Experimental discovery of nodal chains

NASA Astrophysics Data System (ADS)

Yan, Qinghui; Liu, Rongjuan; Yan, Zhongbo; Liu, Boyuan; Chen, Hongsheng; Wang, Zhong; Lu, Ling

2018-05-01

Three-dimensional Weyl and Dirac nodal points1 have attracted widespread interest across multiple disciplines and in many platforms but allow for few structural variations. In contrast, nodal lines2-4 can have numerous topological configurations in momentum space, forming nodal rings5-9, nodal chains10-15, nodal links16-20 and nodal knots21,22. However, nodal lines are much less explored because of the lack of an ideal experimental realization23-25. For example, in condensed-matter systems, nodal lines are often fragile to spin-orbit coupling, located away from the Fermi level, coexist with energy-degenerate trivial bands or have a degeneracy line that disperses strongly in energy. Here, overcoming all these difficulties, we theoretically predict and experimentally observe nodal chains in a metallic-mesh photonic crystal having frequency-isolated linear band-touching rings chained across the entire Brillouin zone. These nodal chains are protected by mirror symmetry and have a frequency variation of less than 1%. We use angle-resolved transmission measurements to probe the projected bulk dispersion and perform Fourier-transformed field scans to map out the dispersion of the drumhead surface state. Our results establish an ideal nodal-line material for further study of topological line degeneracies with non-trivial connectivity and consequent wave dynamics that are richer than those in Weyl and Dirac materials.

Spinless hourglass nodal-line semimetals

NASA Astrophysics Data System (ADS)

Takahashi, Ryo; Hirayama, Motoaki; Murakami, Shuichi

2017-10-01

Nodal-line semimetals, one of the topological semimetals, have degeneracy along nodal lines where the band gap is closed. In many cases, the nodal lines appear accidentally, and in such cases it is impossible to determine whether the nodal lines appear or not, only from the crystal symmetry and the electron filling. In this paper, for spinless systems, we show that in specific space groups at 4 N +2 fillings (8 N +4 fillings including the spin degree of freedom), presence of the nodal lines is required regardless of the details of the systems. Here, the spinless systems refer to crystals where the spin-orbit coupling is negligible and the spin degree of freedom can be omitted because of the SU(2) spin degeneracy. In this case the shape of the band structure around these nodal lines is like an hourglass, and we call this a spinless hourglass nodal-line semimetal. We construct a model Hamiltonian as an example and we show that it is always in the spinless hourglass nodal-line semimetal phase even when the model parameters are changed without changing the symmetries of the system. We also establish a list of all the centrosymmetric space groups, under which spinless systems always have hourglass nodal lines, and illustrate where the nodal lines are located. We propose that Al3FeSi2 , whose space-group symmetry is Pbcn (No. 60), is one of the nodal-line semimetals arising from this mechanism.

RELATIVISTIC MAGNETOHYDRODYNAMICS: RENORMALIZED EIGENVECTORS AND FULL WAVE DECOMPOSITION RIEMANN SOLVER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anton, Luis; MartI, Jose M; Ibanez, Jose M

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, andmore » 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.« less

On the implementation of an accurate and efficient solver for convection-diffusion equations

NASA Astrophysics Data System (ADS)

Wu, Chin-Tien

In this dissertation, we examine several different aspects of computing the numerical solution of the convection-diffusion equation. The solution of this equation often exhibits sharp gradients due to Dirichlet outflow boundaries or discontinuities in boundary conditions. Because of the singular-perturbed nature of the equation, numerical solutions often have severe oscillations when grid sizes are not small enough to resolve sharp gradients. To overcome such difficulties, the streamline diffusion discretization method can be used to obtain an accurate approximate solution in regions where the solution is smooth. To increase accuracy of the solution in the regions containing layers, adaptive mesh refinement and mesh movement based on a posteriori error estimations can be employed. An error-adapted mesh refinement strategy based on a posteriori error estimations is also proposed to resolve layers. For solving the sparse linear systems that arise from discretization, goemetric multigrid (MG) and algebraic multigrid (AMG) are compared. In addition, both methods are also used as preconditioners for Krylov subspace methods. We derive some convergence results for MG with line Gauss-Seidel smoothers and bilinear interpolation. Finally, while considering adaptive mesh refinement as an integral part of the solution process, it is natural to set a stopping tolerance for the iterative linear solvers on each mesh stage so that the difference between the approximate solution obtained from iterative methods and the finite element solution is bounded by an a posteriori error bound. Here, we present two stopping criteria. The first is based on a residual-type a posteriori error estimator developed by Verfurth. The second is based on an a posteriori error estimator, using local solutions, developed by Kay and Silvester. Our numerical results show the refined mesh obtained from the iterative solution which satisfies the second criteria is similar to the refined mesh obtained from

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.

Nodal surface semimetals: Theory and material realization

NASA Astrophysics Data System (ADS)

Wu, Weikang; Liu, Ying; Li, Si; Zhong, Chengyong; Yu, Zhi-Ming; Sheng, Xian-Lei; Zhao, Y. X.; Yang, Shengyuan A.

2018-03-01

We theoretically study the three-dimensional topological semimetals with nodal surfaces protected by crystalline symmetries. Different from the well-known nodal-point and nodal-line semimetals, in these materials, the conduction and valence bands cross on closed nodal surfaces in the Brillouin zone. We propose different classes of nodal surfaces, both in the absence and in the presence of spin-orbit coupling (SOC). In the absence of SOC, a class of nodal surfaces can be protected by space-time inversion symmetry and sublattice symmetry and characterized by a Z2 index, while another class of nodal surfaces are guaranteed by a combination of nonsymmorphic twofold screw-rotational symmetry and time-reversal symmetry. We show that the inclusion of SOC will destroy the former class of nodal surfaces but may preserve the latter provided that the inversion symmetry is broken. We further generalize the result to magnetically ordered systems and show that protected nodal surfaces can also exist in magnetic materials without and with SOC, given that certain magnetic group symmetry requirements are satisfied. Several concrete nodal-surface material examples are predicted via the first-principles calculations. The possibility of multi-nodal-surface materials is discussed.

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

NASA Technical Reports Server (NTRS)

Padovan, J.; Lackney, J.

1986-01-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, W.; Almgren, A.; Bell, J.

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 Godunovmore » scheme, whereas the parabolic part is solved implicitly with a first-order backward Euler method.« less

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

PubMed Central

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. PMID:28448591

Transport Corrections in Nodal Diffusion Codes for HTR Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 solutionmore » 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.« less

MILAMIN 2 - Fast MATLAB FEM solver

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Robust doubly charged nodal lines and nodal surfaces in centrosymmetric systems

NASA Astrophysics Data System (ADS)

Bzdušek, Tomáš; Sigrist, Manfred

2017-10-01

Weyl points in three spatial dimensions are characterized by a Z -valued charge—the Chern number—which makes them stable against a wide range of perturbations. A set of Weyl points can mutually annihilate only if their net charge vanishes, a property we refer to as robustness. While nodal loops are usually not robust in this sense, it has recently been shown using homotopy arguments that in the centrosymmetric extension of the AI symmetry class they nevertheless develop a Z2 charge analogous to the Chern number. Nodal loops carrying a nontrivial value of this Z2 charge are robust, i.e., they can be gapped out only by a pairwise annihilation and not on their own. As this is an additional charge independent of the Berry π -phase flowing along the band degeneracy, such nodal loops are, in fact, doubly charged. In this manuscript, we generalize the homotopy discussion to the centrosymmetric extensions of all Atland-Zirnbauer classes. We develop a tailored mathematical framework dubbed the AZ +I classification and show that in three spatial dimensions such robust and multiply charged nodes appear in four of such centrosymmetric extensions, namely, AZ +I classes CI and AI lead to doubly charged nodal lines, while D and BDI support doubly charged nodal surfaces. We remark that no further crystalline symmetries apart from the spatial inversion are necessary for their stability. We provide a description of the corresponding topological charges, and develop simple tight-binding models of various semimetallic and superconducting phases that exhibit these nodes. We also indicate how the concept of robust and multiply charged nodes generalizes to other spatial dimensions.

