular element is interpolated using Legendre-Gauss-Lobatto (LGL) function leading to a more accurate local solutions than in the case of simple DG. We have tested the numerical scheme for poroelastic media in 1D and 2D case, and solution obtained for the systems offers high accuracy in results over other methods such as finite difference , finite volume and pseudo-spectral. The nodal nature of our approach makes it easy to convert the application into a multi-threaded algorithm

  9. 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

  10. An iterative solver for the 3D Helmholtz equation

    NASA Astrophysics Data System (ADS)

    Belonosov, Mikhail; Dmitriev, Maxim; Kostin, Victor; Neklyudov, Dmitry; Tcheverda, Vladimir

    2017-09-01

    We develop a frequency-domain iterative solver for numerical simulation of acoustic waves in 3D heterogeneous media. It is based on the application of a unique preconditioner to the Helmholtz equation that ensures convergence for Krylov subspace iteration methods. Effective inversion of the preconditioner involves the Fast Fourier Transform (FFT) and numerical solution of a series of boundary value problems for ordinary differential equations. Matrix-by-vector multiplication for iterative inversion of the preconditioned matrix involves inversion of the preconditioner and pointwise multiplication of grid functions. Our solver has been verified by benchmarking against exact solutions and a time-domain solver.

  11. 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)

  12. GPU accelerated kinetic solvers for rarefied gas dynamics

    NASA Astrophysics Data System (ADS)

    Zabelok, Sergey A.; Kolobov, Vladimir I.; Arslanbekov, Robert R.

    2012-11-01

    GPU-acceleration is applied to the Boltzmann solver with adaptive Cartesian mesh in the Unified Flow Solver framework. NVIDIA CUDA technology is used with threads being grouped in thread blocks by points of Korobov sequences in each cell for computing the collision integral and by points in coordinate space for the free-molecular flow stage. GPU-accelerated Boltzmann solver with octree Cartesian mesh has been tested on several computer systems. Speedup of several times for GPU-based code compared to single-core CPU computations on the same machines has been observed.

  13. Nodal metastasis and elective nodal level treatment in sinonasal small-cell and sinonasal undifferentiated carcinoma: a surveillance, epidemiology and end results analysis

    PubMed Central

    Mitra, Nandita; Alonso-Basanta, Michelle; Adappa, Nithin D; Palmer, James N; O'Malley, Bert W; Rassekh, Christopher H; Chalian, Ara; Cohen, Roger B; Lin, Alexander

    2016-01-01

    Objective: Risk of nodal involvement in patients with sinonasal small-cell carcinoma and sinonasal undifferentiated carcinoma (SNUC) has not been well defined because of their rarity. We describe a population-based assessment of specific nodal level involvement in this group of rare neuroectodermal tumours. Methods: The Surveillance, Epidemiology and End Results (SEER) database from 2004 to 2011 identified patients with SNUC and sinonasal small-cell carcinoma. Overall neck involvement and individual nodal level involvement at presentation were assessed, and comparison was made with a contemporaneous cohort of patients with a borderline clinically significant risk of nodal involvement and recurrence. Results: Of 141 patients, 31 (22%) had gross nodal involvement at presentation (range 14–33% by site and histology). Non-nasal, non-ethmoid site with SNUC histology has the highest rates of initial nodal involvement, whereas higher stage and size do not predict for higher nodal involvement rates. Bilateral Levels 2–3 for all sinonasal small cell; Levels 2–3 for nasal or ethmoid SNUC; and bilateral Levels 1–3 in non-nasal/non-ethmoid SNUC have the highest rates of involvement compared with a clinical reference standard. Conclusion: We found high rates of initial nodal involvement in all SNUC and sinonasal small-cell carcinoma. We found higher initial involvement of Levels 2 and 3 and in certain cases to the Level 1 nodal levels, hypothesizing benefit for elective treatment to those levels. Advances in knowledge: With small single-institution series reporting conflicting nodal involvement rates, our data support high rates of nodal presentation at diagnosis, hypothesizing benefit for elective nodal treatment in this cohort. PMID:26559439

  14. Wind-US Unstructured Flow Solutions for a Transonic Diffuser

    NASA Technical Reports Server (NTRS)

    Mohler, Stanley R., Jr.

    2005-01-01

    The Wind-US Computational Fluid Dynamics flow solver computed flow solutions for a transonic diffusing duct. The calculations used an unstructured (hexahedral) grid. The Spalart-Allmaras turbulence model was used. Static pressures along the upper and lower wall agreed well with experiment, as did velocity profiles. The effect of the smoothing input parameters on convergence and solution accuracy was investigated. The meaning and proper use of these parameters are discussed for the benefit of Wind-US users. Finally, the unstructured solver is compared to the structured solver in terms of run times and solution accuracy.

  15. Flow Solver for Incompressible Rectangular Domains

    NASA Technical Reports Server (NTRS)

    Kalb, Virginia L.

    2008-01-01

    This is an extension of the Flow Solver for Incompressible 2-D Drive Cavity software described in the preceding article. It solves the Navier-Stokes equations for incompressible flow using finite differencing on a uniform, staggered grid. There is a runtime choice of either central differencing or modified upwinding for the convective term. The domain must be rectangular, but may have a rectangular walled region within it. Currently, the position of the interior region and exterior boundary conditions are changed by modifying parameters in the code and recompiling. These features make it possible to solve a variety of classical fluid flow problems such as an L-shaped cavity, channel flow, or wake flow past a square cylinder. The code uses fourth-order Runge-Kutta time-stepping and overall second-order spatial accuracy. This software permits the walled region to be positioned such that flow past a square cylinder, an L-shaped cavity, and the flow over a back-facing step can all be solved by reconfiguration. Also, this extension has an automatic detection of periodicity, as well as use of specialized data structure for ease of configuring domain decomposition and computing convergence in overlap regions.

  16. Advanced Multigrid Solvers for Fluid Dynamics

    NASA Technical Reports Server (NTRS)

    Brandt, Achi

    1999-01-01

    The main objective of this project has been to support the development of multigrid techniques in computational fluid dynamics that can achieve "textbook multigrid efficiency" (TME), which is several orders of magnitude faster than current industrial CFD solvers. Toward that goal we have assembled a detailed table which lists every foreseen kind of computational difficulty for achieving it, together with the possible ways for resolving the difficulty, their current state of development, and references. We have developed several codes to test and demonstrate, in the framework of simple model problems, several approaches for overcoming the most important of the listed difficulties that had not been resolved before. In particular, TME has been demonstrated for incompressible flows on one hand, and for near-sonic flows on the other hand. General approaches were advanced for the relaxation of stagnation points and boundary conditions under various situations. Also, new algebraic multigrid techniques were formed for treating unstructured grid formulations. More details on all these are given below.

  17. 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.

  18. 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.

  19. 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.

  20. A RADIATION TRANSFER SOLVER FOR ATHENA USING SHORT CHARACTERISTICS

    SciTech Connect

    Davis, Shane W.; Stone, James M.; Jiang Yanfei

    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.

  1. 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.

  2. 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.

  3. 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.

  4. Intra and interfraction mediastinal nodal region motion: implications for internal target volume expansions.

    PubMed

    Thomas, Jonathan G; Kashani, Rojano; Balter, James M; Tatro, Daniel; Kong, Feng-Ming; Pan, Charlie C

    2009-01-01

    The purpose of this study was to determine the intra and interfraction motion of mediastinal lymph node regions. Ten patients with nonsmall-cell lung cancer underwent controlled inhale and exhale computed tomography (CT) scans during two sessions (40 total datasets) and mediastinal nodal stations 1-8 were outlined. Corresponding CT scans from different sessions were registered to remove setup error and, in this reference frame, the centroid of each nodal station was compared for right-left (RL), anterior-posterior (AP), and superior-inferior (SI) displacement. In addition, an anisotropic volume expansion encompassing the change of the nodal region margins in all directions was used. Intrafraction displacement was determined by comparing same session inhale-exhale scans. Interfraction reproducibility of nodal regions was determined by comparing the same respiratory phase scans between two sessions. Intrafraction displacement of centroid varied between nodal stations. All nodal regions moved posteriorly and superiorly with exhalation, and inferior nodal stations showed the most motion. Based on anisotropic expansion, nodal regions expanded mostly in the RL direction from inhale to exhale. The interpatient variations in intrafraction displacement were large compared with the displacements themselves. Moreover, there was substantial interfractional displacement ( approximately 5 mm). Mediastinal lymph node regions clearly move during breathing. In addition, deformation of nodal regions between inhale and exhale occurs. The degree of motion and deformation varies by station and by individual. This study indicates the potential advantage of characterizing individualized nodal region motion to safely maximize conformality of mediastinal nodal targets.

  5. Experiences Running a Parallel Answer Set Solver on Blue Gene

    NASA Astrophysics Data System (ADS)

    Schneidenbach, Lars; Schnor, Bettina; Gebser, Martin; Kaminski, Roland; Kaufmann, Benjamin; Schaub, Torsten

    This paper presents the concept of parallelisation of a solver for Answer Set Programming (ASP). While there already exist some approaches to parallel ASP solving, there was a lack of a parallel version of the powerful clasp solver. We implemented a parallel version of clasp based on message-passing. Experimental results on Blue Gene P/L indicate the potential of such an approach.

  6. 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.

  7. 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.

  8. Radial nodalization effects on BWR (boiling water reactor) stability calculations

    SciTech Connect

    March-Leuba, J.

    1990-01-01

    Computer simulations have shown that stability calculations in boiling water reactors (BWRs) are very sensitive to a number of input parameters and modeling assumptions. In particular, the number of thermohydraulic regions (i.e., channels) used in the calculation can affect the results of decay ratio calculations by as much as 30%. This paper presents the background theory behind the observed effects of radial nodalization in BWR stability calculations. The theory of how a radial power distribution can be simulated in time or frequency domain codes by using representative'' regions is developed. The approximations involved in this method of solution are reviewed, and some examples of the effect of radial nodalization are presented based on LAPUR code solutions. 2 refs., 4 figs., 2 tabs.

  9. A composite grid solver for conjugate heat transfer in fluid-structure systems

    SciTech Connect

    Henshaw, William D. Chand, Kyle K.

    2009-06-01

    We describe a numerical method for modeling temperature-dependent fluid flow coupled to heat transfer in solids. This approach to conjugate heat transfer can be used to compute transient and steady state solutions to a wide range of fluid-solid systems in complex two- and three-dimensional geometry. Fluids are modeled with the temperature-dependent incompressible Navier-Stokes equations using the Boussinesq approximation. Solids with heat transfer are modeled with the heat equation. Appropriate interface equations are applied to couple the solutions across different domains. The computational region is divided into a number of sub-domains corresponding to fluid domains and solid domains. There may be multiple fluid domains and multiple solid domains. Each fluid or solid sub-domain is discretized with an overlapping grid. The entire region is associated with a composite grid which is the union of the overlapping grids for the sub-domains. A different physics solver (fluid solver or solid solver) is associated with each sub-domain. A higher-level multi-domain solver manages the entire solution process. We propose and analyze some centered discrete approximations to the interface equations that have some desirable stability properties. The coupled interface equations may be solved directly when using explicit time-stepping methods in the sub-domains, resulting in a strongly coupled approach. The stability of the interface treatment in this case is independent of the relative sizes of the material properties in the two domains with the time-step only depending on the usual von Neumann conditions for each sub-domain. For implicit time-stepping methods we solve the interface equations in a weakly coupled fashion to avoid forming a coupled implicit system across all sub-domains. The convergence of this approach does depend on the relative sizes of the thermal conductivities and diffusivities. We analyze different iteration strategies for solving these implicit equations

  10. NODAL PATHWAY GENES ARE DOWNREGULATED IN FACIAL ASYMMETRY

    PubMed Central

    Nicot, Romain; Hottenstein, Molly; Raoul, Gwenael; Ferri, Joel; Horton, Michael; Tobias, John W.; Barton, Elisabeth; Gelé, Patrick; Sciote, James J.

    2014-01-01

    Purpose Facial asymmetry is a common comorbid condition in patients with jaw deformation malocclusion. Heritability of malocclusion is advancing rapidly, but very little is known regarding genetic contributions to asymmetry. This study identifies differences in expression of key asymmetry-producing genes which are down regulated in facial asymmetry patients. Material and Methods Masseter muscle samples were collected during BSSO orthognathic surgery to correct skeletal-based malocclusion. Patients were classified as Class II or III and open or deep bite malocclusion with or without facial asymmetry. Muscle samples were analyzed for gene expression differences on Affymetrix HT2.0 microarray global expression chips. Results Overall gene expression was different for asymmetric patients compared to other malocclusion classifications by principal component analysis (P<0.05). We identified differences in the nodal signaling pathway (NSP) which promotes development of mesoderm and endoderm and left-right patterning during embryogenesis. Nodal and Lefty expression was 1.39–1.84 fold greater (P<3.41×10−5) whereas integral membrane Nodal-modulators Nomo1,2,3 were −5.63 to −5.81 (P<3.05×10−4) less in asymmetry subjects. Fold differences among intracellular pathway members were negative in the range of −7.02 to −2.47 (P<0.003). Finally Pitx2, a upstream effector of Nodal known to influence the size of type II skeletal muscle fibers was also significantly decreased in facial asymmetry (P<0.05). Conclusions When facial asymmetry is part of skeletal malocclusion there are decreases of NSP genes in masseter muscle. This data suggests that the NSP is down regulated to help promote development of asymmetry. Pitx2 expression differences also contributed to both skeletal and muscle development in this condition. PMID:25364968

  11. PoroTomo: Nodal Seismometer Active Source Data Sample

    SciTech Connect

    Kurt Feigl

    2016-03-25

    This data is in sac format and includes recordings of two active source events from 238 three-component nodal seismometers deployed at Bradys Hot Springs geothermal field as part of the PoroTomo project. The source was a viberoseis truck operating in P-wave vibrational mode and generating a swept-frequency signal. The files are 33 seconds long starting 4 seconds before each sweep was initiated. There is some overlap in the file times.

  12. 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.

  13. Histogenesis of metaplastic breast carcinoma and axillary nodal metastases.

    PubMed

    Osako, Tomo; Horii, Rie; Ogiya, Akiko; Iijima, Kotaro; Iwase, Takuji; Akiyama, Futoshi

    2009-02-01

    A 40-year-old breast-feeding woman presented with left breast swelling. On physical examination a 7 cm mass was found in the breast. Because biopsy demonstrated malignant tissue, mastectomy with axillary nodal dissection was performed. Pathological findings were consistent with metaplastic breast carcinoma with nodal metastases. The primary tumor consisted of three types of invasion: ductal, squamous, and sarcomatous. Furthermore, three morphological transitions were observed: ductal-squamous, ductal-sarcomatous, and squamous-sarcomatous. Ductal-squamous (12/18 microscopy slides) and squamous-sarcomatous transitions (10/18) were more commonly observed than ductal-sarcomatous transition (3/18). Furthermore, immunohistochemistry showed loss of epithelial marker (cytokeratin) and acquisition of mesenchymal markers (vimentin and alpha-smooth muscle actin) in the sarcomatous component. These findings suggested that epithelial-mesenchymal transition had occurred in the tumor and that two pathways, ductal-squamous-sarcomatous and ductal-sarcomatous transition, were involved in progression of metaplastic breast carcinoma. The main pathway appeared to be ductal-squamous-sarcomatous transition. Regarding the nodal metastases, of 13 positive nodes, ductal, squamous, and sarcomatous components were observed in 13, seven, and two nodes, respectively. Moreover, as in the primary tumor, ductal-squamous and squamous-sarcomatous transitions were observed. This suggested that the ductal component metastasized to the nodes and that epithelial-mesenchymal transition subsequently occurred within the nodes.

  14. 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.

  15. 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.

  16. Topological phase transitions in line-nodal superconductors

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    Fathoming interplay between symmetry and topology of many-electron wave functions has deepened our understanding of quantum many-body systems, particularly after the discovery of topological insulators. Topology of electron wave functions often enforces and protects emergent gapless excitation, and symmetry is intrinsically tied to the topological protection of the excitations. Namely, unless the symmetry is broken, the topological nature of the excitations is intact. We show intriguing phenomena of interplay between symmetry and topology in three-dimensional topological phase transitions associated with line-nodal superconductors. More specifically, we discover an exotic universality class out of topological line-nodal superconductors. The order parameter of broken symmetries is strongly correlated with underlying line-nodal fermions, and this gives rise to a large anomalous dimension in sharp contrast to that of the Landau-Ginzburg theory. Remarkably, hyperscaling violation and emergent relativistic scaling appear in spite of the presence of nonrelativistic fermionic excitation. We also propose characteristic experimental signatures around the phase transitions, for example, a linear phase boundary in a temperature-tuning parameter phase diagram, and discuss the implication of recent experiments in pnictides and heavy-fermion systems.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. A Comparison of Stiff ODE Solvers for Astrochemical Kinetics Problems

    NASA Astrophysics Data System (ADS)

    Nejad, Lida A. M.

    2005-09-01

    The time dependent chemical rate equations arising from astrochemical kinetics problems are described by a system of stiff ordinary differential equations (ODEs). In this paper, using three astrochemical models of varying physical and computational complexity, and hence different degrees of stiffness, we present a comprehensive performance survey of a set of well-established ODE solver packages from the ODEPACK collection, namely LSODE, LSODES, VODE and VODPK. For completeness, we include results from the GEAR package in one of the test models. The results demonstrate that significant performance improvements can be obtained over GEAR which is still being used by many astrochemists by default. We show that a simple appropriate ordering of the species set results in a substantial improvement in the performance of the tested ODE solvers. The sparsity of the associated Jacobian matrix can be exploited and results using the sparse direct solver routine LSODES show an extensive reduction in CPU time without any loss in accuracy. We compare the performance and the computed abundances of one model with a 175 species set and a reduced set of 88 species, keeping all physical and chemical parameters identical with both sets.We found that the calculated abundances using two different size models agree quite well. However, with no extra computational effort and more reliable results, it is possible for the computation to be many times faster with the larger species set than the reduced set, depending on the use of solvers, the ordering and the chosen options. It is also shown that though a particular solver with certain chosen parameters may have severe difficulty or even fail to complete a run over the required integration time, another solver can easily complete the run with a wider range of control parameters and options. As a result of the superior performance of LSODES for the solution of astrochemical kinetics systems, we have tailor-made a sparse version of the VODE

  3. A two-dimensional, semi-analytic expansion method for nodal calculations

    SciTech Connect

    Palmtag, Scott P.

    1995-08-01

    Most modern nodal methods used today are based upon the transverse integration procedure in which the multi-dimensional flux shape is integrated over the transverse directions in order to produce a set of coupled one-dimensional flux shapes. The one-dimensional flux shapes are then solved either analytically or by representing the flux shape by a finite polynomial expansion. While these methods have been verified for most light-water reactor applications, they have been found to have difficulty predicting the large thermal flux gradients near the interfaces of highly-enriched MOX fuel assemblies. A new method is presented here in which the neutron flux is represented by a non-seperable, two-dimensional, semi-analytic flux expansion. The main features of this method are (1) the leakage terms from the node are modeled explicitly and therefore, the transverse integration procedure is not used, (2) the corner point flux values for each node are directly edited from the solution method, and a corner-point interpolation is not needed in the flux reconstruction, (3) the thermal flux expansion contains hyperbolic terms representing analytic solutions to the thermal flux diffusion equation, and (4) the thermal flux expansion contains a thermal to fast flux ratio term which reduces the number of polynomial expansion functions needed to represent the thermal flux. This new nodal method has been incorporated into the computer code COLOR2G and has been used to solve a two-dimensional, two-group colorset problem containing uranium and highly-enriched MOX fuel assemblies. The results from this calculation are compared to the results found using a code based on the traditional transverse integration procedure.

  4. Cripto recruits Furin and PACE4 and controls Nodal trafficking during proteolytic maturation.

    PubMed

    Blanchet, Marie-Hélène; Le Good, J Ann; Mesnard, Daniel; Oorschot, Viola; Baflast, Stéphane; Minchiotti, Gabriella; Klumperman, Judith; Constam, Daniel B

    2008-10-08

    The glycosylphosphatidylinositol (GPI)-anchored proteoglycan Cripto binds Nodal and its type I receptor Alk4 to activate Smad2,3 transcription factors, but a role during Nodal precursor processing has not been described. We show that Cripto also binds the proprotein convertases Furin and PACE4 and localizes Nodal processing at the cell surface. When coexpressed as in early embryonic cells, Cripto and uncleaved Nodal already associated during secretion, and a Cripto-interacting region in the Nodal propeptide potentiated the effect of proteolytic maturation on Nodal signalling. Disruption of the trans-Golgi network (TGN) by brefeldin A blocked secretion, but export of Cripto and Nodal to the cell surface was not inhibited, indicating that Nodal is exposed to extracellular convertases before entering the TGN/endosomal system. Density fractionation and antibody uptake experiments showed that Cripto guides the Nodal precursor in detergent-resistant membranes to endocytic microdomains marked by GFP-Flotillin. We conclude that Nodal processing and endocytosis are coupled in signal-receiving cells.