Hopf-link topological nodal-loop semimetals

NASA Astrophysics Data System (ADS)

Zhou, Yao; Xiong, Feng; Wan, Xiangang; An, Jin

2018-04-01

We construct a generic two-band model which can describe topological semimetals with multiple closed nodal loops. All the existing multi-nodal-loop semimetals, including the nodal-net, nodal-chain, and Hopf-link states, can be examined within the same framework. Based on a two-nodal-loop model, the corresponding drumhead surface states for these topologically different bulk states are studied and compared with each other. The connection of our model with Hopf insulators is also discussed. Furthermore, to identify experimentally these topologically different semimetal states, especially to distinguish the Hopf-link from unlinked ones, we also investigate their Landau levels. It is found that the Hopf-link state can be characterized by the existence of a quadruply degenerate zero-energy Landau band, regardless of the direction of the magnetic field.

Nodal-chain metals.

PubMed

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

2016-10-06

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 (IrF 4 ), as well as in other compounds of this class of materials. Using IrF 4 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.

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

Development of Tokamak Transport Solvers for Stiff Confinement Systems

NASA Astrophysics Data System (ADS)

St. John, H. E.; Lao, L. L.; Murakami, M.; Park, J. M.

2006-10-01

Leading transport models such as GLF23 [1] and MM95 [2] describe turbulent plasma energy, momentum and particle flows. In order to accommodate existing transport codes and associated solution methods effective diffusivities have to be derived from these turbulent flow models. This can cause significant problems in predicting unique solutions. We have developed a parallel transport code solver, GCNMP, that can accommodate both flow based and diffusivity based confinement models by solving the discretized nonlinear equations using modern Newton, trust region, steepest descent and homotopy methods. We present our latest development efforts, including multiple dynamic grids, application of two-level parallel schemes, and operator splitting techniques that allow us to combine flow based and diffusivity based models in tokamk simulations. 6pt [1] R.E. Waltz, et al., Phys. Plasmas 4, 7 (1997). [2] G. Bateman, et al., Phys. Plasmas 5, 1793 (1998).

A case of nodal malignant lymphoma presenting with arterial bleeding related to its duodenal penetration.

PubMed

Miyake, Takakazu; Iida, Tomoya; Masaki, Yoshiharu; Onodera, Kei; Kubo, Toshiyuki; Yamashita, Kentaro; Yamano, Hiroo; Nakase, Hiroshi

2018-06-01

A 62-year-old man with a chief complaint of dysphagia visited our hospital. Enhanced computed tomography showed the tumor near the duodenal wall and lymphadenopathy in the left supraclavicular fossa and para-aortic lymph node. Upper gastrointestinal endoscopy showed an ulcer accompanied with a fistula in the anterior wall of duodenal bulb, suggesting that the tumor penetrated into duodenal wall. Biopsy from the lymph node in the left supraclavicular fossa indicated diffuse large B-cell lymphoma. Although chemotherapy was planned, massive arterial bleeding occurred from the part of duodenal penetration. Endoscopic hemostasis was unsuccessfully performed. Therefore, we performed transcathether arterial embolization for hemostasis. After the procedure, the patient received six cycles of chemotherapy, and he achieved complete response. He has been alive 5 years without recurrence. There were many cases of gastrointestinal bleeding from primary gastrointestinal lymphomas, while there were few cases with nodal involvement by malignant lymphoma resulting in bleeding from gastrointestinal tract. We herein report a case of duodenal bleeding by nodal involvement of diffuse large B-cell lymphoma with review of literature.

Solving regularly and singularly perturbed reaction-diffusion equations in three space dimensions

NASA Astrophysics Data System (ADS)

Moore, Peter K.

2007-06-01

In [P.K. Moore, Effects of basis selection and h-refinement on error estimator reliability and solution efficiency for higher-order methods in three space dimensions, Int. J. Numer. Anal. Mod. 3 (2006) 21-51] a fixed, high-order h-refinement finite element algorithm, Href, was introduced for solving reaction-diffusion equations in three space dimensions. In this paper Href is coupled with continuation creating an automatic method for solving regularly and singularly perturbed reaction-diffusion equations. The simple quasilinear Newton solver of Moore, (2006) is replaced by the nonlinear solver NITSOL [M. Pernice, H.F. Walker, NITSOL: a Newton iterative solver for nonlinear systems, SIAM J. Sci. Comput. 19 (1998) 302-318]. Good initial guesses for the nonlinear solver are obtained using continuation in the small parameter ɛ. Two strategies allow adaptive selection of ɛ. The first depends on the rate of convergence of the nonlinear solver and the second implements backtracking in ɛ. Finally a simple method is used to select the initial ɛ. Several examples illustrate the effectiveness of the algorithm.

Quantum oscillations in nodal line systems

NASA Astrophysics Data System (ADS)

Yang, Hui; Moessner, Roderich; Lim, Lih-King

2018-04-01

We study signatures of magnetic quantum oscillations in three-dimensional nodal line semimetals at zero temperature. The extended nature of the degenerate bands can result in a Fermi surface geometry with topological genus one, as well as a Fermi surface of electron and hole pockets encapsulating the nodal line. Moreover, the underlying two-band model to describe a nodal line is not unique, in that there are two classes of Hamiltonian with distinct band topology giving rise to the same Fermi-surface geometry. After identifying the extremal cyclotron orbits in various magnetic field directions, we study their concomitant Landau levels and resulting quantum oscillation signatures. By Landau-fan-diagram analyses, we extract the nontrivial π Berry phase signature for extremal orbits linking the nodal line.

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.

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.)

A contemporary view of atrioventricular nodal physiology.

PubMed

Markowitz, Steven M; Lerman, Bruce B

2018-06-16

In delaying transmission of the cardiac impulse from the atria to the ventricles, the atrioventricular (AV) node serves a critical function in augmenting ventricular filling during diastole and limiting the ventricular response during atrial tachyarrhythmias. The complex structure of the nodal region, however, also provides the substrate for reentrant rhythms. Recent discoveries have elucidated the cellular basis and anatomical determinants of slow conduction in the node. Based on analysis of gap junction proteins, distinct structural components of the AV node have been defined, including the compact node, right and left inferior nodal extensions, the lower nodal bundle, and transitional tissue. Emerging evidence supports the role of the inferior nodal extensions in mediating slow pathway conduction. The most common form of reentry involving the node, slow-fast AV nodal reentrant tachycardia (AVNRT), utilizes the inferior nodal extensions for anterograde slow pathway conduction; the structures responsible for retrograde fast pathway activation in the superior septum are less well defined and likely heterogeneous. Atypical forms of AVNRT arise from circuits that activate at least one of the inferior extensions in the retrograde direction.

A high-order semi-explicit discontinuous Galerkin solver for 3D incompressible flow with application to DNS and LES of turbulent channel flow

NASA Astrophysics Data System (ADS)

Krank, Benjamin; Fehn, Niklas; Wall, Wolfgang A.; Kronbichler, Martin

2017-11-01

We present an efficient discontinuous Galerkin scheme for simulation of the incompressible Navier-Stokes equations including laminar and turbulent flow. We consider a semi-explicit high-order velocity-correction method for time integration as well as nodal equal-order discretizations for velocity and pressure. The non-linear convective term is treated explicitly while a linear system is solved for the pressure Poisson equation and the viscous term. The key feature of our solver is a consistent penalty term reducing the local divergence error in order to overcome recently reported instabilities in spatially under-resolved high-Reynolds-number flows as well as small time steps. This penalty method is similar to the grad-div stabilization widely used in continuous finite elements. We further review and compare our method to several other techniques recently proposed in literature to stabilize the method for such flow configurations. The solver is specifically designed for large-scale computations through matrix-free linear solvers including efficient preconditioning strategies and tensor-product elements, which have allowed us to scale this code up to 34.4 billion degrees of freedom and 147,456 CPU cores. We validate our code and demonstrate optimal convergence rates with laminar flows present in a vortex problem and flow past a cylinder and show applicability of our solver to direct numerical simulation as well as implicit large-eddy simulation of turbulent channel flow at Reτ = 180 as well as 590.