  5. Euler/Navier-Stokes Solvers Applied to Ducted Fan Configurations

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

    Due to noise considerations, ultra high bypass ducted fans have become a more viable design. These ducted fans typically consist of a rotor stage containing a wide chord fan and a stator stage. One of the concerns for this design is the classical flutter that keeps occurring in various unducted fan blade designs. These flutter are catastrophic and are to be avoided in the flight envelope of the engine. Some numerical investigations by Williams, Cho and Dalton, have suggested that a duct around a propeller makes it more unstable. This needs to be further investigated. 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 be available. Aerodynamic solvers based on unsteady three-dimensional analysis will provide accurate and fast solutions and are best suited for aeroelastic analysis. The Euler solvers capture significant physics of the flowfield and are reasonably fast. An aerodynamic solver Ref. based on Euler equations had been developed under a separate grant from NASA Lewis in the past. Under the current grant, this solver has been modified to calculate the aeroelastic characteristics of unducted and ducted rotors. Even though, the aeroelastic solver based on three-dimensional Euler equations is computationally efficient, it is still very expensive to investigate the effects of multiple stages on the aeroelastic characteristics. In order to investigate the effects of multiple stages, a two-dimensional multi stage aeroelastic solver was also developed under this task, in collaboration with Dr. T. S. R. Reddy of the University of Toledo. Both of these solvers were applied to several test cases and validated against experimental data, where available.

  6. Tumor Budding in Intestinal Type Gastric Adenocarcinoma is Associated with Nodal Metastasis and Recurrence.

    PubMed

    Olsen, Stephen; Linda, Jin; Fields, Ryan C; Yan, Yan; Nalbantoglu, ILKe

    2017-04-17

    Gastric adenocarcinoma (GAC) is a common cause of cancer-related death worldwide. GAC can be classified as intestinal or diffuse. Intestinal type cancers are common and reported to have a better prognosis compared to diffuse cancers. Studies have shown the presence and amount of tumor budding in intestinal carcinomas of the colon and esophagus to predict nodal metastasis and recurrence. Our aim is to determine if tumor budding in intestinal type GAC correlates with prognostic features. One hundred four patients treated with primary surgical excision between 1999-2013 were identified. Histologic type (intestinal, diffuse, or mixed), tumor grade, T-stage, and lymph node status were evaluated. Tumor bud scores were assigned to all intestinal type cancers using methods previously described for colorectal adenocarcinoma. Scores of <1 were designated as low and ≥1 as high. Tumor characteristics were as follows: 52 intestinal (50%), 36 diffuse (35%) and 16 mixed (15%). Of the 52 cases with intestinal histology, 4 were well (8%), 28 were moderately (54%), and 20 were poorly differentiated (38%). Thirty-three (63%) of the intestinal tumors had high tumor bud scores. Cases with high scores were associated with higher T-stage, N-stage, and grade (P<.001, P<.001, and P=.002). These also had a higher likelihood of recurrence (P=.007). In our cohort, high tumor bud scores in intestinal type GAC have higher T-stage, N-stage, grade, and likelihood of recurrence. Assessment of tumor budding may guide clinical management in a subset of patients. Copyright © 2017. Published by Elsevier Inc.

  7. CD20-Positive nodal natural killer/T-cell lymphoma with cutaneous involvement.

    PubMed

    Tsai, Yi-Chiun; Chen, Chi-Kuan; Wu, Yu-Hung

    2015-09-01

    CD20-positive natural killer (NK)/T-cell lymphoma is extremely rare. We describe a case of a CD20-positive nodal NK/T-cell lymphoma with cutaneous involvement in a 32-year-old man. The patient presented with fever, night sweats, right inguinal lymphadenopathy and multiple violaceous to erythematous nodules and plaques on the back and bilateral legs. Immunohistochemical analysis showed diffusely and strongly positive staining for CD3, CD3 epsilon, CD43, CD56, TIA-1 and CD20 but negative staining for other B-cell markers, including CD79a and PAX-5 and T-cell markers CD5 and CD7. The tumor cell nuclei were diffusely positive for Epstein-Barr virus-encoded RNA in situ hybridization. A partial clinical response was observed after chemotherapy, indicated by the decreased size of the lymph nodes and skin lesions. It is a diagnostic challenge to deal with lymphoma cells that present with the surface proteins of both T- and B-cells.

  8. Endogenous Nodal promotes melanoma undergoing epithelial-mesenchymal transition via Snail and Slug in vitro and in vivo

    PubMed Central

    Guo, Qiang; Ning, Fen; Fang, Rui; Wang, Hong-Sheng; Zhang, Ge; Quan, Mei-Yu; Cai, Shao-Hui; Du, Jun

    2015-01-01

    Nodal, an important embryonic morphogen, has been reported to modulate tumorigenesis. Epithelial-mesenchymal transition (EMT) plays an important role in cancer metastasis. We have previously reported that recombinant Nodal treatment can promote melanoma undergoing EMT, but the effects of endogenous Nodal on EMT are still unknown. Here we generated both Nodal-overexpression and -knockdown stable cell lines to investigate the in vitro and in vivo characteristics of Nodal-induced EMT in murine melanoma cells. Nodal-overexpression cells displayed increased migration ability, accompanied by typical phenotype changes of EMT. In contrast, Nodal-knockdown stable cells repressed the EMT phenotype as well as reduced cell motility. Results of animal experiments confirmed that overexpression of Nodal can promote the metastasis of melanoma tumor in vivo. Mechanistically, we found that Nodal-induced expression of Snail and Slug involves its activation of ALK/Smads and PI3k/AKT pathways, which is an important process in the Nodal-induced EMT. However, we also found that the EMT phenotype was not completely inhibited by blocking the paracrine activity of Nodal in Nodal overexpression cell line suggesting the presence of additional mechanism(s) in the Nodal-induced EMT. This study provides a better understanding of Nodal function in melanoma, and suggests targeting Nodal as a potential strategy for melanoma therapey. PMID:26269769

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

    PubMed

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

    2013-07-01

    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. Sorghum and millet were grown in a split-pot system that allowed the primary and nodal roots to be watered separately. 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) partitioning to nodal root length from primary roots

  10. Performance Models for the Spike Banded Linear System Solver

    DOE PAGES

    Manguoglu, Murat; Saied, Faisal; Sameh, Ahmed; ...

    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

  11. A robust HLLC-type Riemann solver for strong shock

    NASA Astrophysics Data System (ADS)

    Shen, Zhijun; Yan, Wei; Yuan, Guangwei

    2016-03-01

    It is well known that for the Eulerian equations the numerical schemes that can accurately capture contact discontinuity usually suffer from some disastrous carbuncle phenomenon, while some more dissipative schemes, such as the HLL scheme, are free from this kind of shock instability. Hybrid schemes to combine a dissipative flux with a less dissipative flux can cure the shock instability, but also may lead to other problems, such as certain arbitrariness of choosing switching parameters or contact interface becoming smeared. In order to overcome these drawbacks, this paper proposes a simple and robust HLLC-type Riemann solver for inviscid, compressible gas flows, which is capable of preserving sharp contact surface and is free from instability. The main work is to construct a HLL-type Riemann solver and a HLLC-type Riemann solver by modifying the shear viscosity of the original HLL and HLLC methods. Both of the two new schemes are positively conservative under some typical wavespeed estimations. Moreover, a linear matrix stability analysis for the proposed schemes is accomplished, which illustrates the HLLC-type solver with shear viscosity is stable whereas the HLL-type solver with vorticity wave is unstable. Our arguments and numerical experiments demonstrate that the inadequate dissipation associated to the shear wave may be a unique reason to cause the instability.

  12. 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.

  13. 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.

  14. Topological nodal-line semimetal in nonsymmorphic Cmce -phase Ag2S

    NASA Astrophysics Data System (ADS)

    Huang, Huaqing; Jin, Kyung-Hwan; Liu, Feng

    2017-09-01

    Based on first-principles calculations and symmetry analysis, we discovery that the Ag2S with C m c e symmetry is a topological nodal-line semimetal in the absence of spin-orbit coupling. A single nodal loop as protected by the glide symmetry exists around the center of the Brillouin zone, dispersing slightly in the momentum space to form both electron and hole pockets around the loop. Moreover, a nearly flat drumheadlike surface state appears on the (001) surface of this material. The nodal-line semimetal phase and its drumheadlike surface states are expected to be experimentally detectable in C m c e -phase Ag2S because spin-orbit coupling will only open a negligible gap comparing to the energy dispersion of the nodal loop. Our finding provides a different member to the growing family of nodal-line semimetals with a single nodal loop structure.

  15. Topological Dirac nodal lines and surface charges in fcc alkaline earth metals

    NASA Astrophysics Data System (ADS)

    Hirayama, Motoaki; Okugawa, Ryo; Miyake, Takashi; Murakami, Shuichi

    2017-01-01

    In nodal-line semimetals, the gaps close along loops in k space, which are not at high-symmetry points. Typical mechanisms for the emergence of nodal lines involve mirror symmetry and the π Berry phase. Here we show via ab initio calculations that fcc calcium (Ca), strontium (Sr) and ytterbium (Yb) have topological nodal lines with the π Berry phase near the Fermi level, when spin-orbit interaction is neglected. In particular, Ca becomes a nodal-line semimetal at high pressure. Owing to nodal lines, the Zak phase becomes either π or 0, depending on the wavevector k, and the π Zak phase leads to surface polarization charge. Carriers eventually screen it, leaving behind large surface dipoles. In materials with nodal lines, both the large surface polarization charge and the emergent drumhead surface states enhance Rashba splitting when heavy adatoms are present, as we have shown to occur in Bi/Sr(111) and in Bi/Ag(111).

  16. Topological nodal line semimetals with and without spin-orbital coupling

    NASA Astrophysics Data System (ADS)

    Fang, Chen; Chen, Yige; Kee, Hae-Young; Fu, Liang

    2015-08-01

    We theoretically study three-dimensional topological semimetals (TSMs) with nodal lines protected by crystalline symmetries. Compared to TSMs with point nodes, e.g., Weyl semimetals and Dirac semimetals, where the conduction and the valence bands touch at discrete points, in these TSMs the two bands cross at closed lines in the Brillouin zone. We propose two different classes of symmetry protected nodal lines in the absence and in the presence of spin-orbital coupling (SOC), respectively. In the former, we discuss nodal lines that are protected by a combination of inversion symmetry and time-reversal symmetry, yet, unlike previously studied nodal lines in the same symmetry class, each nodal line has a Z2 monopole charge and can only be created (annihilated) in pairs. In the second class, with SOC, we show that a nonsymmorphic symmetry (screw axis) protects a four-band crossing nodal line in systems having both inversion and time-reversal symmetries.

  17. 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Topological Dirac nodal lines and surface charges in fcc alkaline earth metals.

    PubMed

    Hirayama, Motoaki; Okugawa, Ryo; Miyake, Takashi; Murakami, Shuichi

    2017-01-11

    In nodal-line semimetals, the gaps close along loops in k space, which are not at high-symmetry points. Typical mechanisms for the emergence of nodal lines involve mirror symmetry and the π Berry phase. Here we show via ab initio calculations that fcc calcium (Ca), strontium (Sr) and ytterbium (Yb) have topological nodal lines with the π Berry phase near the Fermi level, when spin-orbit interaction is neglected. In particular, Ca becomes a nodal-line semimetal at high pressure. Owing to nodal lines, the Zak phase becomes either π or 0, depending on the wavevector k, and the π Zak phase leads to surface polarization charge. Carriers eventually screen it, leaving behind large surface dipoles. In materials with nodal lines, both the large surface polarization charge and the emergent drumhead surface states enhance Rashba splitting when heavy adatoms are present, as we have shown to occur in Bi/Sr(111) and in Bi/Ag(111).

  19. A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality

    NASA Astrophysics Data System (ADS)

    Noël, Emily S.; Verhoeven, Manon; Lagendijk, Anne Karine; Tessadori, Federico; Smith, Kelly; Choorapoikayil, Suma; den Hertog, Jeroen; Bakkers, Jeroen

    2013-11-01

    Breaking left-right symmetry in bilateria is a major event during embryo development that is required for asymmetric organ position, directional organ looping and lateralized organ function in the adult. Asymmetric expression of Nodal-related genes is hypothesized to be the driving force behind regulation of organ laterality. Here we identify a Nodal-independent mechanism that drives asymmetric heart looping in zebrafish embryos. In a unique mutant defective for the Nodal-related southpaw gene, preferential dextral looping in the heart is maintained, whereas gut and brain asymmetries are randomized. As genetic and pharmacological inhibition of Nodal signalling does not abolish heart asymmetry, a yet undiscovered mechanism controls heart chirality. This mechanism is tissue intrinsic, as explanted hearts maintain ex vivo retain chiral looping behaviour and require actin polymerization and myosin II activity. We find that Nodal signalling regulates actin gene expression, supporting a model in which Nodal signalling amplifies this tissue-intrinsic mechanism of heart looping.

  20. An efficient transport solver for tokamak plasmas

    DOE PAGES

    Park, Jin Myung; Murakami, Masanori; St. John, H. E.; ...

    2017-01-03

    A simple approach to efficiently solve a coupled set of 1-D diffusion-type transport equations with a stiff transport model for tokamak plasmas is presented based on the 4th order accurate Interpolated Differential Operator scheme along with a nonlinear iteration method derived from a root-finding algorithm. Here, numerical tests using the Trapped Gyro-Landau-Fluid model show that the presented high order method provides an accurate transport solution using a small number of grid points with robust nonlinear convergence.

  1. 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.

  2. 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.

  3. An adaptive fast multipole accelerated Poisson solver for complex geometries

    NASA Astrophysics Data System (ADS)

    Askham, T.; Cerfon, A. J.

    2017-09-01

    We present a fast, direct and adaptive Poisson solver for complex two-dimensional geometries based on potential theory and fast multipole acceleration. More precisely, the solver relies on the standard decomposition of the solution as the sum of a volume integral to account for the source distribution and a layer potential to enforce the desired boundary condition. The volume integral is computed by applying the FMM on a square box that encloses the domain of interest. For the sake of efficiency and convergence acceleration, we first extend the source distribution (the right-hand side in the Poisson equation) to the enclosing box as a C0 function using a fast, boundary integral-based method. We demonstrate on multiply connected domains with irregular boundaries that this continuous extension leads to high accuracy without excessive adaptive refinement near the boundary and, as a result, to an extremely efficient ;black box; fast solver.

  4. Overset Techniques for Hypersonic Multibody Configurations with the DPLR Solver

    NASA Technical Reports Server (NTRS)

    Hyatt, Andrew James; Prabhu, Dinesh K.; Boger, David A.

    2010-01-01

    Three unit problems in shock-shock/shock-boundary layer interactions are considered in the evaluation overset techniques with the Data Parallel Line Relaxation (DPLR) computational fluid dynamics solver, a three dimensional Navier-Stokes solver . The unit problems considered are those of two stacked hemispherical cylinders (of different diameters and lengths, and at various orientations relative to each other or relative to the nozzle axis) tested in a hypersonic wind tunnel. These problems are taken as representative of a Two-Stage-To-Orbit design. The objective of the present presentation would be to discuss the techniques used to develop suitable overset grid systems and then evaluate their respective solutions by comparing to corresponding point matched grid solutions and experimental data. Both successful and unsuccessful techniques would be discussed. All solutions would be calculated using the DPLR solver and SUGGAR will be used to develop the domain connectivity information.

  5. General Equation Set Solver for Compressible and Incompressible Turbomachinery Flows

    NASA Technical Reports Server (NTRS)

    Sondak, Douglas L.; Dorney, Daniel J.

    2002-01-01

    Turbomachines for propulsion applications operate with many different working fluids and flow conditions. The flow may be incompressible, such as in the liquid hydrogen pump in a rocket engine, or supersonic, such as in the turbine which may drive the hydrogen pump. Separate codes have traditionally been used for incompressible and compressible flow solvers. The General Equation Set (GES) method can be used to solve both incompressible and compressible flows, and it is not restricted to perfect gases, as are many compressible-flow turbomachinery solvers. An unsteady GES turbomachinery flow solver has been developed and applied to both air and water flows through turbines. It has been shown to be an excellent alternative to maintaining two separate codes.

  6. Advanced Fast 3D Electromagnetic Solver for Microwave Tomography Imaging.

    PubMed

    Simonov, Nikolai; Kim, Bo-Ra; Lee, Kwang-Jae; Jeon, Soon-Ik; Son, Seong-Ho

    2017-06-07

    This paper describes a fast forward electromagnetic solver (FFS) for the image reconstruction algorithm of our microwave tomography (MT) system. Our apparatus is a preclinical prototype of a biomedical imaging system, designed for the purpose of early breast cancer detection. It operates in the 3-6 GHz frequency band using a circular array of probe antennas immersed in a matching liquid; it produces image reconstructions of the permittivity and conductivity profiles of the breast under examination. Our reconstruction algorithm solves the electromagnetic inverse problem and takes into account the real electromagnetic properties of the probe antenna array as well as the influence of the patient's body and that of the upper metal screen sheet. This FFS algorithm is much faster than conventional electromagnetic simulation solvers. In comparison, in the same PC, the CST solver takes ~45 min, while the FFS takes ~1 s of effective simulation time for the same electromagnetic model of a numerical breast phantom.

  7. Numerical comparison of Riemann solvers for astrophysical hydrodynamics

    NASA Astrophysics Data System (ADS)

    Klingenberg, Christian; Schmidt, Wolfram; Waagan, Knut

    2007-11-01

    The idea of this work is to compare a new positive and entropy stable approximate Riemann solver by Francois Bouchut with a state-of the-art algorithm for astrophysical fluid dynamics. We implemented the new Riemann solver into an astrophysical PPM-code, the Prometheus code, and also made a version with a different, more theoretically grounded higher order algorithm than PPM. We present shock tube tests, two-dimensional instability tests and forced turbulence simulations in three dimensions. We find subtle differences between the codes in the shock tube tests, and in the statistics of the turbulence simulations. The new Riemann solver increases the computational speed without significant loss of accuracy.

  8. 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.

  9. Transversality in scalar reaction-diffusion equations on a circle

    NASA Astrophysics Data System (ADS)

    Czaja, Radoslaw; Rocha, Carlos

    We prove that stable and unstable manifolds of hyperbolic periodic orbits for general scalar reaction-diffusion equations on a circle always intersect transversally. The argument also shows that for a periodic orbit there are no homoclinic connections. The main tool used in the proofs is Matano's zero number theory dealing with the Sturm nodal properties of the solutions.

  10. 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.

  11. 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.

  12. Magnon nodal-line semimetals and drumhead surface states in anisotropic pyrochlore ferromagnets

    NASA Astrophysics Data System (ADS)

    Mook, Alexander; Henk, Jürgen; Mertig, Ingrid

    2017-01-01

    We introduce a type of topological magnon matter: the magnonic pendant to electronic nodal-line semimetals. Magnon spectra of anisotropic pyrochlore ferromagnets feature twofold degeneracies of magnon bands along a closed loop in reciprocal space. These magnon nodal lines are topologically protected by the coexistence of inversion and time-reversal symmetry; they require the absence of spin-orbit interaction (no Dzyaloshinskii-Moriya interaction). We calculate the topological invariants of the nodal lines and show that details of the associated magnon drumhead surface states depend strongly on the termination of the surface. Magnon nodal-line semimetals complete the family of topological magnons in three-dimensional ferromagnetic materials.

  13. Radiotherapy studies and extra-nodal non-Hodgkin lymphomas, progress and challenges.

    PubMed

    Specht, L

    2012-06-01

    Extra-nodal lymphomas may arise in any organ, and different histological subtypes occur in distinct patterns. Prognosis and treatment depend not only on the histological subtype and disease extent, but also on the particular involved extra-nodal organ. The clinical course and response to treatment for the more common extra-nodal organs, e.g. stomach, Waldeyer's ring, skin and brain, are fairly well known and show significant variation. A few randomised trials have been carried out testing the role of radiotherapy in these lymphomas. However, for most extra-nodal lymphomas, randomised trials have not been carried out, and treatment decisions are made on small patient series and extrapolations from nodal lymphomas. Hopefully, wide international collaboration will make controlled clinical trials possible in the less common extra-nodal lymphomas. Modern highly conformal radiotherapy allows better coverage of extra-nodal lymphomatous involvement with better sparing of normal tissues. The necessary radiation doses and volumes need to be defined for the different extra-nodal lymphoma entities. The challenge is to optimise the use of radiotherapy in the modern multimodality treatment of extra-nodal lymphomas.

  14. 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.

  15. Nonlinear Least Squares Curve Fitting with Microsoft Excel Solver

    NASA Astrophysics Data System (ADS)

    Harris, Daniel C.

    1998-01-01

    "Solver" is a powerful tool in the Microsoft Excel spreadsheet that provides a simple means of fitting experimental data to nonlinear functions. The procedure is so easy to use and its mode of operation is so obvious that it is excellent for students to learn the underlying principle of lease squares curve fitting. This article introduces the method of fitting nonlinear functions with Solver and extends the treatment to weighted least squares and to the estimation of uncertainties in the least-squares parameters.

  16. An Easy Method To Accelerate An Iterative Algebraic Equation Solver

    SciTech Connect

    Yao, Jin

    2014-01-06

    This article proposes to add a simple term to an iterative algebraic equation solver with an order n convergence rate, and to raise the order of convergence to (2n - 1). In particular, a simple algebraic equation solver with the 5th order convergence but uses only 4 function values in each iteration, is described in details. When this scheme is applied to a Newton-Raphson method of the quadratic convergence for a system of algebraic equations, a cubic convergence can be achieved with an low overhead cost of function evaluation that can be ignored as the size of the system increases.