Unstructured Polyhedral Mesh Thermal Radiation Diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baudron, Anne-Marie, E-mail: anne-marie.baudron@cea.fr; CEA-DRN/DMT/SERMA, CEN-Saclay, 91191 Gif sur Yvette Cedex; Lautard, Jean-Jacques, E-mail: jean-jacques.lautard@cea.fr

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 ofmore » 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.« less

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.

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

PubMed

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.

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

PubMed Central

Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

2012-01-01

An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

Nodal signalling and asymmetry of the nervous system

PubMed Central

Signore, Iskra A.; Palma, Karina

2016-01-01

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’. PMID:27821531

Maternal nodal and zebrafish embryogenesis.

PubMed

Bennett, James T; Stickney, Heather L; Choi, Wen-Yee; Ciruna, Brian; Talbot, William S; Schier, Alexander F

2007-11-08

In fish and amphibians, the dorsal axis is specified by the asymmetric localization of maternally provided components of the Wnt signalling pathway. Gore et al. suggest that the Nodal signal Squint (Sqt) is required as a maternally provided dorsal determinant in zebrafish. Here we test their proposal and show that the maternal activities of sqt and the related Nodal gene cyclops (cyc) are not required for dorsoventral patterning.

WIND Flow Solver Released

NASA Technical Reports Server (NTRS)

Towne, Charles E.

1999-01-01

The WIND code is a general-purpose, structured, multizone, compressible flow solver that can be used to analyze steady or unsteady flow for a wide range of geometric configurations and over a wide range of flow conditions. WIND is the latest product of the NPARC Alliance, a formal partnership between the NASA Lewis Research Center and the Air Force Arnold Engineering Development Center (AEDC). WIND Version 1.0 was released in February 1998, and Version 2.0 will be released in February 1999. The WIND code represents a merger of the capabilities of three existing computational fluid dynamics codes--NPARC (the original NPARC Alliance flow solver), NXAIR (an Air Force code used primarily for unsteady store separation problems), and NASTD (the primary flow solver at McDonnell Douglas, now part of Boeing).

Occult nodal metastasis in solid carcinomata

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

1987-01-01

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

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

An oscillation-free flow solver based on flux reconstruction

NASA Astrophysics Data System (ADS)

Aguerre, Horacio J.; Pairetti, Cesar I.; Venier, Cesar M.; Márquez Damián, Santiago; Nigro, Norberto M.

2018-07-01

In this paper, a segregated algorithm is proposed to suppress high-frequency oscillations in the velocity field for incompressible flows. In this context, a new velocity formula based on a reconstruction of face fluxes is defined eliminating high-frequency errors. In analogy to the Rhie-Chow interpolation, this approach is equivalent to including a flux-based pressure gradient with a velocity diffusion in the momentum equation. In order to guarantee second-order accuracy of the numerical solver, a set of conditions are defined for the reconstruction operator. To arrive at the final formulation, an outlook over the state of the art regarding velocity reconstruction procedures is presented comparing them through an error analysis. A new operator is then obtained by means of a flux difference minimization satisfying the required spatial accuracy. The accuracy of the new algorithm is analyzed by performing mesh convergence studies for unsteady Navier-Stokes problems with analytical solutions. The stabilization properties of the solver are then tested in a problem where spurious numerical oscillations arise for the velocity field. The results show a remarkable performance of the proposed technique eliminating high-frequency errors without losing accuracy.

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.

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.).

An HLLC Riemann solver for resistive relativistic magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Miranda-Aranguren, S.; Aloy, M. A.; Rembiasz, T.

2018-05-01

We present a new approximate Riemann solver for the augmented system of equations of resistive relativistic magnetohydrodynamics that belongs to the family of Harten-Lax-van Leer contact wave (HLLC) solvers. In HLLC solvers, the solution is approximated by two constant states flanked by two shocks separated by a contact wave. The accuracy of the new approximate solver is calibrated through 1D and 2D test problems.

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

Inverse design of centrifugal compressor vaned diffusers in inlet shear flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zangeneh, M.

1996-04-01

A three-dimensional inverse design method in which the blade (or vane) geometry is designed for specified distributions of circulation and blade thickness is applied to the design of centrifugal compressor vaned diffusers. Two generic diffusers are designed, one with uniform inlet flow (equivalent to a conventional design) and the other with a sheared inlet flow. The inlet shear flow effects are modeled in the design method by using the so-called ``Secondary Flow Approximation`` in which the Bernoulli surfaces are convected by the tangentially mean inviscid flow field. The difference between the vane geometry of the uniform inlet flow and nonuniformmore » inlet flow diffusers is found to be most significant from 50 percent chord to the trailing edge region. The flows through both diffusers are computed by using Denton`s three-dimensional inviscid Euler solver and Dawes` three-dimensional Navier-Stokes solver under sheared in-flow conditions. The predictions indicate improved pressure recovery and internal flow field for the diffuser designed for shear inlet flow conditions.« less

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.

Topological transport in Dirac nodal-line semimetals

NASA Astrophysics Data System (ADS)

Rui, W. B.; Zhao, Y. X.; Schnyder, Andreas P.

2018-04-01

Topological nodal-line semimetals are characterized by one-dimensional Dirac nodal rings that are protected by the combined symmetry of inversion P and time-reversal T . The stability of these Dirac rings is guaranteed by a quantized ±π Berry phase and their low-energy physics is described by a one-parameter family of (2+1)-dimensional quantum field theories exhibiting the parity anomaly. Here we study the Berry-phase supported topological transport of P T -invariant nodal-line semimetals. We find that small inversion breaking allows for an electric-field-induced anomalous transverse current, whose universal component originates from the parity anomaly. Due to this Hall-like current, carriers at opposite sides of the Dirac nodal ring flow to opposite surfaces when an electric field is applied. To detect the topological currents, we propose a dumbbell device, which uses surface states to filter charges based on their momenta. Suggestions for experiments and device applications are discussed.

Risk of Nodal Metastasis in Major Salivary Gland Adenoid Cystic Carcinoma.

PubMed

Megwalu, Uchechukwu C; Sirjani, Davud

2017-04-01

Objective To determine the risk of nodal metastasis, examine risk factors for nodal metastasis, and evaluate the impact of nodal metastasis on survival in patients with major salivary gland adenoid cystic carcinoma. Study Design Retrospective cohort study from a large population- based cancer database. Methods Data were extracted from the SEER 18 database (Surveillance, Epidemiology, and End Results) of the National Cancer Institute. The study cohort included 720 patients diagnosed with major salivary gland adenoid cystic carcinoma between 1988 and 2013. Results The overall rate of lymph node metastasis was 17%. T3 disease (odds ratio, 4.74) and T4 disease (odds ratio, 9.24) were associated with increased risk of nodal metastasis. Age, sex, and site were not associated with nodal metastasis. Nodal metastasis was associated with worse overall survival (hazard ratio, 2.56) and disease-specific survival (hazard ratio, 3.27), after adjusting for T stage, presence of distant metastasis, site, surgical resection, radiotherapy, neck dissection, age, sex, race, marital status, and year of diagnosis. Conclusion Major salivary gland adenoid cystic carcinoma carries significant risk of nodal metastasis. Advanced T stage is associated with increased risk of nodal metastasis. Nodal metastasis is associated with worse survival.

Chiral topological insulating phases from three-dimensional nodal loop semimetals

NASA Astrophysics Data System (ADS)

Li, Linhu; Yin, Chuanhao; Chen, Shu; Araujo, Miguel

We begin with a minimal model of three-dimensional nodal loop semimetals, and study the effect of anticommuting gap terms. The resulting topological insulating phases are protected by a chiral symmetry, and can be characterized by a winding number defined along the nodal loop. We illustrate the geometric relation between the nodal loop and the gap terms, which has a correspondence to the nodal loop winding number. We further investigate a lattice model and study its edge states under open boundary condition. The edge states hold Dirac cones with the same number as the summation of the winding numbers of each nodal loop in the first Brillouin zone.

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.

Topological Nodal-Net Semimetal in a Graphene Network Structure

NASA Astrophysics Data System (ADS)

Wang, Jian-Tao; Nie, Simin; Weng, Hongming; Kawazoe, Yoshiyuki; Chen, Changfeng

2018-01-01

Topological semimetals are characterized by the nodal points in their electronic structure near the Fermi level, either discrete or forming a continuous line or ring, which are responsible for exotic properties related to the topology of bulk bands. Here we identify by ab initio calculations a distinct topological semimetal that exhibits nodal nets comprising multiple interconnected nodal lines in bulk and have two coupled drumheadlike flat bands around the Fermi level on its surface. This nodal net semimetal state is proposed to be realized in a graphene network structure that can be constructed by inserting a benzene ring into each C- C bond in the bct-C4 lattice or by a crystalline modification of the (5,5) carbon nanotube. These results expand the realm of nodal manifolds in topological semimetals, offering a new platform for exploring novel physics in these fascinating materials.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evoli, Carmelo; Gaggero, Daniele; Vittino, Andrea

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 tomore » 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.« less

New core-reflector boundary conditions for transient nodal reactor calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, E.K.; Kim, C.H.; Joo, H.K.

1995-09-01

New core-reflector boundary conditions designed for the exclusion of the reflector region in transient nodal reactor calculations are formulated. Spatially flat frequency approximations for the temporal neutron behavior and two types of transverse leakage approximations in the reflector region are introduced to solve the transverse-integrated time-dependent one-dimensional diffusion equation and then to obtain relationships between net current and flux at the core-reflector interfaces. To examine the effectiveness of new core-reflector boundary conditions in transient nodal reactor computations, nodal expansion method (NEM) computations with and without explicit representation of the reflector are performed for Laboratorium fuer Reaktorregelung und Anlagen (LRA) boilingmore » water reactor (BWR) and Nuclear Energy Agency Committee on Reactor Physics (NEACRP) pressurized water reactor (PWR) rod ejection kinetics benchmark problems. Good agreement between two NEM computations is demonstrated in all the important transient parameters of two benchmark problems. A significant amount of CPU time saving is also demonstrated with the boundary condition model with transverse leakage (BCMTL) approximations in the reflector region. In the three-dimensional LRA BWR, the BCMTL and the explicit reflector model computations differ by {approximately}4% in transient peak power density while the BCMTL results in >40% of CPU time saving by excluding both the axial and the radial reflector regions from explicit computational nodes. In the NEACRP PWR problem, which includes six different transient cases, the largest difference is 24.4% in the transient maximum power in the one-node-per-assembly B1 transient results. This difference in the transient maximum power of the B1 case is shown to reduce to 11.7% in the four-node-per-assembly computations. As for the computing time, BCMTL is shown to reduce the CPU time >20% in all six transient cases of the NEACRP PWR.« less

Nodal portraits of quantum billiards: Domains, lines, and statistics

NASA Astrophysics Data System (ADS)

Jain, Sudhir Ranjan; Samajdar, Rhine

2017-10-01

This is a comprehensive review of the nodal domains and lines of quantum billiards, emphasizing a quantitative comparison of theoretical findings to experiments. The nodal statistics are shown to distinguish not only between regular and chaotic classical dynamics but also between different geometric shapes of the billiard system itself. How a random superposition of plane waves can model chaotic eigenfunctions is discussed and the connections of the complex morphology of the nodal lines thereof to percolation theory and Schramm-Loewner evolution are highlighted. Various approaches to counting the nodal domains—using trace formulas, graph theory, and difference equations—are also illustrated with examples. The nodal patterns addressed pertain to waves on vibrating plates and membranes, acoustic and electromagnetic modes, wave functions of a "particle in a box" as well as to percolating clusters, and domains in ferromagnets, thus underlining the diversity and far-reaching implications of the problem.

Ensemble Grouping Strategies for Embedded Stochastic Collocation Methods Applied to Anisotropic Diffusion Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

D'Elia, M.; Edwards, H. C.; Hu, J.

Previous work has demonstrated that propagating groups of samples, called ensembles, together through forward simulations can dramatically reduce the aggregate cost of sampling-based uncertainty propagation methods [E. Phipps, M. D'Elia, H. C. Edwards, M. Hoemmen, J. Hu, and S. Rajamanickam, SIAM J. Sci. Comput., 39 (2017), pp. C162--C193]. However, critical to the success of this approach when applied to challenging problems of scientific interest is the grouping of samples into ensembles to minimize the total computational work. For example, the total number of linear solver iterations for ensemble systems may be strongly influenced by which samples form the ensemble whenmore » applying iterative linear solvers to parameterized and stochastic linear systems. In this paper we explore sample grouping strategies for local adaptive stochastic collocation methods applied to PDEs with uncertain input data, in particular canonical anisotropic diffusion problems where the diffusion coefficient is modeled by truncated Karhunen--Loève expansions. Finally, we demonstrate that a measure of the total anisotropy of the diffusion coefficient is a good surrogate for the number of linear solver iterations for each sample and therefore provides a simple and effective metric for grouping samples.« less

Ensemble Grouping Strategies for Embedded Stochastic Collocation Methods Applied to Anisotropic Diffusion Problems

DOE PAGES

D'Elia, M.; Edwards, H. C.; Hu, J.; ...

2018-01-18

Previous work has demonstrated that propagating groups of samples, called ensembles, together through forward simulations can dramatically reduce the aggregate cost of sampling-based uncertainty propagation methods [E. Phipps, M. D'Elia, H. C. Edwards, M. Hoemmen, J. Hu, and S. Rajamanickam, SIAM J. Sci. Comput., 39 (2017), pp. C162--C193]. However, critical to the success of this approach when applied to challenging problems of scientific interest is the grouping of samples into ensembles to minimize the total computational work. For example, the total number of linear solver iterations for ensemble systems may be strongly influenced by which samples form the ensemble whenmore » applying iterative linear solvers to parameterized and stochastic linear systems. In this paper we explore sample grouping strategies for local adaptive stochastic collocation methods applied to PDEs with uncertain input data, in particular canonical anisotropic diffusion problems where the diffusion coefficient is modeled by truncated Karhunen--Loève expansions. Finally, we demonstrate that a measure of the total anisotropy of the diffusion coefficient is a good surrogate for the number of linear solver iterations for each sample and therefore provides a simple and effective metric for grouping samples.« less

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...

Reduction of numerical diffusion in three-dimensional vortical flows using a coupled Eulerian/Lagrangian solution procedure

NASA Technical Reports Server (NTRS)

Felici, Helene M.; Drela, Mark

1993-01-01

A new approach based on the coupling of an Eulerian and a Lagrangian solver, aimed at reducing the numerical diffusion errors of standard Eulerian time-marching finite-volume solvers, is presented. The approach is applied to the computation of the secondary flow in two bent pipes and the flow around a 3D wing. Using convective point markers the Lagrangian approach provides a correction of the basic Eulerian solution. The Eulerian flow in turn integrates in time the Lagrangian state-vector. A comparison of coarse and fine grid Eulerian solutions makes it possible to identify numerical diffusion. It is shown that the Eulerian/Lagrangian approach is an effective method for reducing numerical diffusion errors.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 examinedmore » 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.« less

NHDS: The New Hampshire Dispersion Relation Solver

NASA Astrophysics Data System (ADS)

Verscharen, Daniel; Chandran, Benjamin D. G.

2018-04-01

NHDS is the New Hampshire Dispersion Relation Solver. This article describes the numerics of the solver and its capabilities. The code is available for download on https://github.com/danielver02/NHDS.