  17. Von Neumann stability analysis of globally divergence-free RKDG schemes for the induction equation using multidimensional Riemann solvers

    NASA Astrophysics Data System (ADS)

    Balsara, Dinshaw S.; Käppeli, Roger

    2017-05-01

    In this paper we focus on the numerical solution of the induction equation using Runge-Kutta Discontinuous Galerkin (RKDG)-like schemes that are globally divergence-free. The induction equation plays a role in numerical MHD and other systems like it. It ensures that the magnetic field evolves in a divergence-free fashion; and that same property is shared by the numerical schemes presented here. The algorithms presented here are based on a novel DG-like method as it applies to the magnetic field components in the faces of a mesh. (I.e., this is not a conventional DG algorithm for conservation laws.) The other two novel building blocks of the method include divergence-free reconstruction of the magnetic field and multidimensional Riemann solvers; both of which have been developed in recent years by the first author. Since the method is linear, a von Neumann stability analysis is carried out in two-dimensions to understand its stability properties. The von Neumann stability analysis that we develop in this paper relies on transcribing from a modal to a nodal DG formulation in order to develop discrete evolutionary equations for the nodal values. These are then coupled to a suitable Runge-Kutta timestepping strategy so that one can analyze the stability of the entire scheme which is suitably high order in space and time. We show that our scheme permits CFL numbers that are comparable to those of traditional RKDG schemes. We also analyze the wave propagation characteristics of the method and show that with increasing order of accuracy the wave propagation becomes more isotropic and free of dissipation for a larger range of long wavelength modes. This makes a strong case for investing in higher order methods. We also use the von Neumann stability analysis to show that the divergence-free reconstruction and multidimensional Riemann solvers are essential algorithmic ingredients of a globally divergence-free RKDG-like scheme. Numerical accuracy analyses of the RKDG

  18. Pseudospin Vortex Ring with a Nodal Line in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Lim, Lih-King; Moessner, Roderich

    2017-01-01

    We present a model of a topological semimetal in three dimensions whose energy spectrum exhibits a nodal line acting as a vortex ring; this in turn is linked by a pseudospin structure akin to that of a smoke ring. Contrary to a Weyl point node spectrum, the vortex ring gives rise to Skyrmionic pseudospin patterns in cuts on both sides of the nodal ring plane; this pattern covers the full Brillouin zone, thus leading to a fully extended chiral Fermi arc and a new, "maximal," anomalous Hall effect in a 3D semimetal. Tuning a model parameter shrinks the vortex ring until it vanishes, giving way to a pair of Weyl nodes of opposite chirality. This establishes a connection between two distinct momentum-space topologies—that of a vortex ring (a circle of singularity) and a monopole-antimonopole pair (two point singularities). We present the model both as a low-energy continuum and a two-band tight-binding lattice model. Its simplicity permits an analytical computation of its Landau level spectrum.

  19. 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.

  20. Amyloid precursor protein at node of Ranvier modulates nodal formation

    PubMed Central

    Xu, De-En; Zhang, Wen-Min; Yang, Zara Zhuyun; Zhu, Hong-Mei; Yan, Ke; Li, Shao; Bagnard, Dominique; Dawe, Gavin S; Ma, Quan-Hong; Xiao, Zhi-Cheng

    2014-01-01

    Amyloid precursor protein (APP), commonly associated with Alzheimer disease, is upregulated and distributes evenly along the injured axons, and therefore, also known as a marker of demyelinating axonal injury and axonal degeneration. However, the physiological distribution and function of APP along myelinated axons was unknown. We report that APP aggregates at nodes of Ranvier (NOR) in the myelinated central nervous system (CNS) axons but not in the peripheral nervous system (PNS). At CNS NORs, APP expression co-localizes with tenascin-R and is flanked by juxtaparanodal potassium channel expression demonstrating that APP localized to NOR. In APP-knockout (KO) mice, nodal length is significantly increased, while sodium channels are still clustered at NORs. Moreover, APP KO and APP-overexpressing transgenic (APP TG) mice exhibited a decreased and an increased thickness of myelin in spinal cords, respectively, although the changes are limited in comparison to their littermate WT mice. The thickness of myelin in APP KO sciatic nerve also increased in comparison to that in WT mice. Our observations indicate that APP acts as a novel component at CNS NORs, modulating nodal formation and has minor effects in promoting myelination. PMID:25482638

  1. Dirac Magnon Nodal Loops in Quasi-2D Quantum Magnets.

    PubMed

    Owerre, S A

    2017-07-31

    In this report, we propose a new concept of one-dimensional (1D) closed lines of Dirac magnon nodes in two-dimensional (2D) momentum space of quasi-2D quantum magnetic systems. They are termed "2D Dirac magnon nodal-line loops". We utilize the bilayer honeycomb ferromagnets with intralayer coupling J and interlayer coupling J L , which is realizable in the honeycomb chromium compounds CrX3 (X ≡ Br, Cl, and I). However, our results can also exist in other layered quasi-2D quantum magnetic systems. Here, we show that the magnon bands of the bilayer honeycomb ferromagnets overlap for J L  ≠ 0 and form 1D closed lines of Dirac magnon nodes in 2D momentum space. The 2D Dirac magnon nodal-line loops are topologically protected by inversion and time-reversal symmetry. Furthermore, we show that they are robust against weak Dzyaloshinskii-Moriya interaction Δ DM  < J L and possess chiral magnon edge modes.

  2. Tumor satellite in predicting occult nodal metastasis of tongue cancer.

    PubMed

    Yang, Tsung-Lin; Lou, Pei-Jen; Chang, Yih-Leong; Wu, Chen-Tu; Wang, Cheng-Ping; Ko, Jenq-Yuh

    2011-10-01

    Tongue cancer is well known to have a high potential for locoregional metastasis. However, controversy about electively treating the neck in early-stage tongue cancer remains. Although many risk factors related to cervical occult nodal metastasis (ONM) have been investigated, the ability of the tumor to spread, a phenomenon that results from the intrinsic property of the tumor and its interaction with the surrounding environment, has seldom been addressed. Retrospective case series with chart review. Tertiary referral hospital of university. Patients with early-stage squamous cell carcinoma of the oral tongue. In 71 eligible enrolled patients, ONM was detected in 19 (27%) patients, while the results were negative (ONM(-)) in 52 (73%) patients. The average tumor satellite distance (TSD) in the ONM(+) group was 4.1 ± 4.3 mm, in contrast to that in the ONM(-) group (1.0 ± 1.5 mm; P < .001). When stratified by increased TSD values, the significance of the difference between the 2 groups increased. For clinical applications, the optimal TSD threshold for determining the ONM probability was 3.5 mm. Multivariate analyses demonstrated that TSD was an independent prognosticator. The results indicate that TSD is a feasible pathological parameter that is useful for determining the status of cervical nodal metastasis. It can be used as an indicator of potential cervical subclinical disease and as a guideline for deciding the necessity and modality of neck treatment.

  3. Intra- and Inter-Fraction Mediastinal Nodal Region Motion: Implications for Internal Target Volume Expansions

    PubMed Central

    Thomas, Jonathan G.; Kashani, Rojano; Balter, James M.; Tatro, Daniel; Kong, Feng-Ming; Pan, Charlie C.

    2009-01-01

    Purpose/Objective The purpose of this study is to determine the intra- and inter-fraction motion of mediastinal lymph node regions. Materials/Methods Ten patients with non-small cell lung cancer underwent controlled inhale and exhale CT scans during two sessions (40 total data sets) and mediastinal nodal stations 1–8 [Chapet, et al, IJROBP 2005;63:170–8] were outlined. Corresponding CT scans from different sessions were registered to remove setup error and in this reference frame, the center-of-mass (COM) of each nodal station was compared for right-left (RL), anterior-posterior (AP), and superior-inferior (SI) displacement. In addition, an anisotropic volume expansion encompassing the change of the nodal region margins in all directions was used. Intra-fraction displacement was determined by comparing same session inhale-exhale scans. Inter-fraction reproducibility of nodal regions was determined by comparing the same respiratory phase scans between two sessions. Results Intra-fraction displacement of COM varied between nodal stations. All nodal regions moved posteriorly and superiorly with exhalation, and inferior nodal stations showed the most motion. Based on anisotropic expansion, nodal regions expanded mostly in the RL direction from inhale to exhale. The inter-patient variations in intra-fraction displacement were large compared to the displacements themselves. Moreover, there was substantial inter-fractional displacement (∼5 mm). Conclusions Mediastinal lymph node regions clearly move during breathing. Additionally, deformation of nodal regions between inhale and exhale occurs. The degree of motion and deformation varies by station and by individual. This study indicates the potential advantage of characterizing individualized nodal region motion to safely maximize conformality of mediastinal nodal targets. PMID:19410142

  4. The impact of audit and feedback on nodal harvest in colorectal cancer

    PubMed Central

    2011-01-01

    Background Adequate nodal harvest (≥ 12 lymph nodes) in colorectal cancer has been shown to optimize staging and proposed as a quality indicator of colorectal cancer care. An audit within a single health district in Nova Scotia, Canada presented and published in 2002, revealed that adequate nodal harvest occurred in only 22% of patients. The goal of this current study was to identify factors associated with adequate nodal harvest, and specifically to examine the impact of the audit and feedback strategy on nodal harvest. Methods This population-based study included all patients undergoing resection for primary colorectal cancer in Nova Scotia, Canada, from 01 January 2001 to 31 December 2005. Linkage of the provincial cancer registry with other databases (hospital discharge, physician claims data, and national census data) provided clinicodemographic, diagnostic, and treatment-event data. Factors associated with adequate nodal harvest were examined using multivariate logistic regression. The specific interaction between year and health district was examined to identify any potential effect of dissemination of the previously-performed audit. Results Among the 2,322 patients, the median nodal harvest was 8; overall, 719 (31%) had an adequate nodal harvest. On multivariate analysis, audited health district (p < 0.0001), year (p < 0.0001), younger age (p < 0.0001), non-emergent surgery (p < 0.0001), more advanced stage (p = 0.008), and previous cancer history (p = 0.03) were associated with an increased likelihood of an adequate nodal harvest. Interaction between year and audited health district was identified (p = 0.006) such that the increase in adequate nodal harvest over time was significantly greater in the audited health district. Conclusions Improvements in colorectal cancer nodal harvest did occur over time. A published audit demonstrating suboptimal nodal harvest appeared to be an effective knowledge translation tool, though more so for the audited health

  5. Fast Multilevel Solvers for a Class of Discrete Fourth Order Parabolic Problems

    SciTech Connect

    Zheng, Bin; Chen, Luoping; Hu, Xiaozhe; Chen, Long; Nochetto, Ricardo H.; Xu, Jinchao

    2016-03-05

    In this paper, we study fast iterative solvers for the solution of fourth order parabolic equations discretized by mixed finite element methods. We propose to use consistent mass matrix in the discretization and use lumped mass matrix to construct efficient preconditioners. We provide eigenvalue analysis for the preconditioned system and estimate the convergence rate of the preconditioned GMRes method. Furthermore, we show that these preconditioners only need to be solved inexactly by optimal multigrid algorithms. Our numerical examples indicate that the proposed preconditioners are very efficient and robust with respect to both discretization parameters and diffusion coefficients. We also investigate the performance of multigrid algorithms with either collective smoothers or distributive smoothers when solving the preconditioner systems.

  6. 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.

  7. Expression of the polycomb‐group gene BMI1 is related to an unfavourable prognosis in primary nodal DLBCL

    PubMed Central

    van Galen, Joost C; Muris, Jettie J F; Oudejans, Joost J; Vos, Wim; Giroth, Cindy P E; Ossenkoppele, Gert J; Otte, Arie P; Raaphorst, Frank M; Meijer, Chris J L M

    2007-01-01

    Background Clinical outcome in patients with diffuse large B cell lymphomas (DLBCL) is highly variable and poorly predictable. Microarray studies showed that patients with DLBCL with a germinal centre B cell‐like (GCB) phenotype have a better prognosis than those with an activated B cell‐like (ABC) phenotype. The BMI1 proto‐oncogene was identified as one of the genes present in the signature of the ABC type of DLBCL, associated with a poor prognosis. Objectives (1) To investigate, in primary nodal DLBCL, the expression of BMI1 and its association with clinical outcome and DLBCL signature; (2) to look for an association between BMI1 expression and the expression of its putative downstream targets p14ARF and p16INK4a. Results BMI1 expression was found to be associated with poor clinical outcome, but not clearly with an ABC‐like phenotype of DLBCL. Expression of BMI1 was frequently, but not always, related to low levels of expression of p14ARF and p16INK4a. Conclusion Expression of BMI1 is associated with an unfavourable clinical outcome of primary nodal DLBCL. PMID:16837630

  8. Mapping patterns of nodal metastases in esophageal carcinoma: rethinking the clinical target volume for supraclavicular nodal irradiation

    PubMed Central

    Luo, Yijun; Liu, Yuhui; Wang, Xiaoli; Zhang, Bin; Yu, Jinming; Wang, Chengang; Huang, Yong

    2016-01-01

    Background To map detail distribution of metastatic supraclavicular (SCV) lymph nodes (LN) in esophageal cancer (EC) patients and determine the precise radiation therapy clinical target volume (CTV). Methods A total of 101 thoracic esophageal carcinoma patients after surgery experienced SCV LN metastasis were retrospectively examined. The SCV region is further divided into four subgroups. Using hand drawings registration, nodes were mapped to a template computed tomogram to provide a visual impression of nodal frequencies and anatomic distribution. Results In all, 158 nodes were considered to be clinical metastatic in the SCV region in the 101 patients, 74 on the left and 84 on the right. Seven of 158 (4.4%) positive LN were located in group I, 78 of 158 (49.37%) were located in group II, 72 of 158 nodes (45.6%) were located in group III, 1 of 158 (0.63%) located in group IV. Conclusions According to our results, the SCV group II and group III are considered to be the high risk regions of esophageal squamous cell carcinoma (ESCC) LN metastasis, which were defined as elective nodal irradiation (ENI) areas. PMID:28066592

  9. 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.…

  10. 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).

  11. 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.…

  12. PSH3D fast Poisson solver for petascale DNS

    NASA Astrophysics Data System (ADS)

    Adams, Darren; Dodd, Michael; Ferrante, Antonino

    2016-11-01

    Direct numerical simulation (DNS) of high Reynolds number, Re >= O (105) , turbulent flows requires computational meshes >= O (1012) grid points, and, thus, the use of petascale supercomputers. DNS often requires the solution of a Helmholtz (or Poisson) equation for pressure, which constitutes the bottleneck of the solver. We have developed a parallel solver of the Helmholtz equation in 3D, PSH3D. The numerical method underlying PSH3D combines a parallel 2D Fast Fourier transform in two spatial directions, and a parallel linear solver in the third direction. For computational meshes up to 81923 grid points, our numerical results show that PSH3D scales up to at least 262k cores of Cray XT5 (Blue Waters). PSH3D has a peak performance 6 × faster than 3D FFT-based methods when used with the 'partial-global' optimization, and for a 81923 mesh solves the Poisson equation in 1 sec using 128k cores. Also, we have verified that the use of PSH3D with the 'partial-global' optimization in our DNS solver does not reduce the accuracy of the numerical solution of the incompressible Navier-Stokes equations.

  13. Development of multiphase CFD flow solver in OpenFOAM

    NASA Astrophysics Data System (ADS)

    Rollins, Chad; Luo, Hong; Dinh, Nam

    2016-11-01

    We are developing a pressure-based multiphase (Eulerian) CFD solver using OpenFOAM with Reynolds-averaged turbulence stress modeling. Our goal is the evaluation and improvement of the current OpenFOAM two-fluid (Eulerian) solver in boiling channels with a motivation to produce a more consistent modeling and numerics treatment. The difficulty lies in the prescense of the many forces and models that are tightly non-linearly coupled in the solver. Therefore, the solver platform will allow not only the modeling, but the tracking as well, of the effects of the individual components (various interfacial forces/heat transfer models) and their interactions. This is essential for the development of a robust and efficient solution method. There has be a lot of work already performed in related areas that generally indicates a lack of robustness of the solution methods. The objective here is therefore to identify and develop remedies for numerical/modeling issues through a systematic approach to verification and validation, taking advantage of the open source nature of OpenFOAM. The presentation will discuss major findings, and suggest strategies for robust and consistent modeling (probably, a more consistent treatment of heat transfer models with two-fluid models in the near-wall cells).

  14. Thinking Process of Naive Problem Solvers to Solve Mathematical Problems

    ERIC Educational Resources Information Center

    Mairing, Jackson Pasini

    2017-01-01

    Solving problems is not only a goal of mathematical learning. Students acquire ways of thinking, habits of persistence and curiosity, and confidence in unfamiliar situations by learning to solve problems. In fact, there were students who had difficulty in solving problems. The students were naive problem solvers. This research aimed to describe…

  15. Hypersonic simulations using open-source CFD and DSMC solvers

    NASA Astrophysics Data System (ADS)

    Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

    2016-11-01

    Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

  16. A new fast direct solver for the boundary element method

    NASA Astrophysics Data System (ADS)

    Huang, S.; Liu, Y. J.

    2017-04-01

    A new fast direct linear equation solver for the boundary element method (BEM) is presented in this paper. The idea of the new fast direct solver stems from the concept of the hierarchical off-diagonal low-rank matrix. The hierarchical off-diagonal low-rank matrix can be decomposed into the multiplication of several diagonal block matrices. The inverse of the hierarchical off-diagonal low-rank matrix can be calculated efficiently with the Sherman-Morrison-Woodbury formula. In this paper, a more general and efficient approach to approximate the coefficient matrix of the BEM with the hierarchical off-diagonal low-rank matrix is proposed. Compared to the current fast direct solver based on the hierarchical off-diagonal low-rank matrix, the proposed method is suitable for solving general 3-D boundary element models. Several numerical examples of 3-D potential problems with the total number of unknowns up to above 200,000 are presented. The results show that the new fast direct solver can be applied to solve large 3-D BEM models accurately and with better efficiency compared with the conventional BEM.

  17. Assessment of Linear Finite-Difference Poisson-Boltzmann Solvers

    PubMed Central

    Wang, Jun; Luo, Ray

    2009-01-01

    CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. PMID:20063271

  18. Coordinate Projection-based Solver for ODE with Invariants

    SciTech Connect

    Serban, Radu

    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. Time-varying Riemann solvers for conservation laws on networks

    NASA Astrophysics Data System (ADS)

    Garavello, Mauro; Piccoli, Benedetto

    We consider a conservation law on a network and generic Riemann solvers at nodes depending on parameters, which can be seen as control functions. Assuming that the parameters have bounded variation as functions of time, we prove existence of solutions to Cauchy problems on the whole network.

  20. Parallel Solver for H(div) Problems Using Hybridization and AMG

    SciTech Connect

    Lee, Chak S.; Vassilevski, Panayot S.

    2016-01-15

    In this paper, a scalable parallel solver is proposed for H(div) problems discretized by arbitrary order finite elements on general unstructured meshes. The solver is based on hybridization and algebraic multigrid (AMG). Unlike some previously studied H(div) solvers, the hybridization solver does not require discrete curl and gradient operators as additional input from the user. Instead, only some element information is needed in the construction of the solver. The hybridization results in a H1-equivalent symmetric positive definite system, which is then rescaled and solved by AMG solvers designed for H1 problems. Weak and strong scaling of the method are examined through several numerical tests. Our numerical results show that the proposed solver provides a promising alternative to ADS, a state-of-the-art solver [12], for H(div) problems. In fact, it outperforms ADS for higher order elements.

  1. 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.

  2. Prevention of AV Nodal Reentry Tachycardia by Oral Amiodarone: An Alternative Mechanism of Action

    PubMed Central

    Gold, Robert L.; Haffajee, Charles I.; Entes, Kenneth L.

    1987-01-01

    A 73-year-old man was noted to have atrioventricular (AV) nodal reentry tachycardia, which was induced during programmed electrical stimulation. After 1 month of oral amiodarone therapy, AV nodal reentry tachycardia was prevented by the prolongation of atrial refractoriness and not by direct action on the AV node itself. (Texas Heart Institute Journal 1987; 14:99-101) PMID:15227337

  3. Prognostic value of whole-body SUVmax of nodal and extra-nodal lesions detected by 18F-FDG PET/CT in extra-nodal NK/T-cell lymphoma

    PubMed Central

    Gale, Robert Peter; Wang, Li; Xu, Ji; Qu, Xiao-Yan; Fan, Lei; Li, Tian-Lv; Li, Jian-Yong; Xu, Wei

    2017-01-01

    We analyzed data from 54 newly-diagnosed persons with extra-nodal natural killer/T-cell (NK/T) lymphoma, who had a pretreatment 18F-FDG PET/CT study, to determine whether the sum of SUVmax of all the nodal and extra-nodal lesions predicted progression-free survival (PFS) and/or overall survival (OS). Three models (WB1SUVmax, WB2SUVmax, WB3SUVmax) based on the basis of the sum of SUVmax of the whole-body SUVmax of 11 nodal and 10 extra-nodal lesions were tested. The discrimination value of these models was evaluated using time-dependent receiver-operator characteristic (ROC) curves and corresponding areas under the curve (AUC) in training and validation cohorts. Findings were validated in an independent cohort of 15 subjects. ROC curve analysis showed the optimal cut-off values for WB1SUVmax, WB2SUVmax and WB3SUVmax were 15.8 (sensitivity 92%, specificity 67%, AUC 0.811; P<0.001), 12.7 (sensitivity 96%; specificity 57%; AUC 0.785; P<0.001) and 15.8 (sensitivity 88%; specificity 70%; AUC 0.793; P<0.001). Multivariate analyses indicated WB3SUVmax was independently associated with PFS (hazard ratio [HR]=3.67, 95% confidence interval [95% CI]=1.19, 11.29; P=0.023) and OS (HR= 4.51 [1.02, 19.91]; P=0.047). WB3SUVmax calculated based of the sum of the SUVmax of 3 nodal and 10 extra-nodal lesions was significantly associated with PFS and OS. PMID:27974685

  4. 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).

  5. 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)

  6. 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.

  7. 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

  8. Advanced computational methods for nodal diffusion, Monte Carlo, and S{sub n} problems. Final Report

    SciTech Connect

    1994-12-31

    The work addresses basic computational difficulties that arise in the numerical simulation of neutral particle radiation transport: discretized radiation transport problems, iterative methods, selection of parameters, and extension of current algorithms.

  9. 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

  10. Augmented weighted diamond form of the linear nodal scheme for Cartesian coordinate systems

    SciTech Connect

    Walters, W.F.

    1985-01-01

    The equations of the high order linear nodal numerical scheme are cast in an augmented weighted difference form for three-dimensional Cartesian nodes. The coupling exhibited by these equations indicate that this new algorithm is simpler and hence faster than previous nodal schemes of this degree of accuracy. A well-logging problem and a fast reactor problem are examined. The new scheme developed here is compared with the classical linear-linear nodal scheme and the diamond difference scheme. For the well-logging problem, it is found that the new scheme is both faster and simpler than the classical linear-linear nodal scheme while sacrificing little in accuracy. Even though the new scheme is more accurate than the diamond difference scheme for the reactor problem, the results indicate that state of the art acceleration methods are needed for nodal schemes.

  11. 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.

  12. Nodal staging of colorectal carcinomas and sentinel nodes

    PubMed Central

    Cserni, G

    2003-01-01

    This review surveys the staging systems used for the classification of colorectal carcinomas, including the TNM system, and focuses on the assessment of the nodal stage of the disease. It reviews the quantitative requirements for a regional metastatic work up, and some qualitative features of lymph nodes that may help in the selection of positive and negative lymph nodes. Identification of the sentinel lymph nodes (those lymph nodes that have direct drainage from the primary tumour site) is one such qualitative feature that is claimed to allow the upstaging of colorectal carcinomas via an oriented, enhanced pathological work up. Current evidence in favour of a change in the requisite of assessing as may lymph nodes as is possible, and concentrating the efforts on only a selected number of lymph nodes, is weak. PMID:12719450

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

    PubMed Central

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

    2016-01-01

    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. PMID:26886954

  14. CAISO flicks switch on nodal scheme and lights stay on

    SciTech Connect

    2009-06-15

    In 2000-01, two years after introducing a competitive wholesale power auction in California - with a separate day-ahead zonal market operated by the California Power Exchange and a zonal market for ancillary services and balancing energy operated by the California Independent System Operator (CAISO) - the California market collapsed from exorbitant prices, flagrant gaming, and abuse of market power. Nine years later, CAISO introduced a nodal pricing auction for the wholesale market in April, replacing the zonal scheme, which was among many causes of the original market's demise. With nearly 3,000 nodes on the network, high prices in one region do not affect prices everywhere on the system. After investing some $200 million to upgrade the software, countless delays, and 18 months of market simulation and testing, the new auction was introduced and nothing unusual happened.

  15. Improving the Accuracy of High-Order Nodal Transport Methods

    SciTech Connect

    Azmy, Y.Y.; Buscaglia, G.C.; Zamonsky, O.M.

    1999-09-27

    This paper outlines some recent advances towards improving the accuracy of neutron transport calculations using the Arbitrarily High Order Transport-Nodal (AHOT-N) Method. These advances consist of several contributions: (a) A formula for the spatial weights that allows for the polynomial order to be raised arbitrarily high without suffering adverse effects from round-off error; (b) A reconstruction technique for the angular flux, based upon a recursive formula, that reduces the pointwise error by one ordeq (c) An a posterior error indicator that estimates the true error and its distribution throughout the domain, so that it can be used for adaptively refining the approximation. Present results are mainly for ID, extension to 2D-3D is in progress.

  16. Improving the Accuracy of High-Order Nodal Transport Methods

    SciTech Connect

    Azmy, Y.Y.; Buscaglia, G.C.; Zamonsky, O.M.

    1999-09-27

    This paper outlines some recent advances towards improving the accuracy of neutron calculations using the Arbitrarily High Order Transport-Nodal (AHOT-N) Method. These transport advances consist of several contributions: (a) A formula for the spatial weights that allows for the polynomial order to be raised arbitrarily high without suffering from pollution from round-off, error; (b) A reconstruction technique for the angular flux, based upon a recursive formula, that reduces the pointwise error by one order; (c) An a posterior error indicator that estimates the true error and its distribution throughout the domain, so that it can be used for adaptively reftig the approximation. Present results are mainly for ID, extension to 2D-3D is in progress.

  17. 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.

  18. 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.

  19. Nodal domains on isospectral quantum graphs: the resolution of isospectrality?

    NASA Astrophysics Data System (ADS)

    Band, Ram; Shapira, Talia; Smilansky, Uzy

    2006-11-01

    We present and discuss isospectral quantum graphs which are not isometric. These graphs are the analogues of the isospectral domains in {\\bb R}^{2} which were introduced recently in Gordon et al (1992 Bull. Am. Math. Soc. 27 134-8), Chapman (1995 Am. Math. Mon. 102 124), Buser et al (1994 Int. Math. Res. Not. 9 391-400), Okada and Shudo (2001 J. Phys. A: Math. Gen. 34 5911-22), Jakobson et al (2006 J. Comput. Appl. Math. 194 141-55) and Levitin et al (2006 J. Phys. A: Math. Gen. 39 2073-82)) all based on Sunada's construction of isospectral domains (Sunada T 1985 Ann. Math. 121 196-86). After presenting some of the properties of these graphs, we discuss a few examples which support the conjecture that by counting the nodal domains of the corresponding eigenfunctions one can resolve the isospectral ambiguity.

  20. On-line application of the PANTHER advanced nodal code

    SciTech Connect

    Hutt, P.K.; Knight, M.P. )

    1992-01-01

    Over the last few years, Nuclear Electric has developed an integrated core performance code package for both light water reactors (LWRs) and advanced gas-cooled reactors (AGRs) that can perform a comprehensive range of calculations for fuel cycle design, safety analysis, and on-line operational support for such plants. The package consists of the following codes: WIMS for lattice physics, PANTHER whole reactor nodal flux and AGR thermal hydraulics, VIPRE for LWR thermal hydraulics, and ENIGMA for fuel performance. These codes are integrated within a UNIX-based interactive system called the Reactor Physics Workbench (RPW), which provides an interactive graphic user interface and quality assurance records/data management. The RPW can also control calculational sequences and data flows. The package has been designed to run both off-line and on-line accessing plant data through the RPW.

  1. 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

  2. Reactivation of Embryonic Nodal Signaling is Associated with Tumor Progression and Promotes the Growth of Prostate Cancer Cells

    PubMed Central

    Lawrence, Mitchell G.; Margaryan, Naira V.; Loessner, Daniela; Collins, Angus; Kerr, Kris M.; Turner, Megan; Seftor, Elisabeth A.; Stephens, Carson R.; Lai, John; BioResource, APC; Postovit, Lynne-Marie; Clements, Judith A.; Hendrix, Mary J.C.

    2011-01-01

    Background Nodal is a member of the Transforming Growth Factor β (TGFβ) superfamily that directs embryonic patterning and promotes the plasticity and tumorigenicity of tumor cells, but its role in the prostate is unknown. The goal of this study was to characterize the expression and function of Nodal in prostate cancer and determine whether, like other TGFβ ligands, it modulates androgen receptor (AR) activity. Methods Nodal expression was investigated using immunohistochemistry of tissue microarrays and Western blots of prostate cell lines. The functional role of Nodal was examined using Matrigel and soft agar growth assays. Cross-talk between Nodal and AR signaling was assessed with luciferase reporter assays and expression of endogenous androgen regulated genes. Results Significantly increased Nodal expression was observed in cancer compared with benign prostate specimens. Nodal was only expressed by DU145 and PC3 cells. All cell lines expressed Nodal’s co-receptor, Cripto-1, but lacked Lefty, a critical negative regulator of Nodal signaling. Recombinant human Nodal triggered downstream Smad2 phosphorylation in DU145 and LNCaP cells, and stable transfection of pre-pro-Nodal enhanced the growth of LNCaP cells in Matrigel and soft agar. Finally, Nodal attenuated AR signaling, reducing the activity of a PSA promoter construct in luciferase assays and down-regulating the endogenous expression of androgen regulated genes. Conclusions An aberrant Nodal signaling pathway is re-expressed and functionally active in prostate cancer cells. PMID:21656830

  3. Value of ADC measurements for nodal staging after chemoradiation in locally advanced rectal cancer—a per lesion validation study

    PubMed Central

    Lambregts, Doenja M. J.; Maas, Monique; Riedl, Robert G.; Bakers, Frans C. H.; Verwoerd, Jan L.; Kessels, Alfons G. H.; Lammering, Guido; Boetes, Carla; Beets, Geerard L.

    2010-01-01

    Objectives To evaluate the performance of diffusion-weighted MRI (DWI) in addition to T2-weighted (T2W) MRI for nodal restaging after chemoradiation in rectal cancer. Methods Thirty patients underwent chemoradiation followed by MRI (1.5 T) and surgery. Imaging consisted of T2W-MRI and DWI (b0, 500, 1000). On T2W-MRI, nodes were scored as benign/malignant by two independent readers (R1, R2). Mean apparent diffusion coefficient (ADC) was measured for each node. Diagnostic performance was compared for T2W-MRI, ADC and T2W+ADC, using a per lesion histological validation. Results ADC was higher for the malignant nodes (1.43 ± 0.38 vs 1.19 ± 0.27 *10−3 mm2/s, p < 0.001). Area under the ROC curve/sensitivity/specificity were 0.88/65%/93% (R1) and 0.95/71%/91% (R2) using T2W-MRI; 0.66/53%/82% using ADC (mean of two readers); and 0.91/56%/98% (R1) and 0.96/56%/99% (R2) using T2W+ADC. There was no significant difference between T2W-MRI and T2W+ADC. Interobserver reproducibility was good for T2W-MRI (κ0.73) and ADC (intraclass correlation coefficient 0.77). Conclusions After chemoradiation, ADC measurements may have potential for nodal characterisation, but DWI on its own is not reliable. Addition of DWI to T2W-MRI does not improve accuracy and T2W-MRI is already sufficiently accurate. PMID:20730540

  4. Nodal promotes mir206 expression to control convergence and extension movements during zebrafish gastrulation.

    PubMed

    Liu, Xiuli; Ma, Yuanqing; Zhang, Congwei; Wei, Shi; Cao, Yu; Wang, Qiang

    2013-10-20

    Nodal, a member of the transforming growth factor β (TGF-β) superfamily, has been shown to play a role in mesendoderm induction and gastrulation movements. The activity of Nodal signaling can be modulated by microRNAs (miRNAs) as previously reported, but little is known about which miRNAs are regulated by Nodal during gastrulation. In the present study, we found that the expression of mir206, one of the most abundant miRNAs during zebrafish early embryo development, is regulated by Nodal signaling. Abrogation of Nodal signal activity results in defective convergence and extension (CE) movements, and these cell migration defects can be rescued by supplying an excess of mir206, suggesting that mir206 acts downstream of Nodal signaling to regulate CE movements. Furthermore, in mir206 morphants, the expression of cell adhesion molecule E-cadherin is significantly increased, while the key transcriptional repressor of E-cadherin, snail1a, is depressed. Our study uncovers a novel mechanism by which Nodal-regulated mir206 modulates gastrulation movements in connection with the Snail/E-cadherin pathway.

  5. Xantivin suppresses the activity of EGF-CFC genes to regulate nodal signaling.

    PubMed

    Tanegashima, Kousuke; Haramoto, Yoshikazu; Yokota, Chika; Takahashi, Shuji; Asashima, Makoto

    2004-06-01

    Lefty, antivin and related genes act in a feedback inhibition mechanism for nodal signaling at a number of stages of vertebrate embryogenesis. To analyze the function of the feedback inhibitor of nodal signaling, Xantivin in Xenopus embryos, we designed a morpholino antisense oligonucleotide (XatvMO) for this gene. XatvMO caused the expansion of mesodermal tissue and head defects. XatvMO-injected gastrulae showed up-regulated expression of the mesodermal markers Xbra, Xwnt8, Xnot, and Chordin, suggesting expansion of the trunk-tail organizer. As expected, depletion of Xantivin also up-regulated nodal signaling as confirmed by the enhanced ectopic expression of Xantivin mRNA, a known target gene of nodal signaling. Furthermore, we investigated the relationship between Xantivin and the EGF-CFC gene FRL-1, which is a component of the nodal receptor. In animal cap assays, FRL-1 could not induce expression of nodal-responsive genes, but could up-regulate expression of these genes when FRL-1 was coinjected with a low dose of Xnr1; coinjection of Xantivin suppressed this up-regulation by FRL-1. We also found that Xantivin can rescue the caudalized phenotype induced by overexpression of FRL-1. Co-immunoprecipitation assays showed that Xantivin interacted with the EGF-CFC proteins, FRL-1 and cripto. Taken together, these results suggest that Xantivin opposes the activity of EGF-CFC genes and thereby antagonizes nodal signaling.

  6. Nodal signals mediate interactions between the extra-embryonic and embryonic tissues in zebrafish.

    PubMed

    Fan, Xiang; Hagos, Engda G; Xu, Bo; Sias, Christina; Kawakami, Koichi; Burdine, Rebecca D; Dougan, Scott T

    2007-10-15

    In many vertebrates, extra-embryonic tissues are important signaling centers that induce and pattern the germ layers. In teleosts, the mechanism by which the extra-embryonic yolk syncytial layer (YSL) patterns the embryo is not understood. Although the Nodal-related protein Squint is expressed in the YSL, its role in this tissue is not known. We generated a series of stable transgenic lines with GFP under the control of squint genomic sequences. In all species, nodal-related genes induce their own expression through a positive feedback loop. We show that two tissue specific enhancers in the zebrafish squint gene mediate the response to Nodal signals. Expression in the blastomeres depends upon a conserved Nodal response element (NRE) in the squint first intron, while expression in the extra-embryonic enveloping layer (EVL) is mediated by an element upstream of the transcription start site. Targeted depletion experiments demonstrate that the zebrafish Nodal-related proteins Squint and Cyclops are required in the YSL for endoderm and head mesoderm formation. Thus, Nodal signals mediate interactions between embryonic and extra-embryonic tissues in zebrafish that maintain nodal-related gene expression in the margin. Our results demonstrate a high degree of functional conservation between the extra-embryonic tissues of mouse and zebrafish.

  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

    2004-08-04

    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.

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

    PubMed Central

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

    2004-01-01

    Nodals are signaling factors of the transforming growth factor-β (TGFβ) 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 γ-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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. A 3-D upwind Euler solver for unstructured meshes

    NASA Technical Reports Server (NTRS)

    Barth, Timothy J.

    1991-01-01

    A three-dimensional finite-volume upwind Euler solver is developed for unstructured meshes. The finite-volume scheme solves for solution variables at vertices of the mesh and satisfies the integral conservation law on nonoverlapping polyhedral control volumes surrounding vertices of the mesh. The schene achieves improved solution accuracy by assuming a piecewise linear variation of the solution in each control volume. This improved spatial accuracy hinges heavily upon the calculation of the solution gradient in each control volume given pointwise values of the solution at vertices of the mesh. Several algorithms are discussed for obtaining these gradients. Details concerning implementation procedures and data structures are discussed. Sample calculations for inviscid Euler flow about isolated aircraft wings at subsonic and transonic speeds are compared with established Euler solvers as well as experiment.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. Menu-Driven Solver Of Linear-Programming Problems

    NASA Technical Reports Server (NTRS)

    Viterna, L. A.; Ferencz, D.

    1992-01-01

    Program assists inexperienced user in formulating linear-programming problems. A Linear Program Solver (ALPS) computer program is full-featured LP analysis program. Solves plain linear-programming problems as well as more-complicated mixed-integer and pure-integer programs. Also contains efficient technique for solution of purely binary linear-programming problems. Written entirely in IBM's APL2/PC software, Version 1.01. Packed program contains licensed material, property of IBM (copyright 1988, all rights reserved).

  6. 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.

  7. 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.

  8. 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.

  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. Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations

    PubMed Central

    Mohapatra, Bhagyalaxmi; Casey, Brett; Li, Hua; Ho-Dawson, Trang; Smith, Liana; Fernbach, Susan D.; Molinari, Laura; Niesh, Stephen R.; Jefferies, John Lynn; Craigen, William J.; Towbin, Jeffrey A.; Belmont, John W.; Ware, Stephanie M.

    2009-01-01

    NODAL and its signaling pathway are known to play a key role in specification and patterning of vertebrate embryos. Mutations in several genes encoding components of the NODAL signaling pathway have previously been implicated in the pathogenesis of human left–right (LR) patterning defects. Therefore, NODAL, a member of TGF-β superfamily of developmental regulators, is a strong candidate to be functionally involved in congenital LR axis patterning defects or heterotaxy. Here we have investigated whether variants in NODAL are present in patients with heterotaxy and/or isolated cardiovascular malformations (CVM) thought to be caused by abnormal heart tube looping. Analysis of a large cohort of cases (n = 269) affected with either classic heterotaxy or looping CVM revealed four different missense variants, one in-frame insertion/deletion and two conserved splice site variants in 14 unrelated subjects (14/269, 5.2%). Although similar with regard to other associated defects, individuals with the NODAL mutations had a significantly higher occurrence of pulmonary valve atresia (P = 0.001) compared with cases without a detectable NODAL mutation. Functional analyses demonstrate that the missense variant forms of NODAL exhibit significant impairment of signaling as measured by decreased Cripto (TDGF-1) co-receptor-mediated activation of artificial reporters. Expression of these NODAL proteins also led to reduced induction of Smad2 phosphorylation and impaired Smad2 nuclear import. Taken together, these results support a role for mutations and rare deleterious variants in NODAL as a cause for sporadic human LR patterning defects. PMID:19064609

  11. Conformational features and binding affinities to Cripto, ALK7 and ALK4 of Nodal synthetic fragments.

    PubMed

    Calvanese, Luisa; Sandomenico, Annamaria; Caporale, Andrea; Focà, Annalia; Focà, Giuseppina; D'Auria, Gabriella; Falcigno, Lucia; Ruvo, Menotti

    2015-04-01

    Nodal, a member of the TGF-β superfamily, is a potent embryonic morphogen also implicated in tumor progression. As for other TGF-βs, it triggers the signaling functions through the interaction with the extracellular domains of type I and type II serine/threonine kinase receptors and with the co-receptor Cripto. Recently, we reported the molecular models of Nodal in complex with its type I receptors (ALK4 and ALK7) as well as with Cripto, as obtained by homology modeling and docking simulations. From such models, potential binding epitopes have been identified. To validate such hypotheses, a series of mutated Nodal fragments have been synthesized. These peptide analogs encompass residues 44-67 of the Nodal protein, corresponding to the pre-helix loop and the H3 helix, and reproduce the wild-type sequence or bear some modifications to evaluate the hot-spot role of modified residues in the receptor binding. Here, we show the structural characterization in solution by CD and NMR of the Nodal peptides and the measurement of binding affinity toward Cripto by surface plasmon resonance. Data collected by both conformational analyses and binding measurements suggest a role for Y58 of Nodal in the recognition with Cripto and confirm that previously reported for E49 and E50. Surface plasmon resonance binding assays with recombinant proteins show that Nodal interacts in vitro also with ALK7 and ALK4 and preliminary data, generated using the Nodal synthetic fragments, suggest that Y58 of Nodal may also be involved in the recognition with these protein partners.

  12. Cerberus-Nodal-Lefty-Pitx signaling cascade controls left-right asymmetry in amphioxus.

    PubMed

    Li, Guang; Liu, Xian; Xing, Chaofan; Zhang, Huayang; Shimeld, Sebastian M; Wang, Yiquan

    2017-04-04

    Many bilaterally symmetrical animals develop genetically programmed left-right asymmetries. In vertebrates, this process is under the control of Nodal signaling, which is restricted to the left side by Nodal antagonists Cerberus and Lefty. Amphioxus, the earliest diverging chordate lineage, has profound left-right asymmetry as a larva. We show that Cerberus, Nodal, Lefty, and their target transcription factor Pitx are sequentially activated in amphioxus embryos. We then address their function by transcription activator-like effector nucleases (TALEN)-based knockout and heat-shock promoter (HSP)-driven overexpression. Knockout of Cerberus leads to ectopic right-sided expression of Nodal, Lefty, and Pitx, whereas overexpression of Cerberus represses their left-sided expression. Overexpression of Nodal in turn represses Cerberus and activates Lefty and Pitx ectopically on the right side. We also show Lefty represses Nodal, whereas Pitx activates Nodal These data combine in a model in which Cerberus determines whether the left-sided gene expression cassette is activated or repressed. These regulatory steps are essential for normal left-right asymmetry to develop, as when they are disrupted embryos may instead form two phenotypic left sides or two phenotypic right sides. Our study shows the regulatory cassette controlling left-right asymmetry was in place in the ancestor of amphioxus and vertebrates. This includes the Nodal inhibitors Cerberus and Lefty, both of which operate in feedback loops with Nodal and combine to establish asymmetric Pitx expression. Cerberus and Lefty are missing from most invertebrate lineages, marking this mechanism as an innovation in the lineage leading to modern chordates.