Code Verification of the HIGRAD Computational Fluid Dynamics Solver

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 verificationmore » 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.« less

Nodal domains of a non-separable problem—the right-angled isosceles triangle

NASA Astrophysics Data System (ADS)

Aronovitch, Amit; Band, Ram; Fajman, David; Gnutzmann, Sven

2012-03-01

We study the nodal set of eigenfunctions of the Laplace operator on the right-angled isosceles triangle. A local analysis of the nodal pattern provides an algorithm for computing the number νn of nodal domains for any eigenfunction. In addition, an exact recursive formula for the number of nodal domains is found to reproduce all existing data. Eventually, we use the recursion formula to analyse a large sequence of nodal counts statistically. Our analysis shows that the distribution of nodal counts for this triangular shape has a much richer structure than the known cases of regular separable shapes or completely irregular shapes. Furthermore, we demonstrate that the nodal count sequence contains information about the periodic orbits of the corresponding classical ray dynamics.

Nodal weighting factor method for ex-core fast neutron fluence evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiang, R. T.

The nodal weighting factor method is developed for evaluating ex-core fast neutron flux in a nuclear reactor by utilizing adjoint neutron flux, a fictitious unit detector cross section for neutron energy above 1 or 0.1 MeV, the unit fission source, and relative assembly nodal powers. The method determines each nodal weighting factor for ex-core neutron fast flux evaluation by solving the steady-state adjoint neutron transport equation with a fictitious unit detector cross section for neutron energy above 1 or 0.1 MeV as the adjoint source, by integrating the unit fission source with a typical fission spectrum to the solved adjointmore » flux over all energies, all angles and given nodal volume, and by dividing it with the sum of all nodal weighting factors, which is a normalization factor. Then, the fast neutron flux can be obtained by summing the various relative nodal powers times the corresponding nodal weighting factors of the adjacent significantly contributed peripheral assembly nodes and times a proper fast neutron attenuation coefficient over an operating period. A generic set of nodal weighting factors can be used to evaluate neutron fluence at the same location for similar core design and fuel cycles, but the set of nodal weighting factors needs to be re-calibrated for a transition-fuel-cycle. This newly developed nodal weighting factor method should be a useful and simplified tool for evaluating fast neutron fluence at selected locations of interest in ex-core components of contemporary nuclear power reactors. (authors)« less

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.

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.

A 3D approximate maximum likelihood localization solver

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

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.

Observation of a nodal chain with Dirac surface states in Ti B2

NASA Astrophysics Data System (ADS)

Yi, C.-J.; Lv, B. Q.; Wu, Q. S.; Fu, B.-B.; Gao, X.; Yang, M.; Peng, X.-L.; Li, M.; Huang, Y.-B.; Richard, P.; Shi, M.; Li, G.; Yazyev, Oleg V.; Shi, Y.-G.; Qian, T.; Ding, H.

2018-05-01

Topological nodal-line semimetals (TNLSMs) are characterized by symmetry-protected band crossings extending along one-dimensional lines in momentum space. The nodal lines exhibit a variety of possible configurations, such as nodal ring, nodal link, nodal chain, and nodal knot. Here, using angle-resolved photoemission spectroscopy, we observe nodal rings on the orthogonal kz=0 and kx=0 planes of the Brillouin zone in Ti B2 . The nodal rings connect with each other on the intersecting line Γ-K of the orthogonal planes forming a remarkable nodal-chain structure. Furthermore, we observe surface states (SSs) on the (001) cleaved surface, which are consistent with the calculated SSs considering the contribution from both Ti and B terminations. The calculated SSs have novel Dirac-cone-like band structures, which are distinct from the usual drumhead SSs with a single flatband proposed in other TNLSMs.

Nodal lines and nodal loops in nonsymmorphic odd-parity superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Bounded fractional diffusion in geological media: Definition and Lagrangian approximation

USGS Publications Warehouse

Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang

2016-01-01

Spatiotemporal Fractional-Derivative Models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and non-zero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing non-zero-value spatial-nonlocal boundary conditions with directional super-diffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eularian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the non-local and non-symmetric fractional diffusion. For a non-zero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite do mains to those with any size and boundary conditions.

Eigenvalue Solvers for Modeling Nuclear Reactors on Leadership Class Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaybaugh, R. N.; Ramirez-Zweiger, M.; Pandya, Tara

In this paper, three complementary methods have been implemented in the code Denovo that accelerate neutral particle transport calculations with methods that use leadership-class computers fully and effectively: a multigroup block (MG) Krylov solver, a Rayleigh quotient iteration (RQI) eigenvalue solver, and a multigrid in energy (MGE) preconditioner. The MG Krylov solver converges more quickly than Gauss Seidel and enables energy decomposition such that Denovo can scale to hundreds of thousands of cores. RQI should converge in fewer iterations than power iteration (PI) for large and challenging problems. RQI creates shifted systems that would not be tractable without the MGmore » Krylov solver. It also creates ill-conditioned matrices. The MGE preconditioner reduces iteration count significantly when used with RQI and takes advantage of the new energy decomposition such that it can scale efficiently. Each individual method has been described before, but this is the first time they have been demonstrated to work together effectively. The combination of solvers enables the RQI eigenvalue solver to work better than the other available solvers for large reactors problems on leadership-class machines. Using these methods together, RQI converged in fewer iterations and in less time than PI for a full pressurized water reactor core. These solvers also performed better than an Arnoldi eigenvalue solver for a reactor benchmark problem when energy decomposition is needed. The MG Krylov, MGE preconditioner, and RQI solver combination also scales well in energy. Finally, this solver set is a strong choice for very large and challenging problems.« less

Eigenvalue Solvers for Modeling Nuclear Reactors on Leadership Class Machines

DOE PAGES

Slaybaugh, R. N.; Ramirez-Zweiger, M.; Pandya, Tara; ...

2018-02-20

In this paper, three complementary methods have been implemented in the code Denovo that accelerate neutral particle transport calculations with methods that use leadership-class computers fully and effectively: a multigroup block (MG) Krylov solver, a Rayleigh quotient iteration (RQI) eigenvalue solver, and a multigrid in energy (MGE) preconditioner. The MG Krylov solver converges more quickly than Gauss Seidel and enables energy decomposition such that Denovo can scale to hundreds of thousands of cores. RQI should converge in fewer iterations than power iteration (PI) for large and challenging problems. RQI creates shifted systems that would not be tractable without the MGmore » Krylov solver. It also creates ill-conditioned matrices. The MGE preconditioner reduces iteration count significantly when used with RQI and takes advantage of the new energy decomposition such that it can scale efficiently. Each individual method has been described before, but this is the first time they have been demonstrated to work together effectively. The combination of solvers enables the RQI eigenvalue solver to work better than the other available solvers for large reactors problems on leadership-class machines. Using these methods together, RQI converged in fewer iterations and in less time than PI for a full pressurized water reactor core. These solvers also performed better than an Arnoldi eigenvalue solver for a reactor benchmark problem when energy decomposition is needed. The MG Krylov, MGE preconditioner, and RQI solver combination also scales well in energy. Finally, this solver set is a strong choice for very large and challenging problems.« less

BCYCLIC: A parallel block tridiagonal matrix cyclic solver

NASA Astrophysics Data System (ADS)

Hirshman, S. P.; Perumalla, K. S.; Lynch, V. E.; Sanchez, R.

2010-09-01

A block tridiagonal matrix is factored with minimal fill-in using a cyclic reduction algorithm that is easily parallelized. Storage of the factored blocks allows the application of the inverse to multiple right-hand sides which may not be known at factorization time. Scalability with the number of block rows is achieved with cyclic reduction, while scalability with the block size is achieved using multithreaded routines (OpenMP, GotoBLAS) for block matrix manipulation. This dual scalability is a noteworthy feature of this new solver, as well as its ability to efficiently handle arbitrary (non-powers-of-2) block row and processor numbers. Comparison with a state-of-the art parallel sparse solver is presented. It is expected that this new solver will allow many physical applications to optimally use the parallel resources on current supercomputers. Example usage of the solver in magneto-hydrodynamic (MHD), three-dimensional equilibrium solvers for high-temperature fusion plasmas is cited.