  13. 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.

  14. 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.

  15. 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.

  16. NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

    SciTech Connect

    Christensen, Max La Cour; Villa, Umberto E.; Engsig-Karup, Allan P.; Vassilevski, Panayot S.

    2016-01-22

    The paper introduces a nonlinear multigrid solver for mixed nite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstruc- tured problems is the guaranteed approximation property of the AMGe coarse spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method, [5, 11]), were less successful due to lack of such good approximation properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on un- structured meshes should be as powerful/successful as FAS on geometrically re ned meshes. For comparison, Newton's method and Picard iterations with an inner state-of-the-art linear solver is compared to FAS on a nonlinear saddle point problem with applications to porous media ow. It is demonstrated that FAS is faster than Newton's method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate, providing a solver with the potential for mesh-independent convergence on general unstructured meshes.

  17. Error control of iterative linear solvers for integrated groundwater models.

    PubMed

    Dixon, Matthew F; Bai, Zhaojun; Brush, Charles F; Chung, Francis I; Dogrul, Emin C; Kadir, Tariq N

    2011-01-01

    An open problem that arises when using modern iterative linear solvers, such as the preconditioned conjugate gradient method or Generalized Minimum RESidual (GMRES) method, is how to choose the residual tolerance in the linear solver to be consistent with the tolerance on the solution error. This problem is especially acute for integrated groundwater models, which are implicitly coupled to another model, such as surface water models, and resolve both multiple scales of flow and temporal interaction terms, giving rise to linear systems with variable scaling. This article uses the theory of "forward error bound estimation" to explain the correspondence between the residual error in the preconditioned linear system and the solution error. Using examples of linear systems from models developed by the US Geological Survey and the California State Department of Water Resources, we observe that this error bound guides the choice of a practical measure for controlling the error in linear systems. We implemented a preconditioned GMRES algorithm and benchmarked it against the Successive Over-Relaxation (SOR) method, the most widely known iterative solver for nonsymmetric coefficient matrices. With forward error control, GMRES can easily replace the SOR method in legacy groundwater modeling packages, resulting in the overall simulation speedups as large as 7.74×. This research is expected to broadly impact groundwater modelers through the demonstration of a practical and general approach for setting the residual tolerance in line with the solution error tolerance and presentation of GMRES performance benchmarking results.

  18. 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

  19. 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.

  20. Non-linear curve fitting using Microsoft Excel solver.

    PubMed

    Walsh, S; Diamond, D

    1995-04-01

    Solver, an analysis tool incorporated into Microsoft Excel V 5.0 for Windows, has been evaluated for solving non-linear equations. Test and experimental data sets have been processed, and the results suggest that solver can be successfully used for modelling data obtained in many analytical situations (e.g. chromatography and FIA peaks, fluorescence decays and ISE response characteristics). The relatively simple user interface, and the fact that Excel is commonly bundled free with new PCs makes it an ideal tool for those wishing to experiment with solving non-linear equations without having to purchase and learn a completely new package. The dynamic display of the iterative search process enables the user to monitor location of the optimum solution by the search algorithm. This, together with the almost universal availability of Excel, makes solver an ideal vehicle for teaching the principles of iterative non-linear curve fitting techniques. In addition, complete control of the modelling process lies with the user, who must present the raw data and enter the equation of the model, in contrast to many commercial packages bundled with instruments which perform these operations with a 'black-box' approach.

  1. IGA-ADS: Isogeometric analysis FEM using ADS solver

    NASA Astrophysics Data System (ADS)

    Łoś, Marcin M.; Woźniak, Maciej; Paszyński, Maciej; Lenharth, Andrew; Hassaan, Muhamm Amber; Pingali, Keshav

    2017-08-01

    In this paper we present a fast explicit solver for solution of non-stationary problems using L2 projections with isogeometric finite element method. The solver has been implemented within GALOIS framework. It enables parallel multi-core simulations of different time-dependent problems, in 1D, 2D, or 3D. We have prepared the solver framework in a way that enables direct implementation of the selected PDE and corresponding boundary conditions. In this paper we describe the installation, implementation of exemplary three PDEs, and execution of the simulations on multi-core Linux cluster nodes. We consider three case studies, including heat transfer, linear elasticity, as well as non-linear flow in heterogeneous media. The presented package generates output suitable for interfacing with Gnuplot and ParaView visualization software. The exemplary simulations show near perfect scalability on Gilbert shared-memory node with four Intel® Xeon® CPU E7-4860 processors, each possessing 10 physical cores (for a total of 40 cores).

  2. 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).

  3. Detection of 18.6 year nodal induced drought in the Patagonian Andes

    NASA Astrophysics Data System (ADS)

    Currie, Robert G.

    1983-11-01

    Analysis of tree-ring chronologies from the Patagonian Andes yields evidence for the 18.6 yr lunar nodal term in drought/flood. The mean discrepancy between epochs of drought/flood and the nodal tide since AD 1600 is 0.7 ± 2.2 yr, but the polarity of the signal is apparently bimodal. From nodal epoch 1750.0 through 1898.9 drought and tide were in phase, whereas prior to 1750.0 and subsequent to 1898.9 drought and tide were out of phase. There is evidence also for the solar cycle drought signal in the data.

  4. [Method for optimal sensor placement in water distribution systems with nodal demand uncertainties].

    PubMed

    Liu, Shu-Ming; Wu, Xue; Ouyang, Le-Yan

    2013-08-01

    The notion of identification fitness was proposed for optimizing sensor placement in water distribution systems. Nondominated Sorting Genetic Algorithm II was used to find the Pareto front between minimum overlap of possible detection times of two events and the best probability of detection, taking nodal demand uncertainties into account. This methodology was applied to an example network. The solutions show that the probability of detection and the number of possible locations are not remarkably affected by nodal demand uncertainties, but the sources identification accuracy declines with nodal demand uncertainties.

  5. PoroTomo: Map of DAS, Nodal, Vibroseis and Reftek Station Deployment

    SciTech Connect

    Kurt Feigl

    2016-10-15

    Map of DAS, nodal, vibroseis and Reftek stations during March 2016 deployment. The plot on the left has nodal stations labeled; the plot on the right has vibroseis observations labeled. Stations are shown in map-view using Brady's rotated X-Y coordinates with side plots denoting elevation with respect to the WGS84 ellipsoid. Blue circles denote vibroseis data, x symbols denote DAS (cyan for horizontal and magenta for vertical), black asterisks denote Reftek data, and red plus signs denote nodal data. This map can be found on UW-Madison's askja server at /PoroTomo/DATA/MAPS/Deployment_Stations.pdf

  6. On the inverse nodal problems for discontinuous Sturm-Liouville operators

    NASA Astrophysics Data System (ADS)

    Wang, Yu Ping; Yurko, V. A.

    2016-03-01

    In this paper, we discuss the inverse nodal problems for discontinuous Sturm-Liouville operators with Robin boundary conditions. We show that the potential q up to its mean value on the interval [ 0 , 1 ] and coefficients h, H, b/a can be uniquely determined by the twin-dense nodal subset on the subinterval [a0 ,b0 ], a0 <1/2 nodal subset on the interval [a0 ,1/2 ] and additional information, respectively.

  7. 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.

  8. Performance of algebraic multi-grid solvers based on unsmoothed and smoothed aggregation schemes

    NASA Astrophysics Data System (ADS)

    Webster, R.

    2001-08-01

    A comparison is made of the performance of two algebraic multi-grid (AMG0 and AMG1) solvers for the solution of discrete, coupled, elliptic field problems. In AMG0, the basis functions for each coarse grid/level approximation (CGA) are obtained directly by unsmoothed aggregation, an appropriate scaling being applied to each CGA to improve consistency. In AMG1 they are assembled using a smoothed aggregation with a constrained energy optimization method providing the smoothing. Although more costly, smoothed basis functions provide a better (more consistent) CGA. Thus, AMG1 might be viewed as a benchmark for the assessment of the simpler AMG0. Selected test problems for D'Arcy flow in pipe networks, Fick diffusion, plane strain elasticity and Navier-Stokes flow (in a Stokes approximation) are used in making the comparison. They are discretized on the basis of both structured and unstructured finite element meshes. The range of discrete equation sets covers both symmetric positive definite systems and systems that may be non-symmetric and/or indefinite. Both global and local mesh refinements to at least one order of resolving power are examined. Some of these include anisotropic refinements involving elements of large aspect ratio; in some hydrodynamics cases, the anisotropy is extreme, with aspect ratios exceeding two orders. As expected, AMG1 delivers typical multi-grid convergence rates, which for all practical purposes are independent of mesh bandwidth. AMG0 rates are slower. They may also be more discernibly mesh-dependent. However, for the range of mesh bandwidths examined, the overall cost effectiveness of the two solvers is remarkably similar when a full convergence to machine accuracy is demanded. Thus, the shorter solution times for AMG1 do not necessarily compensate for the extra time required for its costly grid generation. This depends on the severity of the problem and the demanded level of convergence. For problems requiring few iterations, where grid

  9. 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.

  10. A universal solver for hyperbolic equations by cubic-polynomial interpolation I. One-dimensional solver

    NASA Astrophysics Data System (ADS)

    Yabe, T.; Aoki, T.

    1991-09-01

    A new numerical method is proposed for general hyperbolic equations. The scheme uses a spatial profile interpolated with a cubic polynomial within a grid cell, and is described in an explicit finite-difference form by assuming that both a physical quantity and its spatial derivative obey the master equation. The method gives stable and less diffusive results even without any flux limiter. It is successfully applied to the KdV equation, a one-dimensional shock-tube problem and a cylindrically converging shock wave.

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

    PubMed

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

    2016-05-03

    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.

  12. A nodal integral method for the Fokker-Planck equation

    SciTech Connect

    McArdle, K.R.; Dorning, J.J. )

    1989-01-01

    The Fokker-Planck equation is important in the kinetic theory of plasmas for the description of long-range coulomb collisions of charged particles. Hence, it is used extensively in modeling fusion devices, such as magnetic mirrors and certain aspects of tokamaks. The authors have developed a nodal integral method (NIM) for the accurate numerical solution of the Fokker-Planck equation, applied it to test problems, and compared the results obtained with those obtained using a finite difference method (FDM). These comparisons show that the NIM is more accurate and more computationally efficient than the FDM, especially in the calculation of particle and energy leakages and when applied to more difficult test problems. The new method significantly extends ideas developed previously to more complicated partial differential equations (PDEs) in two important ways. Since the nonlinearities in the Fokker-Planck equation are considerably more complicated than those that arise in the Navier-Stokes equations and the Boussinesq equations, the NIM developed here extends the general technique farther into the nonlinear regime. Further, since the Fokker-Planck equation is singular at the origin in spherical velocity coordinates, the geometry relevant to most practical problems, special origin equations had to be developed for the computational elements adjacent to the v = 0 boundary.

  13. 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.

  14. 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.

  15. 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.

  16. Left–Right Determination: Involvement of Molecular Motor KIF3, Cilia, and Nodal Flow

    PubMed Central

    Hirokawa, Nobutaka; Tanaka, Yosuke; Okada, Yasushi

    2009-01-01

    Mammalian left–right determination is a good example for how multiple cell biological processes coordinate in the formation of a basic body plan. The leftward movement of fluid at the ventral node, called nodal flow, is the central process in symmetry breaking on the left–right axis. Nodal flow is autonomously generated by the rotation of posteriorly tilted cilia that are built by transport via KIF3 motor on cells of the ventral node. How nodal flow is interpreted to create left–right asymmetry has been a matter of debate. Recent evidence suggests that the leftward movement of sheathed lipidic particles, called nodal vesicular parcels (NVPs), may result in the activation of the noncanonical hedgehog signaling pathway, an asymmetric elevation in intracellular Ca2+ and changes in gene expression. PMID:20066075

  17. A semi-experimental nodal synthesis method for the on-line reconstruction of three-dimensional neutron flux-shapes and reactivity

    SciTech Connect

    Jacqmin, R.P.

    1991-12-10

    The safety and optimal performance of large, commercial, light-water reactors require the knowledge at all time of the neutron-flux distribution in the core. In principle, this information can be obtained by solving the time-dependent neutron diffusion equations. However, this approach is complicated and very expensive. Sufficiently accurate, real-time calculations (time scale of approximately one second) are not yet possible on desktop computers, even with fast-running, nodal kinetics codes. A semi-experimental, nodal synthesis method which avoids the solution of the time-dependent, neutron diffusion equations is described. The essential idea of this method is to approximate instantaneous nodal group-fluxes by a linear combination of K, precomputed, three-dimensional, static expansion-functions. The time-dependent coefficients of the combination are found from the requirement that the reconstructed flux-distribution agree in a least-squares sense with the readings of J ({ge}K) fixed, prompt-responding neutron-detectors. Possible numerical difficulties with the least-squares solution of the ill-conditioned, J-by-K system of equations are brought under complete control by the use of a singular-value-decomposition technique. This procedure amounts to the rearrangement of the original, linear combination of K expansion functions into an equivalent more convenient, linear combination of R ({le}K) orthogonalized modes'' of decreasing magnitude. Exceedingly small modes are zeroed to eliminate any risk of roundoff-error amplification, and to assure consistency with the limited accuracy of the data. Additional modes are zeroed when it is desirable to limit the sensitivity of the results to measurement noise.

  18. A semi-experimental nodal synthesis method for the on-line reconstruction of three-dimensional neutron flux-shapes and reactivity. Final report

    SciTech Connect

    Jacqmin, R.P.

    1991-12-10

    The safety and optimal performance of large, commercial, light-water reactors require the knowledge at all time of the neutron-flux distribution in the core. In principle, this information can be obtained by solving the time-dependent neutron diffusion equations. However, this approach is complicated and very expensive. Sufficiently accurate, real-time calculations (time scale of approximately one second) are not yet possible on desktop computers, even with fast-running, nodal kinetics codes. A semi-experimental, nodal synthesis method which avoids the solution of the time-dependent, neutron diffusion equations is described. The essential idea of this method is to approximate instantaneous nodal group-fluxes by a linear combination of K, precomputed, three-dimensional, static expansion-functions. The time-dependent coefficients of the combination are found from the requirement that the reconstructed flux-distribution agree in a least-squares sense with the readings of J ({ge}K) fixed, prompt-responding neutron-detectors. Possible numerical difficulties with the least-squares solution of the ill-conditioned, J-by-K system of equations are brought under complete control by the use of a singular-value-decomposition technique. This procedure amounts to the rearrangement of the original, linear combination of K expansion functions into an equivalent more convenient, linear combination of R ({le}K) orthogonalized ``modes`` of decreasing magnitude. Exceedingly small modes are zeroed to eliminate any risk of roundoff-error amplification, and to assure consistency with the limited accuracy of the data. Additional modes are zeroed when it is desirable to limit the sensitivity of the results to measurement noise.

  19. The Application of Modern Nodal Methods to Pwr Reactor Physics Analysis.

    NASA Astrophysics Data System (ADS)

    Knight, M. P.

    Available from UMI in association with The British Library. The objective of this research is to develop efficient computational procedures for PWR reactor calculations, based on modern nodal methods. The analytic nodal method, which is characterised by the use of exact exponential expansions in transverse-integrated equations, is implemented within an existing finite-difference code. This shows considerable accuracy and efficiency on standard benchmark problems, very much in line with existing experience with nodal methods. Assembly powers can be calculated to within 2.0% with just one mesh per assembly. The recovery of fine detail from a nodal solution based on such a coarse mesh requires additional effort. Techniques are develolped in this thesis which allow the basic nodal equations to be used in this reconstruction, and therefore provide a consistent approach. Pin powers can be recovered from assembly-averaged values with little further loss of accuracy. A similar investigation is followed with the transverse leakage distribution. An improvement, which uses known local behaviour, is shown to be very effective in some limited applications, but overall provides little advantage over the much simpler quadratic model. For heterogeneous calculations it is essential that the homogenisation techniques are well matched to the nodal method. The asymmetric design of some assemblies provides a severe test. Techniques are devised that allow some overall representation of this asymmetry to be retained in the reactor calculation, even when using one mesh per assembly. Extensions of this procedure provide an almost exact global representation of a heterogeneous assembly. A complete comparison is performed between reactor calculations at one mesh per pin, and at one mesh per assembly using nodal and homogenisation methods. Homogenisation errors and nodal coarse-mesh errors are shown to be very similar, amounting to about 0.1% on reactor eigenvalue, 2.0% on assembly power and

  20. Topological Dirac nodal lines and surface charges in fcc alkaline earth metals

    PubMed Central

    Hirayama, Motoaki; Okugawa, Ryo; Miyake, Takashi; Murakami, Shuichi

    2017-01-01

    In nodal-line semimetals, the gaps close along loops in k space, which are not at high-symmetry points. Typical mechanisms for the emergence of nodal lines involve mirror symmetry and the π Berry phase. Here we show via ab initio calculations that fcc calcium (Ca), strontium (Sr) and ytterbium (Yb) have topological nodal lines with the π Berry phase near the Fermi level, when spin–orbit interaction is neglected. In particular, Ca becomes a nodal-line semimetal at high pressure. Owing to nodal lines, the Zak phase becomes either π or 0, depending on the wavevector k, and the π Zak phase leads to surface polarization charge. Carriers eventually screen it, leaving behind large surface dipoles. In materials with nodal lines, both the large surface polarization charge and the emergent drumhead surface states enhance Rashba splitting when heavy adatoms are present, as we have shown to occur in Bi/Sr(111) and in Bi/Ag(111). PMID:28074835

  1. The nodal inhibitor Coco is a critical target of leftward flow in Xenopus.

    PubMed

    Schweickert, Axel; Vick, Philipp; Getwan, Maike; Weber, Thomas; Schneider, Isabelle; Eberhardt, Melanie; Beyer, Tina; Pachur, Anke; Blum, Martin

    2010-04-27

    Vertebrate laterality, which is manifested by asymmetrically placed organs [1], depends on asymmetric activation of the Nodal signaling cascade in the left lateral plate mesoderm [2]. In fish, amphibians, and mammals, a cilia-driven leftward flow of extracellular fluid acts upstream of the Nodal cascade [3-6]. The direct target of flow has remained elusive. In Xenopus, flow occurs at the gastrocoel roof plate (GRP) in the dorsal midline of the embryo [4, 7]. The GRP is bordered by a second, bilaterally symmetrical Nodal expression domain [8]. Here we identify the Nodal inhibitor Coco as a critical target of flow. Coco and Xenopus Nodal-related 1 (Xnr1) are coexpressed in the lateralmost ciliated GRP cells. Coco becomes downregulated on the left side of the GRP as a direct readout of flow. Ablation of flow prevented Coco repression, whereas Xnr1 expression was independent of flow. Loss of flow-induced laterality defects were rescued by knockdown of Coco on the left side. Parallel knockdown of Coco and Xnr1 in GRP cells restored laterality defects in flow-impaired embryos, demonstrating that Coco acted through GRP-expressed Xnr1. Coco thus acts as a critical target of flow, suggesting that symmetry is broken by flow-mediated left-asymmetric release of Nodal repression at the midline.

  2. Influence of FDG-PET on primary nodal target volume definition for head and neck carcinomas.

    PubMed

    van Egmond, Sylvia L; Piscaer, Vera; Janssen, Luuk M; Stegeman, Inge; Hobbelink, Monique G; Grolman, Wilko; Terhaard, Chris H

    The role of 2-[(18)F]-fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography (PET)/computed tomography (CT) in routine diagnostic staging remains controversial. In case of discordance between FDG-PET and CT, a compromise has to be made between the risk of false positive FDG-PET and the risk of delaying appropriate salvage intervention. Second, with intensity modulated radiation therapy (IMRT), smaller radiation fields allow tissue sparing, but could also lead to more marginal failures. We retrospectively studied 283 patients with head and neck carcinoma scheduled for radiotherapy between 2002 and 2010. We analyzed the influence of FDG-PET/CT versus CT alone on defining nodal target volume definition and evaluated its long-term clinical results. Second, the location of nodal recurrences was related to the radiation regional dose distribution. In 92 patients, CT and FDG-PET, performed in mold, showed discordant results. In 33%, nodal staging was altered by FDG-PET. In 24%, FDG-PET also led to an alteration in nodal treatment, including a nodal upstage of 18% and downstage of 6%. In eight of these 92 patients, a regional recurrence occurred. Only two patients had a recurrence in the discordant node on FDG-PET and CT and both received a boost (high dose radiation). These results support the complementary value of FDG-PET/CT compared to CT alone in defining nodal target volume definition for radiotherapy of head and neck cancer.

  3. Cilia are required for asymmetric nodal induction in the sea urchin embryo.

    PubMed

    Tisler, Matthias; Wetzel, Franziska; Mantino, Sabrina; Kremnyov, Stanislav; Thumberger, Thomas; Schweickert, Axel; Blum, Martin; Vick, Philipp

    2016-08-23

    Left-right (LR) organ asymmetries are a common feature of metazoan animals. In many cases, laterality is established by a conserved asymmetric Nodal signaling cascade during embryogenesis. In most vertebrates, asymmetric nodal induction results from a cilia-driven leftward fluid flow at the left-right organizer (LRO), a ciliated epithelium present during gastrula/neurula stages. Conservation of LRO and flow beyond the vertebrates has not been reported yet. Here we study sea urchin embryos, which use nodal to establish larval LR asymmetry as well. Cilia were found in the archenteron of embryos undergoing gastrulation. Expression of foxj1 and dnah9 suggested that archenteron cilia were motile. Cilia were polarized to the posterior pole of cells, a prerequisite of directed flow. High-speed videography revealed rotating cilia in the archenteron slightly before asymmetric nodal induction. Removal of cilia through brief high salt treatments resulted in aberrant patterns of nodal expression. Our data demonstrate that cilia - like in vertebrates - are required for asymmetric nodal induction in sea urchin embryos. Based on these results we argue that the anterior archenteron represents a bona fide LRO and propose that cilia-based symmetry breakage is a synapomorphy of the deuterostomes.

  4. A Robust Compressible Flow Solver for Studies on Solar Fuel Production in Microwave Plasma

    NASA Astrophysics Data System (ADS)

    Tadayon Mousavi, Samaneh; Koelman, Peter; Groen, Pieter Willem; van Dijk, Jan; Epg/ Applied Physics/ Eindhoven University Of Technology Team; Dutch InstituteFundamental Energy Research (Differ) Team

    2016-09-01

    n order to simulate the dissociation of CO2 with H2O admixture by microwave plasma for the production of solar fuels, we need a multicomponent solver that is able to capture the complex nature of the plasma by combining the chemistry, flow, and electromagnetic field. To achieve this goal, first we developed a robust finite volume compressible flow solver in C++. The solver is implemented in the framework of the PLASIMO software and will be used in complete plasma simulations later on. Due to the compressible nature of the solver, it can be used for simulation of dissociation of CO2 with H2O admixture by supersonic expansion in microwave plasmas. A spatially second order version of this solver is able to reveal the vortex flow structure of the plasmas. Capabilities of this solver are presented by benchmarking against well-established analytical and numerical test cases.

  5. 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.

  6. 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

  7. BMP2 is a positive regulator of Nodal signaling during left-right axis formation in the chicken embryo.

    PubMed

    Schlange, Thomas; Arnold, Hans-Henning; Brand, Thomas

    2002-07-01

    A model of left-right axis formation in the chick involves inhibition of bone morphogenetic proteins by the antagonist Car as a mechanism of upregulating Nodal in the left lateral plate mesoderm. By contrast, expression of CFC, a competence factor, which is absolutely required for Nodal signaling in the lateral plate mesoderm is dependent on a functional BMP signaling pathway. We have therefore investigated the relationship between BMP and Nodal in further detail. We implanted BMP2 and Noggin-expressing cells into the left lateral plate and paraxial mesoderm and observed a strong upregulation of Nodal and its target genes Pitx2 and Nkx3.2. In addition Cfc, the Nodal type II receptor ActrIIa and Snr were found to depend on BMP signaling for their expression. Comparison of the expression domains of Nodal, Bmp2, Car and Cfc revealed co-expression of Nodal, Cfc and Bmp2, while Car and Nodal only partially overlapped. Ectopic application of BMP2, Nodal, and Car as well as combinations of this signaling molecules to the right lateral plate mesoderm revealed that BMP2 and Car need to synergize in order to specify left identity. We propose a novel model of left-right axis formation, which involves BMP as a positive regulator of Nodal signaling in the chick embryo.

  8. Postmastectomy internal mammary nodal irradiation: a long-term outcome.

    PubMed

    Aleknavičius, Eduardas; Atkočius, Vydmantas; Kuzmickienė, Irena; Steponavičienė, Rita

    2014-01-01

    The internal mammary lymph nodes (IMN) have been recognized as a potential site of regional breast cancer spread. The aim of this study was to evaluate the impact of internal mammary node radiotherapy (RT) to on clinical outcomes in breast cancer patients treated with mastectomy and postoperative radiation therapy. This cohort study included 588 patients with breast cancers located in the central and medial quadrants. IMN RT was applied to 320 patients and 268 patients did not receive it IMN RT. Inside the IMN RT group, 165 patients received external beam IMN irradiation (IMN-EB). Mastectomy combined with using Californium-252 neutron source implantation was applied to 155 patients (IMN-BT). Cox proportional hazards modeling was used to determine the influence of IMN RT on clinical outcome. Age, tumor size, lymph nodal status, adjuvant radiotherapy, chemotherapy and hormonal therapy were assessed. IMN-EB resulted in a significant improvement of distant metastasis-free survival, breast cancer-specific survival and overall survival (P=0.033, P=0.037 and P=0.011, respectively). The IMN-EB radiotherapy has a significant impact on event-free survival (HR, 0.67; 95% CI, 0.46-0.91; P=0.043) and breast cancer-specific survival (HR, 0.64; 95% CI, 45-0.91; P=0.013) in patients with moderate-risk (stage T1-2N1). There was no association between IMN RT and clinical outcomes of patients with high-risk disease (stage T3-4N2-3) in any of the study end points. The effects of IMN-EB radiotherapy on event-free survival and breast cancer-specific survival were benefit for women with moderate-risk breast cancer. Copyright © 2014 Lithuanian University of Health Sciences. Production and hosting by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  9. Catheter Ablation of Atypical Atrioventricular Nodal Reentrant Tachycardia.

    PubMed

    Katritsis, Demosthenes G; Marine, Joseph E; Contreras, Fernando M; Fujii, Akira; Latchamsetty, Rakesh; Siontis, Konstantinos C; Katritsis, George D; Zografos, Theodoros; John, Roy M; Epstein, Lawrence M; Michaud, Gregory F; Anter, Elad; Sepahpour, Ali; Rowland, Edward; Buxton, Alfred E; Calkins, Hugh; Morady, Fred; Stevenson, William G; Josephson, Mark E

    2016-11-22

    Because of its low prevalence, data on atypical atrioventricular nodal reentrant tachycardia (AVNRT) are scarce, and the optimal ablation method has not been established. Our study aimed at assessing the efficacy and safety of conventional slow pathway ablation, as applied for typical cases, in atypical AVNRT. We studied 2079 patients with AVNRT subjected to slow pathway ablation. In 113 patients, mean age 48.5±18.1 years, 68 female, atypical AVNRT or coexistent atypical and typical AVNRT without other concomitant arrhythmia was diagnosed. Ablation data and outcomes were compared with a group of age- and sex-matched control patients with typical AVNRT. Fluoroscopy and radiofrequency current delivery times were not different in the atypical and typical groups, 20.3±12.2 versus 20.8±12.9 minutes (P=0.730) and 5.9±5.0 versus 5.5±4.5 minutes (P=0.650), respectively. Slow pathway ablation was accomplished from the right septum in 110 patients, and from the left septum in 3 patients, in the atypical group. There was no need for additional ablation lesions at other anatomic sites, and no cases of atrioventricular block were encountered. Recurrence rates of the arrhythmia were 5.6% in the atypical (6/108 patients) and 1.8% in the typical (2/111 patients) groups in the next 3 months following ablation (P=0.167). Conventional ablation at the anatomic area of the slow pathway is the therapy of choice for symptomatic AVNRT, regardless of whether the typical or atypical form is present. © 2016 American Heart Association, Inc.

  10. 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.

  11. 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.

  12. Evaluating Sparse Linear System Solvers on Scalable Parallel Architectures

    DTIC Science & Technology

    2008-10-01

    iterations will be necessary to assure sufficient accuracy whenever we do not use a direct method to solve (1.3) or (1.5). The overall SPIKE algorithm...boosting is activated, SPIKE is not used as a direct solver but rather as a preconditioner. In this case outer iterations via a Krylov subspace method ...robustness. Preconditioning aims to improve the robustness of iterative methods by transforming the system into M−1Ax = M−1f, or AM−1(Mx) = f. (3.2

  13. Algorithms for parallel flow solvers on message passing architectures

    NASA Technical Reports Server (NTRS)

    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

  14. 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.

  15. 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.

  16. 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.

  17. A Simple Quantum Integro-Differential Solver (SQuIDS)

    NASA Astrophysics Data System (ADS)

    Argüelles Delgado, Carlos A.; Salvado, Jordi; Weaver, Christopher N.

    2015-11-01

    Simple Quantum Integro-Differential Solver (SQuIDS) is a C++ code designed to solve semi-analytically the evolution of a set of density matrices and scalar functions. This is done efficiently by expressing all operators in an SU(N) basis. SQuIDS provides a base class from which users can derive new classes to include new non-trivial terms from the right hand sides of density matrix equations. The code was designed in the context of solving neutrino oscillation problems, but can be applied to any problem that involves solving the quantum evolution of a collection of particles with Hilbert space of dimension up to six.

  18. High Energy Boundary Conditions for a Cartesian Mesh Euler Solver

    NASA Technical Reports Server (NTRS)

    Pandya, Shishir A.; Murman, Scott M.; Aftosmis, Michael J.

    2004-01-01

    Inlets and exhaust nozzles are often omitted or fared over in aerodynamic simulations of aircraft due to the complexities involving in the modeling of engine details such as complex geometry and flow physics. However, the assumption is often improper as inlet or plume flows have a substantial effect on vehicle aerodynamics. A tool for specifying inlet and exhaust plume conditions through the use of high-energy boundary conditions in an established inviscid flow solver is presented. The effects of the plume on the flow fields near the inlet and plume are discussed.

  19. A Navier-Stokes solver for cascade flows

    NASA Technical Reports Server (NTRS)

    Arnone, A.; Swanson, R. C.

    1988-01-01

    A computer code for solving the Reynolds averaged full Navier-Stokes equations has been developed and applied using sheared H-type grids. The Baldwin-Lomax eddy-viscosity model is used for turbulence closure. The integration in time is based on an explicit four-stage Runge-Kutta scheme. Local time stepping, variable coefficient implicit residual smoothing, and a full multigrid method have been implemented to accelerate steady state calculations. Comparisons with experimental data show that the code is an accurate viscous solver and can give very good blade-to-blade predictions for engineering applications in less than 100 multigrid cycles on the finest mesh.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Numerical simulations, analytical expressions, and observations of apsidal and nodal superhumps

    NASA Astrophysics Data System (ADS)

    Montgomery-Bobertz, Michele Marie

    2004-10-01

    We use theory and numerical simulations, as constrained by observations, to better understand nodal and apsidal superhumps in Cataclysmic Variable (CV) systems. We verify the postulated tilted accretion disk theory by generating artificial light curves and associated Fourier transforms containing nodal and/or apsidal superhumps from numerical simulations of tilted accretion disks. We consider main sequence secondaries only. Apsidal superhumps are adequately described by dynamical motions of particles in a progradely precessing accretion disk due to a tidally perturbing secondary less the pressure effects due to the spiral arms. Nodal superhumps are numerically and kinematically described by the secondary tidally inducing a retrograde precession of a disk tilted out of the orbital plane ˜3° 10°. We suggest that disk tilt is neither caused by thermal instabilities nor tidal instabilities that induce apsidal precession. We find that the disk cannot remain tilted by a steady accretion rate typical of SU UMa's that strikes the inner disk. We find that the accretion disk tilt is a pattern that the disk and secondary pass through, and that the secondary maintains facing the minor axis of the elliptical accretion disk. We extend the mass ratio lower to q = 0.025 and the upper limit to q = 0.35 for apsidally precessing systems. We find no mass ratio limit on nodal precession in our simulations with an imposed disk tilt. Our analytical expressions and numerical simulations agree with observations, on average. For nodal precession, we apply the lunisolar precessional theory to CVs. The ratio of our analytical expressions and numerical simulations of apsidal to-nodal precessions is nearly 2:1, the same ratio found in observations and in the lunisolar precessional theory. We question whether V1159 Ori and ER UMa truly are nodally precessing systems. We suggest that TV Col has a non-main sequence secondary and that an extended campaign be conducted. We find that primary mass

  5. Systematic assembly homogenization and local flux reconstruction for nodal method calculations. Final report, January 1, 1990--September 30, 1992

    SciTech Connect

    Dorning, J.J.

    1993-05-01

    The report is divided into three parts. The main mathematical development of the new systematic simultaneous lattice-cell and fuel-assembly homogenization theory derived from the transport equation is summarized in Part I. Also included in Part I is the validation of this systematic homogenization theory and the resulting calculational procedures for coarse-mesh nodal diffusion methods that follow from it, in the form of their application to a simple one-dimensional test problem. The results of the application of this transport-equation-based systematic homogenization theory are summarized in Part II in which its superior accuracy over traditional flux and volume weighted homogenization procedures and over generalized equivalence theory is demonstrated for small and large practical two-dimensional PWR problems. The mathematical development of a second systematic homogenization theory -- this one derived starting from the diffusion equation -- is summarized in Part III where its application to a practical two-dimensional PWR model also is summarized and its superior accuracy over traditional homogenization methods and generalized equivalence theory is demonstrated for this problem.

  6. 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.

  7. On the implicit density based OpenFOAM solver for turbulent compressible flows

    NASA Astrophysics Data System (ADS)

    Fürst, Jiří

    The contribution deals with the development of coupled implicit density based solver for compressible flows in the framework of open source package OpenFOAM. However the standard distribution of OpenFOAM contains several ready-made segregated solvers for compressible flows, the performance of those solvers is rather week in the case of transonic flows. Therefore we extend the work of Shen [15] and we develop an implicit semi-coupled solver. The main flow field variables are updated using lower-upper symmetric Gauss-Seidel method (LU-SGS) whereas the turbulence model variables are updated using implicit Euler method.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. A Hybrid Stiff Solver for the Rayleigh-Plesset Equation

    NASA Astrophysics Data System (ADS)

    Alsayegh, Mutaz; Lee, Chung-Min

    2011-11-01

    We seek to apply efficient computational algorithms to investigate the locations of bubble concentrations in liquid flow. In flows with large velocities, bubbles tend to form in concentrated areas. Moreover, experiments show that bubbles formed at high velocities release large amount of energy once they collapse causing damage to equipment and objects that are in the path of the flow. To gain more insight on the formation of these bubbles, we will first study the dynamics of a single bubble and assume the bubble is a sphere. The dynamics of the bubble in terms of its radius and the driven pressure is modeled by the Rayleigh-Plesset (RP) equation. The RP equation is a second order nonlinear stiff ordinary differential equation (ode) and theoretically, its solution can be obtained numerically using Finite Difference (FD) methods. However, under large pressure variations, the rate of change of the bubble's radius approaches infinity when the bubble is collapsing. Explicit numerical integration methods require time steps of magnitude of (10-12 s) to achieve stable solutions. Iterations under this time scale are highly impractical and require immense CPU time. Therefore, a stiff ode solver is needed to alleviate the computation cost. Therefore, we would like to devise a hybrid algorithm that automatically selects between an explicit method and the stiff ode solver. Once we have a robust implementation, we will use it to process the data and analyze the relations between bubble locations and flow structures.

  13. 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.

  14. Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum.

    PubMed

    Joshi, Dinesh C; Singh, Vijaya; Hunt, Colleen; Mace, Emma; van Oosterom, Erik; Sulman, Richard; Jordan, David; Hammer, Graeme

    2017-01-01

    In sorghum, the growth angle of nodal roots is a major component of root system architecture. It strongly influences the spatial distribution of roots of mature plants in the soil profile, which can impact drought adaptation. However, selection for nodal root angle in sorghum breeding programs has been restricted by the absence of a suitable high throughput phenotyping platform. The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage. The phenotyping platform comprises of 500 soil filled root chambers (50 × 45 × 0.3 cm in size), made of transparent perspex sheets that were placed in metal tubs and covered with polycarbonate sheets. Around 3 weeks after sowing, once the first flush of nodal roots was visible, roots were imaged in situ using an imaging box that included two digital cameras that were remotely controlled by two android tablets. Free software (openGelPhoto.tcl) allowed precise measurement of nodal root angle from the digital images. The reliability and efficiency of the platform was evaluated by screening a large nested association mapping population of sorghum and a set of hybrids in six independent experimental runs that included up to 500 plants each. The platform revealed extensive genetic variation and high heritability (repeatability) for nodal root angle. High genetic correlations and consistent ranking of genotypes across experimental runs confirmed the reproducibility of the platform. This low cost, high throughput root phenotyping platform requires no sophisticated equipment, is adaptable to most glasshouse environments and is well suited to dissect the genetic control of nodal root angle of sorghum. The platform is suitable for use in sorghum breeding programs aiming to improve drought adaptation through root system architecture manipulation.

  15. Utility of SUVmax on (18) F-FDG PET in detecting cervical nodal metastases.

    PubMed

    Lim, Rebecca S M; Ramdave, Shakher; Beech, Paul; Billah, Baki; Karim, Md Nazmul; Smith, Julian A; Safdar, Adnan; Sigston, Elizabeth

    2016-11-08

    The presence of cervical lymph node metastasis is an important prognostic factor for patients with head and neck squamous cell carcinomas (HNSCC). Accurate assessment of lymph node metastasis in these patients is essential for appropriate prognostic and management purposes. Here, we evaluated the effectiveness of the maximum standardized uptake value (SUVmax) on positron emission tomography (PET) in assessing lymph node metastasis in HNSCC prior to surgery. A retrospective review of 74 patients with HNSCC who underwent PET/CT prior to neck dissection were examined. Pre-operative PET/CT scans were reviewed by two experienced nuclear medicine physicians and SUVmax of the largest node in each nodal basin documented. These were compared with the histology results of the neck dissection. A total of 359 nodal basins including 86 basins with metastatic nodes were evaluated. A nodal SUVmax ≥3.16 yielded a sensitivity of 74.4 % and specificity of 84.9 % in detecting metastatic nodes. The nodal SUVmax/Liver SUVmax ratio was found on receiver operating characteristic (ROC) to be effective in detecting metastatic nodes with an area under ROC curve of 0.90. A nodal SUVmax/Liver SUVmax ratio ≥0.90 yielded a sensitivity of 74.1 % and specificity of 93.4 %. By comparison, visual inspection yielded sensitivities of 66.3 and 61.6 % in observers 1 and 2 respectively. The corresponding specificities were 77.7 and 86.5 %. Nodal SUVmax and nodal SUVmax/liver SUVmax are both useful in the pre-operative detection of metastatic nodes with the latter being superior to visual inspection. The ratio is likely to be more useful as it corrects for inter-scanner variability.

  16. Extra-nodal extension is a significant prognostic factor in lymph node positive breast cancer

    PubMed Central

    Aziz, Sura; Wik, Elisabeth; Davidsen, Benedicte; Aas, Hans; Aas, Turid; Akslen, Lars A.

    2017-01-01

    Presence of lymph node (LN) metastasis is a strong prognostic factor in breast cancer, whereas the importance of extra-nodal extension and other nodal tumor features have not yet been fully recognized. Here, we examined microscopic features of lymph node metastases and their prognostic value in a population-based cohort of node positive breast cancer (n = 218), as part of the prospective Norwegian Breast Cancer Screening Program NBCSP (1996–2009). Sections were reviewed for the largest metastatic tumor diameter (TD-MET), nodal afferent and efferent vascular invasion (AVI and EVI), extra-nodal extension (ENE), number of ENE foci, as well as circumferential (CD-ENE) and perpendicular (PD-ENE) diameter of extra-nodal growth. Number of positive lymph nodes, EVI, and PD-ENE were significantly increased with larger primary tumor (PT) diameter. Univariate survival analysis showed that several features of nodal metastases were associated with disease-free (DFS) or breast cancer specific survival (BCSS). Multivariate analysis demonstrated an independent prognostic value of PD-ENE (with 3 mm as cut-off value) in predicting DFS and BCSS, along with number of positive nodes and histologic grade of the primary tumor (for DFS: P = 0.01, P = 0.02, P = 0.01, respectively; for BCSS: P = 0.02, P = 0.008, P = 0.02, respectively). To conclude, the extent of ENE by its perpendicular diameter was independently prognostic and should be considered in line with nodal tumor burden in treatment decisions of node positive breast cancer. PMID:28199370

  17. A case of primary adrenal diffuse large B-cell lymphoma in HIV.

    PubMed

    Malik, Seema; Chapman, Cordelia B-P; Drew, Olivia

    2016-07-01

    Primary adrenal diffuse large B-cell lymphoma in HIV is a very rare, highly aggressive extra-nodal lymphoma. There is only one previous case reported in the literature. Our patient presented with isolated bilateral adrenal masses with no lymphadenopathy or visceral involvement, which made the diagnosis challenging. © The Author(s) 2015.

  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. 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.

  20. Heavy fermions: From nodal metals to super-spins

    NASA Astrophysics Data System (ADS)

    Ramires Neves de Oliveira, Aline

    Condensed matter physics is an area of research which lies at a sweet spot between two complementary perspectives: the atomistic point of view which takes into account all the details of the system of interest; and the framework of universality and emergent phenomena, which allows us to make drastic simplifications to the microscopic description of materials while still being able to explain much of the experimentally observed phenomena. This thesis addresses problems from both perspectives, focusing on heavy fermion systems. Heavy fermion systems are prototype materials for the study of strongly correlations and quantum criticality. Theoretical understanding of these systems is important for the design of new materials and for the fundamental understanding of quantum critical phenomena. This thesis is strongly motivated by recent experiments in an intrinsically quantum critical material, beta-YbAlB 4. This system shows anomalous critical exponents in transport and thermodynamics. In Chapter 2 we construct a phenomenological theory for the heavy fermion metal beta-YbAlB4 based on the Anderson model, taking into account the peculiarities of this specific material. We analyze the consequences of a non-trivial, momentum-dependent, hybridization matrix between f-electrons and conduction electrons, which gives rise to a nodal metal with unusual dispersion and singular thermodynamic properties, in accordance with experiments. In Chapter 3 we analyze the Electron Spin Resonance experiments in this same material and propose a theory including spin-orbit coupling, crystal electric fields and hyperfine coupling which can account for many of the features of the experimentally observed signal. Within a broader perspective on heavy fermion systems, the absence of a single unified theoretical description which can account for the plethora of phenomena observed in this class of materials also motivates us to consider new theoretical approaches. In Chapter 4 we generalize the

  1. 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

  2. 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.