Histogram Analysis of Apparent Diffusion Coefficients for Occult Tonsil Cancer in Patients with Cervical Nodal Metastasis from an Unknown Primary Site at Presentation.

PubMed

Choi, Young Jun; Lee, Jeong Hyun; Kim, Hye Ok; Kim, Dae Yoon; Yoon, Ra Gyoung; Cho, So Hyun; Koh, Myeong Ju; Kim, Namkug; Kim, Sang Yoon; Baek, Jung Hwan

2016-01-01

To explore the added value of histogram analysis of apparent diffusion coefficient (ADC) values over magnetic resonance (MR) imaging and fluorine 18 ((18)F) fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) for the detection of occult palatine tonsil squamous cell carcinoma (SCC) in patients with cervical nodal metastasis from a cancer of an unknown primary site. The institutional review board approved this retrospective study, and the requirement for informed consent was waived. Differences in the bimodal histogram parameters of the ADC values were assessed among occult palatine tonsil SCC (n = 19), overt palatine tonsil SCC (n = 20), and normal palatine tonsils (n = 20). One-way analysis of variance was used to analyze differences among the three groups. Receiver operating characteristic curve analysis was used to determine the best differentiating parameters. The increased sensitivity of histogram analysis over MR imaging and (18)F-FDG PET/CT for the detection of occult palatine tonsil SCC was evaluated as added value. Histogram analysis showed statistically significant differences in the mean, standard deviation, and 50th and 90th percentile ADC values among the three groups (P < .0045). Occult palatine tonsil SCC had a significantly higher standard deviation for the overall curves, mean and standard deviation of the higher curves, and 90th percentile ADC value, compared with normal palatine tonsils (P < .0167). Receiver operating characteristic curve analysis showed that the standard deviation of the overall curve best delineated occult palatine tonsil SCC from normal palatine tonsils, with a sensitivity of 78.9% (15 of 19 patients) and a specificity of 60% (12 of 20 patients). The added value of ADC histogram analysis was 52.6% over MR imaging alone and 15.8% over combined conventional MR imaging and (18)F-FDG PET/CT. Adding ADC histogram analysis to conventional MR imaging can improve the detection sensitivity for occult

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

Bounded fractional diffusion in geological media: Definition and Lagrangian approximation

NASA Astrophysics Data System (ADS)

Zhang, Yong; Green, Christopher T.; LaBolle, Eric M.; Neupauer, Roseanna M.; Sun, HongGuang

2016-11-01

Spatiotemporal fractional-derivative models (FDMs) have been increasingly used to simulate non-Fickian diffusion, but methods have not been available to define boundary conditions for FDMs in bounded domains. This study defines boundary conditions and then develops a Lagrangian solver to approximate bounded, one-dimensional fractional diffusion. Both the zero-value and nonzero-value Dirichlet, Neumann, and mixed Robin boundary conditions are defined, where the sign of Riemann-Liouville fractional derivative (capturing nonzero-value spatial-nonlocal boundary conditions with directional superdiffusion) remains consistent with the sign of the fractional-diffusive flux term in the FDMs. New Lagrangian schemes are then proposed to track solute particles moving in bounded domains, where the solutions are checked against analytical or Eulerian solutions available for simplified FDMs. Numerical experiments show that the particle-tracking algorithm for non-Fickian diffusion differs from Fickian diffusion in relocating the particle position around the reflective boundary, likely due to the nonlocal and nonsymmetric fractional diffusion. For a nonzero-value Neumann or Robin boundary, a source cell with a reflective face can be applied to define the release rate of random-walking particles at the specified flux boundary. Mathematical definitions of physically meaningful nonlocal boundaries combined with bounded Lagrangian solvers in this study may provide the only viable techniques at present to quantify the impact of boundaries on anomalous diffusion, expanding the applicability of FDMs from infinite domains to those with any size and boundary conditions.

Nodal Lymphangiogenesis and Metastasis

PubMed Central

Hirakawa, Satoshi; Detmar, Michael; Kerjaschki, Dontscho; Nagamatsu, Shogo; Matsuo, Keitaro; Tanemura, Atsushi; Kamata, Nobuyuki; Higashikawa, Koichiro; Okazaki, Hidenori; Kameda, Kenji; Nishida-Fukuda, Hisayo; Mori, Hideki; Hanakawa, Yasushi; Sayama, Koji; Shirakata, Yuji; Tohyama, Mikiko; Tokumaru, Sho; Katayama, Ichiro; Hashimoto, Koji

2009-01-01

Nodal lymphangiogenesis promotes distant lymph node (LN) metastasis in experimental cancer models. However, the role of nodal lymphangiogenesis in distant metastasis and in the overall survival of cancer patients remains unknown. Therefore, we investigated mechanisms that might facilitate regional and distant LN metastasis in extramammary Paget’s disease (EMPD). We retrospectively analyzed the impact of tumor-induced lymphatic vessel activation on the survival of 116 patients, the largest cohort with EMPD studied to date. Nodal lymphangiogenesis was significantly increased in metastatic, compared with tumor-free, LNs (P = 0.022). Increased lymphatic invasion within regional LNs was significantly associated with distant metastasis in LN (P = 0.047) and organs (P = 0.003). Thus, invasion within regional LNs is a powerful indicator of systemic tumor spread and reduced patient survival in EMPD (P = 0.0004). Lymphatic vessels associated with tumors expressed stromal cell-derived factor-1 (SDF-1), whereas CXCR4 was expressed on invasive Paget cells undergoing epithelial-mesenchymal transition (EMT)-like process. A431 cells overexpressing Snail expressed increased levels of CXCR4 in the presence of transforming growth factor-β1. Haptotactic migration assays confirmed that Snail-induced EMT-like process promotes tumor cell motility via the CXCR4-SDF-1 axis. Sinusoidal lymphatic endothelial cells and macrophages expressed SDF-1 in subcapsular sinuses of lymph nodes before Paget cell arrival. Our findings reveal that EMT-related features likely promote lymphatic metastasis of EMPD by activating the CXCR4-SDF-1 axis. PMID:19815713

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.

Differences in the Processes of Solving Physics Problems between Good Physics Problem Solvers and Poor Physics Problem Solvers.

ERIC Educational Resources Information Center

Finegold, M.; Mass, R.

1985-01-01

Good problem solvers and poor problem solvers in advanced physics (N=8) were significantly different in their ability in translating, planning, and physical reasoning, as well as in problem solving time; no differences in reliance on algebraic solutions and checking problems were noted. Implications for physics teaching are discussed. (DH)

Rules for Phase Shifts of Quantum Oscillations in Topological Nodal-Line Semimetals

NASA Astrophysics Data System (ADS)

Li, Cequn; Wang, C. M.; Wan, Bo; Wan, Xiangang; Lu, Hai-Zhou; Xie, X. C.

2018-04-01

Nodal-line semimetals are topological semimetals in which band touchings form nodal lines or rings. Around a loop that encloses a nodal line, an electron can accumulate a nontrivial π Berry phase, so the phase shift in the Shubnikov-de Haas (SdH) oscillation may give a transport signature for the nodal-line semimetals. However, different experiments have reported contradictory phase shifts, in particular, in the WHM nodal-line semimetals (W =Zr /Hf , H =Si /Ge , M =S /Se /Te ). For a generic model of nodal-line semimetals, we present a systematic calculation for the SdH oscillation of resistivity under a magnetic field normal to the nodal-line plane. From the analytical result of the resistivity, we extract general rules to determine the phase shifts for arbitrary cases and apply them to ZrSiS and Cu3 PdN systems. Depending on the magnetic field directions, carrier types, and cross sections of the Fermi surface, the phase shift shows rich results, quite different from those for normal electrons and Weyl fermions. Our results may help explore transport signatures of topological nodal-line semimetals and can be generalized to other topological phases of matter.

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.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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].

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.

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.