  3. Plasmapause diffusion

    NASA Technical Reports Server (NTRS)

    Horwitz, J. L.

    1983-01-01

    The Bohm diffusion coefficient and observed electrostatic wave scattering are used as the bases of estimates of the smoothing effect that diffusion may have on steep plasmapause density gradients. The estimate for diffusion resulting from scattering by observed electrostatic waves is found to be much lower than that of the perpendicular Bohm diffusion coefficient for characteristic plasma temperatures and magnetic fields. This diffusion rate estimate may be too small, however, if the wave amplitudes are significantly higher for steep plasmapauses. The effects are therefore negligible for most considerations of macroscopic plasmapause dynamics, but may be significant in limiting drift wave instabilities and similar phenomena driven by the steepness of the plasmapause density gradient.

  4. Nodal signaling activates the Smad2/3 pathway to regulate stem cell-like properties in breast cancer cells

    PubMed Central

    Gong, Wenchen; Sun, Baocun; Sun, Huizhi; Zhao, Xiulan; Zhang, Danfang; Liu, Tieju; Zhao, Nan; Gu, Qiang; Dong, Xueyi; Liu, Fang

    2017-01-01

    Nodal signaling plays several vital roles in the embryogenesis process. However, its reexpression in breast cancer is correlated with cancer progression, metastasis and poor prognosis. Recently, Nodal has also been reported to regulate self-renewal capacity in pancreatic cancer. This study aimed to explore the role of Nodal in breast cancer stem cells (BCSCs) and the underlying mechanisms. Therefore, the immunohistochemistry staining of Nodal in 135 human breast cancer cases was performed to analyzed the relationship of Nodal signaling, clinical outcomes and BCSC marker. And the results showed that high Nodal expression was positively correlated with poor prognosis and BCSC marker expression in breast cancer samples. We further assessed the effects of Nodal in regulating the BCSC properties in breast cancer cell lines and xenografts. Then, SB431542 was administered in vitro and in vivo to explore the function of the Smad2/3 pathway. And we demonstrated that Nodal signaling up-regulated the expression of ALDH1, CD44, CD133, Sox2, Oct4 and Nanog by activating the Smad2/3 pathway, thereby enhancing the tumorigenicity and sphere-forming ability of breast cancer cells. Furthermore, treatment with SB431542 could inhibit the properties of BCSCs in vitro and in vivo. In conclusion, these findings indicate that Nodal signaling may play a vital role in maintaining the BCSC phenotype in breast cancer and serve as a potential target to explore BCSC-specific therapies. PMID:28401007

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

    DOE PAGES

    Bian, Guang; Chang, Tay-Rong; Sankar, Raman; ...

    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

  6. The impact of surgical technique on neck dissection nodal yield: making a difference.

    PubMed

    Lörincz, Balazs B; Langwieder, Felix; Möckelmann, Nikolaus; Sehner, Susanne; Knecht, Rainald

    2016-05-01

    The nodal yield of neck dissections is an independent prognostic factor in several types of head and neck cancer. The authors aimed to determine whether the applied dissection technique has a significant impact on nodal yield. This is a single-institution, prospective study with internal control group (level of evidence: 2A). Data of 150 patients undergoing 223 neck dissections between February 2011 and March 2013 have been collected in a comprehensive cancer centre. Eighty-two patients underwent neck dissection with unwrapping the cervical fascia from lateral to medial, while 68 patients were operated without specifically unwrapping the fascia, in a caudal to cranial fashion. The standardised, horizontal neck dissection technique along the fascial planes resulted in a significantly higher nodal count in Levels I, II, III and IV, as well as in terms of overall nodal yield (mean: n = 22.53) than that of the vertical dissection applied in the control group (mean: n = 15.00). This is the first publication showing a direct correlation between neck dissection nodal yield and surgical technique. Therefore, it is paramount to optimise the applied surgical concept to maximise the oncological benefit.

  7. Interplay between short-range correlated disorder and Coulomb interaction in nodal-line semimetals

    NASA Astrophysics Data System (ADS)

    Wang, Yuxuan; Nandkishore, Rahul M.

    2017-09-01

    In nodal-line semimetals, Coulomb interactions and short-range correlated disorder are both marginal perturbations to the clean noninteracting Hamiltonian. We analyze their interplay using a weak-coupling renormalization group approach. In the clean case, the Coulomb interaction has been found to be marginally irrelevant, leading to Fermi liquid behavior. We extend the analysis to incorporate the effects of disorder. The nodal line structure gives rise to kinematical constraints similar to that for a two-dimensional Fermi surface, which plays a crucial role in the one-loop renormalization of the disorder couplings. For a twofold degenerate nodal loop (Weyl loop), we show that disorder flows to strong coupling along a unique fixed trajectory in the space of symmetry inequivalent disorder couplings. Along this fixed trajectory, all symmetry inequivalent disorder strengths become equal. For a fourfold degenerate nodal loop (Dirac loop), disorder also flows to strong coupling, however, the strengths of symmetry inequivalent disorder couplings remain different. We show that feedback from disorder reverses the sign of the beta function for the Coulomb interaction, causing the Coulomb interaction to flow to strong coupling as well. However, the Coulomb interaction flows to strong coupling asymptotically more slowly than disorder. Extrapolating our results to strong coupling, we conjecture that at low energies nodal line semimetals should be described by a noninteracting nonlinear sigma model. We discuss the relation of our results with possible many-body localization at zero temperatures in such materials.

  8. The distance between breast cancer and the skin is associated with axillary nodal metastasis.

    PubMed

    Eom, Yong Hwa; Kim, Eun Jin; Chae, Byung Joo; Song, Byung Joo; Jung, Sang Seol

    2015-06-01

    More superficially located tumors may be more likely than deeper tumors to metastasize to the axillary nodes via the lymphatics. The aim of this study was to determine whether breast cancer distance from the skin affects axillary node metastasis, ipsilateral breast cancer recurrence, or recurrence-free survival. A total of 1,005 consecutive patients with breast cancer who underwent surgery between January 2003 and December 2009 were selected. The distance of the tumor from the skin was measured from the skin to the most anterior hypoechoic leading edge of the lesion. In total, 603 (68%) patients had no axillary nodal metastasis, and 288 (32%) had axillary nodal metastasis. A breast cancer distance from the skin <3 mm induced more axillary nodal metastasis (P = 0.039). However, no significant correlation was observed between breast cancer distance from the skin <3 mm and ipsilateral breast cancer recurrence (P = 0.788) or recurrence-free survival (P = 0.353). Breast cancers located closer to the skin had a higher incidence of axillary nodal metastasis. Therefore, tumor distance from the skin should be considered when evaluating a patient with breast cancer and considering the risk of nodal metastasis. © 2015 Wiley Periodicals, Inc.

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

    SciTech Connect

    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

    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 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.

  10. 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

  11. Role of Nodal-PITX2C signaling pathway in glucose-induced cardiomyocyte hypertrophy.

    PubMed

    Su, Dongmei; Jing, Sun; Guan, Lina; Li, Qian; Zhang, Huiling; Gao, Xiaobo; Ma, Xu

    2014-06-01

    Pathological cardiac hypertrophy is a major cause of morbidity and mortality in cardiovascular disease. Recent studies have shown that cardiomyocytes, in response to high glucose (HG) stimuli, undergo hypertrophic growth. While much work still needs to be done to elucidate this important mechanism of hypertrophy, previous works have showed that some pathways or genes play important roles in hypertrophy. In this study, we showed that sublethal concentrations of glucose (25 mmol/L) could induce cardiomyocyte hypertrophy with an increase in the cellular surface area and the upregulation of the atrial natriuretic peptide (ANP) gene, a hypertrophic marker. High glucose (HG) treatments resulted in the upregulation of the Nodal gene, which is under-expressed in cardiomyocytes. We also determined that the knockdown of the Nodal gene resisted HG-induced cardiomyocyte hypertrophy. The overexpression of Nodal was able to induce hypertrophy in cardiomyocytes, which was associated with the upregulation of the PITX2C gene. We also showed that increases in the PITX2C expression, in response to Nodal, were mediated by the Smad4 signaling pathway. This study is highly relevant to the understanding of the effects of the Nodal-PITX2C pathway on HG-induced cardiomyocyte hypertrophy, as well as the related molecular mechanisms.

  12. Wing tip vortex calculations with an unstructured adaptive-grid Euler solver

    NASA Technical Reports Server (NTRS)

    Strawn, Roger C.

    1991-01-01

    A solution-adaptive grid method has been developed for computing tip-vortex flowfields around rectangular wings. This method uses subdivision in order to locally refine the grid in regions with high vorticity. Two different flow solvers are used. Each solves the three-dimensional Euler equations on unstructured grids. Computed results are compared to experimentally measured surface pressures and vortex velocities on a NACA 0015 rectangular wing. Predicted results for surface pressures and integrated lift agree well with the experimental data. The predicted size of the rotational vortex core is larger than the experimentally-measured value and the peak velocities are less. This discrepancy appears to be caused by deficiencies in the inviscid Euler-equation model. This model cannot capture the complex viscous effects at the tip that determine the detailed structure of the resulting vortex. In spite of this limitation, the present Euler unstructured adaptive-grid method demonstrates the ability to convert vortical flows with low numerical diffusion. Applications for modeling helicopter rotor wake systems are discussed.

  13. Wing tip vortex calculations with an unstructured adaptive-grid Euler solver

    NASA Technical Reports Server (NTRS)

    Strawn, Roger C.

    1991-01-01

    A solution-adaptive grid method has been developed for computing tip-vortex flowfields around rectangular wings. This method uses subdivision in order to locally refine the grid in regions with high vorticity. Two different flow solvers are used. Each solves the three-dimensional Euler equations on unstructured grids. Computed results are compared to experimentally measured surface pressures and vortex velocities on a NACA 0015 rectangular wing. Predicted results for surface pressures and integrated lift agree well with the experimental data. The predicted size of the rotational vortex core is larger than the experimentally-measured value and the peak velocities are less. This discrepancy appears to be caused by deficiencies in the inviscid Euler-equation model. This model cannot capture the complex viscous effects at the tip that determine the detailed structure of the resulting vortex. In spite of this limitation, the present Euler unstructured adaptive-grid method demonstrates the ability to convert vortical flows with low numerical diffusion. Applications for modeling helicopter rotor wake systems are discussed.

  14. 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.

  15. Diffusion of Ions in Myelinated Nerve Fibers

    PubMed Central

    Palti, Y.; Gold, R.; Stämpfli, R.

    1979-01-01

    The diffusion of ions towards or away from the inner side of the nodal membrane in preparations, the cut ends of which are placed in various media, was investigated. The ion concentration changes were calculated by numerical solution of the unidimensional electrodiffusion equation under a variety of media compositions, axoplasmic diffusion coefficients, and internal anionic compositions. The potassium and cesium ion diffusion along the axon towards the node was determined experimentally by two different electrophysiological methods. On the basis of comparison between the experimental data and the computational predictions the axoplasmic potassium ion diffusion coefficient was determined to be almost equal to that in free aqueous solution, while that of cesium ion was close to one half of that in aqueous solution. Utilizing the values of diffusion parameters thus determined, we solved the electrodiffusion equation for a number of common experimental procedures. We found that in short fibers, cut 0.1-0.2 cm at each side of the node, the concentration approached values close to the new steady-state values within 5-30 min. In long fibers (over 1 cm long) steady-state concentrations were obtained only after a few hours. Under some conditions the internal concentrations transiently overshot the steady-state values. The diffusion potentials generated in the system were also evaluated. The ion concentration changes and generation of diffusion potential cannot be prevented by using side pools with cation content identical to that of the axoplasm. PMID:318061

  16. Fatty Acid Synthase and Acetyl-CoA Carboxylase Are Expressed in Nodal Metastatic Melanoma But Not in Benign Intracapsular Nodal Nevi.

    PubMed

    Saab, Jad; Santos-Zabala, Maria Laureana; Loda, Massimo; Stack, Edward C; Hollmann, Travis J

    2017-06-13

    Melanoma is a potentially lethal form of skin cancer for which the current standard therapy is complete surgical removal of the primary tumor followed by sentinel lymph node biopsy when indicated. Histologic identification of metastatic melanoma in a sentinel node has significant prognostic and therapeutic implications, routinely guiding further surgical management with regional lymphadenectomy. While melanocytes in a lymph node can be identified by routine histopathologic and immunohistochemical examination, the distinction between nodal nevus cells and melanoma can be morphologically problematic. Previous studies have shown that malignant melanoma can over-express metabolic genes such as fatty acid synthase (FASN) and acetyl-CoA carboxylase (ACC). This immunohistochemical study aims to compare the utility of FASN and ACC in differentiating sentinel lymph nodes with metastatic melanomas from those with benign nodal nevi in patients with cutaneous melanoma. Using antibodies against FASN and ACC, 13 sentinel lymph nodes from 13 patients with metastatic melanoma and 14 lymph nodes harboring benign intracapsular nevi from 14 patients with cutaneous malignant melanoma were examined. A diagnosis of nodal melanoma was based on cytologic atypia and histologic comparison with the primary melanoma. All nodal nevi were intracapsular and not trabecular. Immunohistochemistry for Melan-A, S100, human melanoma black 45 (HMB45), FASN, and ACC were performed. The percentage of melanocytes staining with HMB45, FASN, and ACC was determined and graded in 25% increments; staining intensity was graded as weak, moderate, or strong. All metastatic melanomas tested had at least 25% tumor cell staining for both FASN and ACC. Greater than 75% of the tumor cells stained with FAS in 7/13 cases and for ACC in 5/12 cases. Intensity of staining was variable; strong staining for FASN and ACC was observed in 69% and 50% of metastatic melanoma, respectively. HMB45 was negative in 40% of nodal

  17. Evaluation of linear solvers for oil reservoir simulation problems. Part 2: The fully implicit case

    SciTech Connect

    Joubert, W.; Janardhan, R.

    1997-12-01

    A previous paper [Joubert/Biswas 1997] contained investigations of linear solver performance for matrices arising from Amoco`s Falcon parallel oil reservoir simulation code using the IMPES formulation (implicit pressure, explicit saturation). In this companion paper, similar issues are explored for linear solvers applied to matrices arising from more difficult fully implicit problems. The results of numerical experiments are given.

  18. 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.

  19. A Newton-Krylov solver for fast spin-up of online ocean tracers

    NASA Astrophysics Data System (ADS)

    Lindsay, Keith

    2017-01-01

    We present a Newton-Krylov based solver to efficiently spin up tracers in an online ocean model. We demonstrate that the solver converges, that tracer simulations initialized with the solution from the solver have small drift, and that the solver takes orders of magnitude less computational time than the brute force spin-up approach. To demonstrate the application of the solver, we use it to efficiently spin up the tracer ideal age with respect to the circulation from different time intervals in a long physics run. We then evaluate how the spun-up ideal age tracer depends on the duration of the physics run, i.e., on how equilibrated the circulation is.

  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. Experimental validation of a coupled neutron-photon inverse radiation transport solver

    NASA Astrophysics Data System (ADS)

    Mattingly, John; Mitchell, Dean J.; Harding, Lee T.

    2011-10-01

    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 α-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.

  2. A finite element Poisson solver for gyrokinetic particle simulations in a global field aligned mesh

    SciTech Connect

    Nishimura, Y. . E-mail: nishimuy@uci.edu; Lin, Z.; Lewandowski, J.L.V.; Ethier, S.

    2006-05-20

    A new finite element Poisson solver is developed and applied to a global gyrokinetic toroidal code (GTC) which employs the field aligned mesh and thus a logically non-rectangular grid in a general geometry. Employing test cases where the analytical solutions are known, the finite element solver has been verified. The CPU time scaling versus the matrix size employing portable, extensible toolkit for scientific computation (PETSc) to solve the sparse matrix is promising. Taking the ion temperature gradient modes (ITG) as an example, the solution from the new finite element solver has been compared to the solution from the original GTC's iterative solver which is only efficient for adiabatic electrons. Linear and nonlinear simulation results from the two different forms of the gyrokinetic Poisson equation (integral form and the differential form) coincide each other. The new finite element solver enables the implementation of advanced kinetic electron models for global electromagnetic simulations.

  3. 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.

  4. 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.

  5. Polyurethanes: versatile materials and sustainable problem solvers for today's challenges.

    PubMed

    Engels, Hans-Wilhelm; Pirkl, Hans-Georg; Albers, Reinhard; Albach, Rolf W; Krause, Jens; Hoffmann, Andreas; Casselmann, Holger; Dormish, Jeff

    2013-09-02

    Polyurethanes are the only class of polymers that display thermoplastic, elastomeric, and thermoset behavior depending on their chemical and morphological makeup. In addition to compact polyurethanes, foamed variations in particular are very widespread, and they achieve their targeted properties at very low weights. The simple production of sandwich structures and material composites in a single processing step is a key advantage of polyurethane technology. The requirement of energy and resource efficiency increasingly demands lightweight structures. Polyurethanes can serve this requirement by acting as matrix materials or as flexible adhesives for composites. Polyurethanes are indispensable when it comes to high-quality decorative coatings or maintaining the value of numerous objects. They are extremely adaptable and sustainable problem solvers for today's challenges facing our society, all of which impose special demands on materials.

  6. 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

  7. Status Of The UPS Space-Marching Flow Solver

    NASA Technical Reports Server (NTRS)

    Lawerence, Scott L.; VanDalsem, William (Technical Monitor)

    1995-01-01

    The status of the three-dimensional parabolized Navier-Stokes solver UPS is described. The UPS code, initiated at NASA Ames Research Center in 1986, continues to develop and evolve through application to supersonic and hypersonic flow fields. Hypersonic applications have motivated enhancement of the physical modeling capabilities of the code, specifically real gas modeling, boundary conditions, and turbulence and transition modeling. The UPS code has also been modified to enhance robustness and efficiency in order to be practically used in concert with an optimization code for supersonic transport design. These developments are briefly described along with some relevant results for generic test problems obtained during verification of the enhancements. Included developments and results have previously been published and widely disseminated domestically.

  8. 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.

  9. 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.

  10. Performance evaluation of a parallel sparse lattice Boltzmann solver

    SciTech Connect

    Axner, L. Bernsdorf, J. Zeiser, T. Lammers, P. Linxweiler, J. Hoekstra, A.G.

    2008-05-01

    We develop a performance prediction model for a parallelized sparse lattice Boltzmann solver and present performance results for simulations of flow in a variety of complex geometries. A special focus is on partitioning and memory/load balancing strategy for geometries with a high solid fraction and/or complex topology such as porous media, fissured rocks and geometries from medical applications. The topology of the lattice nodes representing the fluid fraction of the computational domain is mapped on a graph. Graph decomposition is performed with both multilevel recursive-bisection and multilevel k-way schemes based on modified Kernighan-Lin and Fiduccia-Mattheyses partitioning algorithms. Performance results and optimization strategies are presented for a variety of platforms, showing a parallel efficiency of almost 80% for the largest problem size. A good agreement between the performance model and experimental results is demonstrated.

  11. 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.

  12. Large-scale linear nonparallel support vector machine solver.

    PubMed

    Tian, Yingjie; Ping, Yuan

    2014-02-01

    Twin support vector machines (TWSVMs), as the representative nonparallel hyperplane classifiers, have shown the effectiveness over standard SVMs from some aspects. However, they still have some serious defects restricting their further study and real applications: (1) They have to compute and store the inverse matrices before training, it is intractable for many applications where data appear with a huge number of instances as well as features; (2) TWSVMs lost the sparseness by using a quadratic loss function making the proximal hyperplane close enough to the class itself. This paper proposes a Sparse Linear Nonparallel Support Vector Machine, termed as L1-NPSVM, to deal with large-scale data based on an efficient solver-dual coordinate descent (DCD) method. Both theoretical analysis and experiments indicate that our method is not only suitable for large scale problems, but also performs as good as TWSVMs and SVMs.

  13. A Coupled Finite Volume Solver for Incompressible Flows

    NASA Astrophysics Data System (ADS)

    Moukalled, F.; Darwish, M.

    2008-09-01

    This paper reports on a pressure-based coupled algorithm for the solution of laminar incompressible flow problems. The implicit pressure-velocity coupling is accomplished by deriving a pressure equation in a way similar to a segregated SIMPLE algorithm with the extended set of equations solved simultaneously and having diagonally dominant coefficients. The superiority of the coupled approach over the segregated approach is demonstrated by solving the lid-driven flow in a square cavity problem using both methodologies and comparing their computational costs. Results indicate that the number of iterations needed by the coupled solver is grid independent. Moreover, recorded CPU time values reveal that the coupled approach substantially reduces the computational cost with the reduction rate for the problem solved increasing as the grid size increases and reaching a value as high as 115.

  14. 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

  15. Progress in developing Poisson-Boltzmann equation solvers.

    PubMed

    Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil

    2013-03-01

    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.

  16. Performance evaluation of a parallel sparse lattice Boltzmann solver

    NASA Astrophysics Data System (ADS)

    Axner, L.; Bernsdorf, J.; Zeiser, T.; Lammers, P.; Linxweiler, J.; Hoekstra, A. G.

    2008-05-01

    We develop a performance prediction model for a parallelized sparse lattice Boltzmann solver and present performance results for simulations of flow in a variety of complex geometries. A special focus is on partitioning and memory/load balancing strategy for geometries with a high solid fraction and/or complex topology such as porous media, fissured rocks and geometries from medical applications. The topology of the lattice nodes representing the fluid fraction of the computational domain is mapped on a graph. Graph decomposition is performed with both multilevel recursive-bisection and multilevel k-way schemes based on modified Kernighan-Lin and Fiduccia-Mattheyses partitioning algorithms. Performance results and optimization strategies are presented for a variety of platforms, showing a parallel efficiency of almost 80% for the largest problem size. A good agreement between the performance model and experimental results is demonstrated.

  17. 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.

  18. 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.

  19. 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.

  20. Accurate derivative evaluation for any Grad–Shafranov solver

    SciTech Connect

    Ricketson, L.F.; Cerfon, A.J.; Rachh, M.; Freidberg, J.P.

    2016-01-15

    We present a numerical scheme that can be combined with any fixed boundary finite element based Poisson or Grad–Shafranov solver to compute the first and second partial derivatives of the solution to these equations with the same order of convergence as the solution itself. At the heart of our scheme is an efficient and accurate computation of the Dirichlet to Neumann map through the evaluation of a singular volume integral and the solution to a Fredholm integral equation of the second kind. Our numerical method is particularly useful for magnetic confinement fusion simulations, since it allows the evaluation of quantities such as the magnetic field, the parallel current density and the magnetic curvature with much higher accuracy than has been previously feasible on the affordable coarse grids that are usually implemented.

  1. Autoantibody responses to nodal and paranodal antigens in chronic inflammatory neuropathies.

    PubMed

    Mathey, E K; Garg, N; Park, S B; Nguyen, T; Baker, S; Yuki, N; Yiannikas, C; Lin, C S; Spies, J M; Ghaoui, R; Barnett, M H; Vucic, S; Pollard, J D; Kiernan, M C

    2017-08-15

    Autoantibodies to nodal/paranodal proteins have been reported in patients with chronic inflammatory demyelinating polyneuropathy (CIDP) and multifocal motor neuropathy (MMN). To determine the frequency of anti-paranodal antibodies in our cohort of CIDP patients and to validate the presence anti-nodal antibodies in MMN, sera were screened for IgG against human neurofascin 155, contactin-1, neurofascin 186 and gliomedin using ELISA. In CIDP patients, 7% were anti-NF155 IgG4 positive and 7% were anti-CNTN1 IgG4 positive. Positive results were confirmed using cell based assays and indirect immunofluorescence on teased nerve fibres. We did not detect IgG autoantibodies against these nodal/paranodal antigens in MMN patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. The role of nodal and internodal responses in gravitropism and autotropism in Galium aparine L

    NASA Technical Reports Server (NTRS)

    Heathcote, D. G.; Brown, A. H. (Principal Investigator)

    1987-01-01

    This time course and location of gravitropically induced curvatures in stems of goosegrass (Gallium aparine L.), a member of the Rubiaceae, have been investigated. In the early stages of the response (0-5 h), curvature develops throughout the growing region, and is followed by an autotropic straightening which affects the internodes only, leading to the production of essentially straight internodes some 15 h after the onset of gravistimulation. Curvatures developing in the nodal regions, however, continue to increase over this period, and are not subject to reversal by autotropism. The nodal curvatures are not entirely dependent on the presence of any other part of the plant, since marked curvatures can be induced in isolated nodal segments. This pattern of response leads ultimately to correction of the growth direction of the plant by means of curvature responses confined exclusively to the nodes, despite the initial participation of both nodes and internodes in the gravitropic reaction.

  3. Potential for Infra-Nodal Heart Block and Cardiogenic Shock With Propofol Administration

    PubMed Central

    Olson, Nicholas; Lim, Michael J.; Ferreira, Scott W.; Mehdirad, Ali A.

    2013-01-01

    We report a case of infra-nodal complete heart block and cardiogenic shock in a previously healthy 64-year-old man after administration of 180 mg of intravenous Propofol. Although bradycardia, hypotension, and heart block are commonly seen with propofol administration, such findings are transient and respond quickly to administration of vagolytic or sympathomimetic agents suggesting an AV nodal mechanism of heart block. Sustained left ventricular systolic dysfunction and cardiogenic shock by an alternative, non-autonomic mechanism has also been described in the setting of Propofol administration. Our case is the first to note sustained complete infra-nodal heart block in this setting. Early recognition of such a complication, restoration of atrio-ventricular (A-V) synchrony with dual chamber pacing, and aggressive circulatory support is essential in bridging such patients to recovery.

  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. Topological nodal line semimetals in the CaP3 family of materials

    NASA Astrophysics Data System (ADS)

    Xu, Qiunan; Yu, Rui; Fang, Zhong; Dai, Xi; Weng, Hongming

    2017-01-01

    By using first-principles calculations and a k .p model analysis, we propose that the three-dimensional topological nodal line semimetal state can be realized in the CaP3 family of materials, which includes CaP3,CaAs3,SrP3,SrAs3, and BaAs3, when spin-orbit coupling (SOC) is ignored. The closed topological nodal line near the Fermi energy is protected by time reversal symmetry and spatial inversion symmetry. Moreover, drumheadlike two-dimensional surface states are also obtained on the c -direction surface of these materials. When SOC is included, the gaps open along the nodal line and these materials become strong topological insulators with Z2 indices as (1 ;010 ) .

  6. Doping-Dependent Nodal Fermi Velocity in Bi-2212 Revealed by High-Resolution ARPES

    SciTech Connect

    Vishik, I. M.

    2011-08-19

    The improved resolution of laser-based angle-resolved photoemission spectroscopy (ARPES) allows reliable access to fine structures in the spectrum. We present a systematic, doping-dependent study of a recently discovered low-energy kink in the nodal dispersion of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} (Bi-2212), which demonstrates the ubiquity and robustness of this kink in underdoped Bi-2212. The renormalization of the nodal velocity due to this kink becomes stronger with underdoping, revealing that the nodal Fermi velocity is non-universal, in contrast to assumed phenomenology. This is used together with laser-ARPES measurements of the gap velocity, v{sub 2}, to resolve discrepancies with thermal conductivity measurements.

  7. Single Nodal Loop of Accidental Degeneracies in Minimal Symmetry: Triclinic CaAs3

    NASA Astrophysics Data System (ADS)

    Quan, Y.; Yin, Z. P.; Pickett, W. E.

    2017-04-01

    The existence of closed loops of degeneracies in crystals has been intimately connected with associated crystal symmetries, raising the following question: What is the minimum symmetry required for topological character, and can one find an example? Triclinic CaAs3 , in the space group P 1 ¯ with only a center of inversion, has been found to display, without need for tuning, a nodal loop of accidental degeneracies with topological character, centered on one face of the Brillouin zone that is otherwise fully gapped. The small loop is very flat in energy, yet is cut four times by the Fermi energy, a condition that results in an intricate repeated touching of inversion related pairs of Fermi surfaces at Weyl points. Spin-orbit coupling lifts the fourfold degeneracy along the loop, leaving trivial Kramers pairs. With its single nodal loop that emerges without protection from any point group symmetry, CaAs3 represents the primal "hydrogen atom" of nodal loop systems.

  8. RW Per - Nodal motion changes its amplitude by 1.4 mag

    NASA Technical Reports Server (NTRS)

    Schaefer, Bradley E.; Fried, Robert E.

    1991-01-01

    RW Per was found to have large secular changes in its eclipse amplitude. In blue light, for example, the amplitude was 3.2 mag in the early 1900s, 2.2 mag in the late 1960s, and 1.75 mag in 1990. Throughout this time, the brightness at maximum was constant in all colors. It is shown that the only possible explanation is nodal motion, where the inclination varies with a period of roughly 100,000 yr. The nodal motion is caused by a third star, for which the light curve, the colors, and the O - C curve already provide evidence. Thus, RW Per is only the fourth known star with large changes of eclipse amplitude and is only the second example of nodal motion.

  9. Dirac nodal lines and induced spin Hall effect in metallic rutile oxides

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Zhang, Yang; Liu, Chao-Xing; Felser, Claudia; Yan, Binghai

    2017-06-01

    We have found Dirac nodal lines (DNLs) in the band structures of metallic rutile oxides IrO2, OsO2, and RuO2 and have revealed a large spin Hall conductivity contributed by these nodal lines, which explains a strong spin Hall effect (SHE) of IrO2 discovered recently. Two types of DNLs exist. The first type forms DNL networks that extend in the whole Brillouin zone and appears only in the absence of spin-orbit coupling (SOC), which induces surface states on the boundary. Because of SOC-induced band anticrossing, a large intrinsic SHE can be realized in these compounds. The second type appears at the Brillouin zone edges and is stable against SOC because of the protection of nonsymmorphic symmetry. Besides reporting these DNL materials, our work reveals the general relationship between DNLs and the SHE, indicating a way to apply Dirac nodal materials for spintronics.

  10. Constructing a polynomial whose nodal set is the three-twist knot 52

    NASA Astrophysics Data System (ADS)

    Dennis, Mark R.; Bode, Benjamin

    2017-06-01

    We describe a procedure that creates an explicit complex-valued polynomial function of three-dimensional space, whose nodal lines are the three-twist knot 52. The construction generalizes a similar approach for lemniscate knots: a braid representation is engineered from finite Fourier series and then considered as the nodal set of a certain complex polynomial which depends on an additional parameter. For sufficiently small values of this parameter, the nodal lines form the three-twist knot. Further mathematical properties of this map are explored, including the relationship of the phase critical points with the Morse-Novikov number, which is nonzero as this knot is not fibred. We also find analogous functions for other simple knots and links. The particular function we find, and the general procedure, should be useful for designing knotted fields of particular knot types in various physical systems.

  11. A Navier-Stokes solver for complex three-dimensional turbulent flows adopting non-linear modelling of the Reynolds stresses

    NASA Astrophysics Data System (ADS)

    Botte, V.; Tourlidakis, A.; Elder, R. L.

    1998-11-01

    A non-linear modelling of the Reynolds stresses has been incorporated into a Navier-Stokes solver for complex three-dimensional geometries. A k- model, adopting a modelling of the turbulent transport which is not based on the eddy viscosity, has been written in generalised co-ordinates and solved with a finite volume approach, using both a GMRES solver and a direct solver for the solution of the linear systems of equations. An additional term, quadratic in the main strain rate, has been introduced into the modelling of the Reynolds stresses to the basic Boussinesq's form; the corresponding constant has been evaluated through comparison with the experimental data. The computational procedure is implemented for the flow analysis in a 90° square section bend and the obtained results show that with the non-linear modelling a much better agreement with the measured data is obtained, both for the velocity and the pressure. The importance of the convection scheme is also discussed, showing how the effect of the non-linear correction added to the Reynolds stresses is effectively hidden by the additional numerical diffusion introduced by a low-order convection scheme as the first-order upwind scheme, thus making the use of higher order schemes necessary.

  12. A fast solver for systems of axisymmetric ring vortices

    SciTech Connect

    Strickland, J.H.; Amos, D.E.

    1990-09-01

    A method which is capable of efficient calculation of the axisymmetric flow field produced by a large system of ring vortices is presented in this report. The system of ring vortices can, in turn, be used to model body surfaces and wakes in incompressible unsteady axisymmetric flow fields. This method takes advantage of source point and field point series expansions which enables one to make calculations for interactions between groups of vortices which are in well separated spatial domains rather than having to consider interactions between every pair of vortices. In this work, series expansions for the stream function of the ring vortex system are obtained. Such expansions explicitly contain the radial and axial velocity components. A Fortran computer code RSOLV has been written to execute the fast solution technique to calculate the stream function and the axial and radial velocity components at points in the flow field. Test cases have been run to optimize the code and to benchmark the truncation errors and CPU time savings associated with the method. Non-dimensional truncation errors for the stream function and total velocity field are on the order of 5 {times} 10{sup {minus}5} and 3 {times} 10{sup {minus}3} respectively. Single precision accuracy produces errors in these quantities up to about 1 {times} 10{sup {minus}5}. For 100 vortices in the field, there is virtually no CPU time savings with the fast solver. For 10,000 vortices in the flow, the fast solver obtains solutions in about 1% to 3% of the time required for the direct solution technique. Simulations of vortices with square and circular cores were run in order to obtain expressions for the self-induced velocities of such vortices. 8 refs., 26 figs.

  13. 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.

  14. 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.

  15. 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.

  16. The 18.6 yr nodal modulation in the tides of Southern European coasts

    NASA Astrophysics Data System (ADS)

    Shaw, A. G. P.; Tsimplis, M. N.

    2010-02-01

    The nodal modulation of the diurnal ( K1 and O1) and semi-diurnal ( M2 and K2) tidal constituents at the coasts of the Mediterranean Sea and the eastern Atlantic is estimated and its spatial variability mapped. Fourteen hourly tide gauge records each spanning more than 18 years are considered in this analysis. Ten tide gauges are located in the Mediterranean Sea and four in the Bay of Biscay. The nodal modulation of the most energetic tidal constituent ( M2) reaches up to 5 cm at the eastern Atlantic coasts, while within the Mediterranean Sea its modulation is in general less than 1.1 cm. The largest K2 nodal modulation found is 3.7 cm in the eastern Atlantic coasts. In the Mediterranean Sea, smaller modulation amplitudes, ranging between 0.4 and 1.4 cm are found. The K1 tide constituent has the largest amplitude nodal modulation within the Mediterranean Sea of 1.9 cm in the north Adriatic Sea, which is also larger than the modulation of this constituent at the eastern Atlantic coasts. The O1 tide constituent has the highest amplitude nodal modulation (1.4 cm) at the eastern Atlantic coasts. In the Mediterranean Sea the maximum value is 1 cm in the north Adriatic Sea. The derived nodal modulations of the diurnal and semi-diurnal constituents follow, in general, the equilibrium tidal theory. The tidal amplitudes for all four components do not indicate significant secular trends for most tide gauges. The tidal phases indicate significant negative trends for all four tidal constituents within the central and eastern Mediterranean Sea.

  17. Threshold primary tumour sizes for nodal and distant metastases in papillary and follicular thyroid cancers.

    PubMed

    Zaman, Maseeh uz; Fatima, Nosheen; Sajjad, Zafar; Akhtar, Jaweed; Islam, Najmul; Masood, Qamar; Ahmed, Asma

    2012-01-01

    In papillary and follicular thyroid cancers (PTC, FTC), nodal and distant metastasis are generally considered important determinants of recurrence and survival, respectively. However, there is no consensus about the threshold primary tumour size (PTS) for these determinants. The aim of this study was to assess size relationships for developing nodal, pulmonary, bone and overall distant metastases. This prospective study covered 139 (93 females and 46 males) consecutive biopsy proven patients with PTC (114/139, mean age 41.0 ± 15.7 years, M: F, 35%:65%) and FTC (25/139, mean age 39.2 ± 14.3 years, M: F: 24%:76%). Average primary tumor size was 23.4 ± 11.1 mm and 26.5 ± 13.1 mm for PTC and FTC respectively (p value=0.223). Nodal metastasis was found more common in PTC than FTC (49% vs 28%, p value <0.05), whereas overall distant metastasis was approximately the same (13% and 24%, p value =0.277); however, bone metastasis was significantly higher in FTC than PTC (24% vs 5%, p value <0.05). Cumulative risk for nodal and distant metastases for FTC and PTC starts at PTS <20 mm and may indicate an unusual aggressive tumor behavior in the studied population. Highest cumulative risk for nodal and pulmonary metastases in PTC and for bone metastasis in FTC was found to be ≥ 50 mm PTS. We conclude that a PTS of <20 mm may indicate an unusual aggressive tumor behavior with highest cumulative risk for nodal and pulmonary metastases in PTC and for bone metastasis in FTC with a cutoff of ≥ 50 mm.

  18. What is the incidence of isolated paraaortic nodal recurrence in grade 1 endometrial carcinoma?

    PubMed

    Abu-Rustum, Nadeem R; Chi, Dennis S; Leitao, Mario; Oke, Eniola A; Hensley, Martee L; Alektiar, Kaled M; Barakat, Richard R

    2008-10-01

    To describe the incidence of isolated paraaortic nodal recurrences in patients with a final diagnosis of grade 1 endometrial carcinoma initially treated with surgery. Records from a prospectively maintained endometrial carcinoma database were reviewed to identify sites of recurrence. Patients with any papillary serous or clear cell carcinoma, leiomyosarcoma, endometrial stromal sarcoma, squamous carcinoma, or adenosarcoma were excluded. Recurrence sites were classified into 4 main categories: 1) pelvic (including vaginal and other soft tissue pelvic sites); 2) abdominal (including peritoneum, omentum and liver); 3) distant (including lung, brain, supraclavicular, and groins); and 4) isolated paraaortic nodal recurrence (including any nodal recurrence between the midcommon iliac to renal vessels). Between 1/93 and 5/06, 1453 patients with endometrial carcinoma met the study inclusion criteria. Final grade distribution included: grade 1 endometrial adenocarcinoma, 310 (21%); grade 2, 578 (40%); grade 3, 481 (33%); and incomplete, 84 (5.8%). In all, 154 patients (11%) had documented recurrences. Recurrence sites for all patients/all grades included: pelvis, 52 (34%); abdomen, 51 (33%); distant, 41 (27%), and isolated paraaortic, 10 (6%). None of the isolated paraaortic recurrences occurred in patients with a final diagnosis of grade 1 carcinoma. Furthermore, 9/10 (90%) isolated paraaortic nodal recurrences were in grade 3 tumors. Only 8 (2.6%) of 310 patients with grade 1 tumors recurred. Sites of recurrence for grade 1 tumors included: abdomen, 3; pelvis, 3; and distant, 2. This large series of endometrial carcinoma patients initially treated with surgery confirms that isolated paraaortic nodal recurrence in women with a final diagnosis of grade 1 endometrial carcinoma is extremely rare. These rare isolated paraaortic nodal recurrences appear to be limited to high-grade endometrial carcinomas.

  19. Cancer of unknown primary patients with midline nodal distribution: midway between poor and favourable prognosis?

    PubMed

    Pentheroudakis, George; Stoyianni, Aikaterini; Pavlidis, Nicholas

    2011-04-01

    Midline nodal cancer of unknown primary (CUP) has varying definitions and an unclear natural history compared to that of extragonadal germ cell cancer (EGCC) and neuroendocrine tumors. We systematically reviewed all published series of patients with midline nodal CUP using three distinct definitions and presented our own retrospective cohort. Sixty four fit patients (median age 64) with poorly differentiated carcinoma or adenocarcinoma in midline nodal areas were treated from 1998 to 2008 at our center. Only two patients had elevated serum germ cell markers. Forty-eight percentage of patients responded to platinum-based chemotherapy (CR 11%). The median survival was 12 months (2-year survival 18%). Good PS (Hazard Ratio HR 0.287, p=0.058) and administration of platinum (HR 0.340, p=0.08) predicted for more favourable outcome. A subgroup of 15 male patients selected with stricter criteria had a CR rate of 33% and median survival of 18 months (2-year survival 24%). We identified 10 series of midline nodal CUP patients defined with discordant criteria. Despite high response rates (35-65%) to platinum chemotherapy, the median survival clustered around 12 months. Predictive factors for superior survival were low tumor bulk, patient fitness, female gender, carcinomatous histology, and absence of visceral metastases. There were differences between midline nodal CUP patients and EGCC as well as neuroendocrine tumors (age, tumor markers, response to therapy, long-term survival). Midline nodal CUP patients are poorly defined, fare less well than EGCC or neuroendocrine cancer and probably constitute a heterogeneous entity with a minority harbouring atypical germ cell cancer. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Nodal Structure and Stimulus Relatedness in Equivalence Classes: Post-Class Formation Preference Tests

    PubMed Central

    Moss-Lourenco, Patricia; Fields, Lanny

    2011-01-01

    Three experiments used postclass formation within-class preference test performances to evaluate the effects of nodal distance on the relatedness of stimuli in equivalence classes. In Experiment 1, two 2-node four-member equivalence classes were established using the simultaneous protocol in which all of the baseline relations were trained together, after which all emergent relations probes were presented together. All training and testing was done using match-to-sample trials that contained two comparisons. After class formation, the effects of nodal distance were evaluated using within-class preference tests that contained samples and both comparisons from the same class. These tests yielded inconsistent performances for most participants. Experiment 2 replicated Experiment 1, but a third null comparison was used on all trials during class formation. Thereafter, virtually all of the within-class probes, for all participants, evoked performances that were consistent with the predicted effects of nodal distance, that is, the selection of comparisons that were nodally closer to the samples. It appears, then, that the establishment of the equivalence classes with a third null comparison induced control by nodal structure of the classes. Experiment 3 demonstrated the generality of these findings with larger classes that contained more nodal separations, that is, three-node five-member classes. Emergent-relations tests conducted immediately after the within-class tests showed the classes to be intact. Thus, the differential relatedness of stimuli in a class or their interchangeability depended on the content of a test trial: within-class probes occasioned responding indicative of differential strength among the stimuli in the class, while cross-class tests occasioned responding indicative of interchangeability of stimuli in the same class. PMID:21547071