Counting nodal domains on surfaces of revolution

NASA Astrophysics Data System (ADS)

Karageorge, Panos D.; Smilansky, Uzy

2008-05-01

We consider eigenfunctions of the Laplace-Beltrami operator on special surfaces of revolution. For this separable system, the nodal domains of the (real) eigenfunctions form a checkerboard pattern, and their number νn is proportional to the product of the angular and the 'surface' quantum numbers. Arranging the wavefunctions by increasing values of the Laplace-Beltrami spectrum, we obtain the nodal sequence, whose statistical properties we study. In particular, we investigate the distribution of the normalized counts \\frac{\

Propagation of diffuse light in a turbid medium with multiple spherical inhomogeneities.

PubMed

Pustovit, Vitaliy N; Markel, Vadim A

2004-01-01

We develop a fast and accurate solver for the forward problem of diffusion tomography in the case of several spherical inhomogeneities. The approach allows one to take into account multiple scattering of diffuse waves between different inhomogeneities. Theoretical results are illustrated with numerical examples; excellent numerical convergence and efficiency are demonstrated. The method is generalized for the case of additional planar diffuse-nondiffuse interfaces and is therefore applicable to the half-space and slab imaging geometries.

Partitioned coupling of advection-diffusion-reaction systems and Brinkman flows

NASA Astrophysics Data System (ADS)

Lenarda, Pietro; Paggi, Marco; Ruiz Baier, Ricardo

2017-09-01

We present a partitioned algorithm aimed at extending the capabilities of existing solvers for the simulation of coupled advection-diffusion-reaction systems and incompressible, viscous flow. The space discretisation of the governing equations is based on mixed finite element methods defined on unstructured meshes, whereas the time integration hinges on an operator splitting strategy that exploits the differences in scales between the reaction, advection, and diffusion processes, considering the global system as a number of sequentially linked sets of partial differential, and algebraic equations. The flow solver presents the advantage that all unknowns in the system (here vorticity, velocity, and pressure) can be fully decoupled and thus turn the overall scheme very attractive from the computational perspective. The robustness of the proposed method is illustrated with a series of numerical tests in 2D and 3D, relevant in the modelling of bacterial bioconvection and Boussinesq systems.

Classification of reflection-symmetry-protected topological semimetals and nodal superconductors

NASA Astrophysics Data System (ADS)

Chiu, Ching-Kai; Schnyder, Andreas P.

2014-11-01

While the topological classification of insulators, semimetals, and superconductors in terms of nonspatial symmetries is well understood, less is known about topological states protected by crystalline symmetries, such as mirror reflections and rotations. In this work, we systematically classify topological semimetals and nodal superconductors that are protected, not only by nonspatial (i.e., global) symmetries, but also by a crystal reflection symmetry. We find that the classification crucially depends on (i) the codimension of the Fermi surface (nodal line or point) of the semimetal (superconductor), (ii) whether the mirror symmetry commutes or anticommutes with the nonspatial symmetries, and (iii) how the Fermi surfaces (nodal lines or points) transform under the mirror reflection and nonspatial symmetries. The classification is derived by examining all possible symmetry-allowed mass terms that can be added to the Bloch or Bogoliubov-de Gennes Hamiltonian in a given symmetry class and by explicitly deriving topological invariants. We discuss several examples of reflection-symmetry-protected topological semimetals and nodal superconductors, including topological crystalline semimetals with mirror Z2 numbers and topological crystalline nodal superconductors with mirror winding numbers.

Acceleration of FDTD mode solver by high-performance computing techniques.

PubMed

Han, Lin; Xi, Yanping; Huang, Wei-Ping

2010-06-21

A two-dimensional (2D) compact finite-difference time-domain (FDTD) mode solver is developed based on wave equation formalism in combination with the matrix pencil method (MPM). The method is validated for calculation of both real guided and complex leaky modes of typical optical waveguides against the bench-mark finite-difference (FD) eigen mode solver. By taking advantage of the inherent parallel nature of the FDTD algorithm, the mode solver is implemented on graphics processing units (GPUs) using the compute unified device architecture (CUDA). It is demonstrated that the high-performance computing technique leads to significant acceleration of the FDTD mode solver with more than 30 times improvement in computational efficiency in comparison with the conventional FDTD mode solver running on CPU of a standard desktop computer. The computational efficiency of the accelerated FDTD method is in the same order of magnitude of the standard finite-difference eigen mode solver and yet require much less memory (e.g., less than 10%). Therefore, the new method may serve as an efficient, accurate and robust tool for mode calculation of optical waveguides even when the conventional eigen value mode solvers are no longer applicable due to memory limitation.

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.

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

PubMed Central

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

2016-01-01

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

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

Hybrid nodal loop metal: Unconventional magnetoresponse and material realization

NASA Astrophysics Data System (ADS)

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

2018-03-01

A nodal loop is formed by a band crossing along a one-dimensional closed manifold, with each point on the loop a linear nodal point in the transverse dimensions, and can be classified as type I or type II depending on the band dispersion. Here, we propose a class of nodal loops composed of both type-I and type-II points, which are hence termed as hybrid nodal loops. Based on first-principles calculations, we predict the realization of such loops in the existing electride material Ca2As . For a hybrid loop, the Fermi surface consists of coexisting electron and hole pockets that touch at isolated points for an extended range of Fermi energies, without the need for fine-tuning. This leads to unconventional magnetic responses, including the zero-field magnetic breakdown and the momentum-space Klein tunneling observable in the magnetic quantum oscillations, as well as the peculiar anisotropy in the cyclotron resonance.

Type-I and type-II topological nodal superconductors with s -wave interaction

NASA Astrophysics Data System (ADS)

Huang, Beibing; Yang, Xiaosen; Xu, Ning; Gong, Ming

2018-01-01

Topological nodal superconductors with protected gapless points in momentum space are generally realized based on unconventional pairings. In this work we propose a minimal model to realize these topological nodal phases with only s -wave interaction. In our model the linear and quadratic spin-orbit couplings along the two orthogonal directions introduce anisotropic effective unconventional pairings in momentum space. This model may support different nodal superconducting phases characterized by either an integer winding number in BDI class or a Z2 index in D class at the particle-hole invariant axes. In the vicinity of the nodal points the effective Hamiltonian can be described by either type-I or type-II Dirac equations, and the Lifshitz transition from type-I nodal phases to type-II nodal phases can be driven by external in-plane magnetic fields. We show that these nodal phases are robust against weak impurities, which only slightly renormalizes the momentum-independent parameters in the impurity-averaged Hamiltonian, thus these phases are possible to be realized in experiments with real semi-Dirac materials. The smoking-gun evidences to verify these phases based on scanning tunneling spectroscopy method are also briefly discussed.

Nodal Topological Phases in s-wave Superfluid of Ultracold Fermionic Gases

NASA Astrophysics Data System (ADS)

Huang, Bei-Bing; Yang, Xiao-Sen

2018-02-01

The gapless Weyl superfluid has been widely studied in the three-dimensional ultracold fermionic superfluid. In contrast to Weyl superfluid, there exists another kind of gapless superfluid with topologically protected nodal lines, which can be regarded as the superfluid counterpart of nodal line semimetal in the condensed matter physics, just as Weyl superfluid with Weyl semimetal. In this paper we study the ground states of the cold fermionic gases in cubic optical lattices with one-dimensional spin-orbit coupling and transverse Zeeman field and map out the topological phase diagram of the system. We demonstrate that in addition to a fully gapped topologically trivial phase, some different nodal line superfluid phases appear when the Zeeman field is adjusted. The presence of topologically stable nodal lines implies the dispersionless zero-energy flat band in a finite region of the surface Brillouin zone. Experimentally these nodal line superfluid states can be detected via the momentum-resolved radio-frequency spectroscopy. The nodal line topological superfluid provide fertile grounds for exploring exotic quantum matters in the context of ultracold atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11547047 and 11504143

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.

Comparing direct and iterative equation solvers in a large structural analysis software system

NASA Technical Reports Server (NTRS)

Poole, E. L.

1991-01-01

Two direct Choleski equation solvers and two iterative preconditioned conjugate gradient (PCG) equation solvers used in a large structural analysis software system are described. The two direct solvers are implementations of the Choleski method for variable-band matrix storage and sparse matrix storage. The two iterative PCG solvers include the Jacobi conjugate gradient method and an incomplete Choleski conjugate gradient method. The performance of the direct and iterative solvers is compared by solving several representative structural analysis problems. Some key factors affecting the performance of the iterative solvers relative to the direct solvers are identified.

Targeting nodal in conjunction with dacarbazine induces synergistic anticancer effects in metastatic melanoma.

PubMed

Hardy, Katharine M; Strizzi, Luigi; Margaryan, Naira V; Gupta, Kanika; Murphy, George F; Scolyer, Richard A; Hendrix, Mary J C

2015-04-01

Metastatic melanoma is a highly aggressive skin cancer with a poor prognosis. Despite a complete response in fewer than 5% of patients, the chemotherapeutic agent dacarbazine (DTIC) remains the reference drug after almost 40 years. More recently, FDA-approved drugs have shown promise but patient outcome remains modest, predominantly due to drug resistance. As such, combinatorial targeting has received increased attention, and will advance with the identification of new molecular targets. One attractive target for improving melanoma therapy is the growth factor Nodal, whose normal expression is largely restricted to embryonic development, but is reactivated in metastatic melanoma. In this study, we sought to determine how Nodal-positive human melanoma cells respond to DTIC treatment and to ascertain whether targeting Nodal in combination with DTIC would be more effective than monotherapy. A single treatment with DTIC inhibited cell growth but did not induce apoptosis. Rather than reducing Nodal expression, DTIC increased the size of the Nodal-positive subpopulation, an observation coincident with increased cellular invasion. Importantly, clinical tissue specimens from patients with melanomas refractory to DTIC therapy stained positive for Nodal expression, both in pre- and post-DTIC tumors, underscoring the value of targeting Nodal. In vitro, anti-Nodal antibodies alone had some adverse effects on proliferation and apoptosis, but combining DTIC treatment with anti-Nodal antibodies decreased cell growth and increased apoptosis synergistically, at concentrations incapable of producing meaningful effects as monotherapy. Targeting Nodal in combination with DTIC therapy holds promise for the treatment of metastatic melanoma. ©2015 American Association for Cancer Research.

Implications of inaccurate clinical nodal staging in pancreatic adenocarcinoma.

PubMed

Swords, Douglas S; Firpo, Matthew A; Johnson, Kirsten M; Boucher, Kenneth M; Scaife, Courtney L; Mulvihill, Sean J

2017-07-01

Many patients with stage I-II pancreatic adenocarcinoma do not undergo resection. We hypothesized that (1) clinical staging underestimates nodal involvement, causing stage IIB to have a greater percent of resected patients and (2) this stage-shift causes discrepancies in observed survival. The Surveillance, Epidemiology, and End Results (SEER) research database was used to evaluate cause-specific survival in patients with pancreatic adenocarcinoma from 2004-2012. Survival was compared using the log-rank test. Single-center data on 105 patients who underwent resection of pancreatic adenocarcinoma without neoadjuvant treatment were used to compare clinical and pathologic nodal staging. In SEER data, medium-term survival in stage IIB was superior to IB and IIA, with median cause-specific survival of 14, 9, and 11 months, respectively (P < .001). Seventy-two percent of stage IIB patients underwent resection vs 28% in IB and 36% in IIA (P < .001). In our institutional data, 12.4% of patients had clinical evidence of nodal involvement vs 69.5% by pathologic staging (P < .001). Among clinical stage IA-IIA patients, 71.6% had nodal involvement by pathologic staging. Both SEER and institutional data support substantial underestimation of nodal involvement by clinical staging. This finding has implications in decisions regarding neoadjuvant therapy and analysis of outcomes in the absence of pathologic staging. Copyright © 2017 Elsevier Inc. All rights reserved.

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. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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.

Evaluation of the use of nodal methods for MTR neutronic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 timemore » limitations such as are required for the RERTR program.« less

Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers

PubMed Central

Cai, Qin; Hsieh, Meng-Juei; Wang, Jun; Luo, Ray

2014-01-01

We implemented and optimized seven finite-difference solvers for the full nonlinear Poisson-Boltzmann equation in biomolecular applications, including four relaxation methods, one conjugate gradient method, and two inexact Newton methods. The performance of the seven solvers was extensively evaluated with a large number of nucleic acids and proteins. Worth noting is the inexact Newton method in our analysis. We investigated the role of linear solvers in its performance by incorporating the incomplete Cholesky conjugate gradient and the geometric multigrid into its inner linear loop. We tailored and optimized both linear solvers for faster convergence rate. In addition, we explored strategies to optimize the successive over-relaxation method to reduce its convergence failures without too much sacrifice in its convergence rate. Specifically we attempted to adaptively change the relaxation parameter and to utilize the damping strategy from the inexact Newton method to improve the successive over-relaxation method. Our analysis shows that the nonlinear methods accompanied with a functional-assisted strategy, such as the conjugate gradient method and the inexact Newton method, can guarantee convergence in the tested molecules. Especially the inexact Newton method exhibits impressive performance when it is combined with highly efficient linear solvers that are tailored for its special requirement. PMID:24723843

Oasis: A high-level/high-performance open source Navier-Stokes solver

NASA Astrophysics Data System (ADS)

Mortensen, Mikael; Valen-Sendstad, Kristian

2015-03-01

Oasis is a high-level/high-performance finite element Navier-Stokes solver written from scratch in Python using building blocks from the FEniCS project (fenicsproject.org). The solver is unstructured and targets large-scale applications in complex geometries on massively parallel clusters. Oasis utilizes MPI and interfaces, through FEniCS, to the linear algebra backend PETSc. Oasis advocates a high-level, programmable user interface through the creation of highly flexible Python modules for new problems. Through the high-level Python interface the user is placed in complete control of every aspect of the solver. A version of the solver, that is using piecewise linear elements for both velocity and pressure, is shown to reproduce very well the classical, spectral, turbulent channel simulations of Moser et al. (1999). The computational speed is strongly dominated by the iterative solvers provided by the linear algebra backend, which is arguably the best performance any similar implicit solver using PETSc may hope for. Higher order accuracy is also demonstrated and new solvers may be easily added within the same framework.

Optical conductivity of three and two dimensional topological nodal-line semimetals

NASA Astrophysics Data System (ADS)

Barati, Shahin; Abedinpour, Saeed H.

2017-10-01

The peculiar shape of the Fermi surface of topological nodal-line semimetals at low carrier concentrations results in their unusual optical and transport properties. We analytically investigate the linear optical responses of three- and two-dimensional nodal-line semimetals using the Kubo formula. The optical conductivity of a three-dimensional nodal-line semimetal is anisotropic. Along the axial direction (i.e., the direction perpendicular to the nodal-ring plane), the Drude weight has a linear dependence on the chemical potential at both low and high carrier dopings. For the radial direction (i.e., the direction parallel to the nodal-ring plane), this dependence changes from linear into quadratic in the transition from low into high carrier concentration. The interband contribution into optical conductivity is also anisotropic. In particular, at large frequencies, it saturates to a constant value for the axial direction and linearly increases with frequency along the radial direction. In two-dimensional nodal-line semimetals, no interband optical transition could be induced and the only contribution to the optical conductivity arises from the intraband excitations. The corresponding Drude weight is independent of the carrier density at low carrier concentrations and linearly increases with chemical potential at high carrier doping.

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

Winding numbers of nodal points in Fe-based superconductors

NASA Astrophysics Data System (ADS)

Chichinadze, Dmitry V.; Chubukov, Andrey V.

2018-03-01

We analyze the nodal points in multiorbital Fe-based superconductors from a topological perspective. We consider the s+- gap structure with accidental nodes, and the d -wave gap with nodes along the symmetry directions. In both cases, the nodal points can be moved by varying an external parameter, e.g., a degree of interpocket pairing. Eventually, the nodes merge and annihilate via a Lifshitz-type transition. We discuss the Lifshitz transition in Fe-based superconductors from a topological point of view. We show, both analytically and numerically, that the merging nodal points have winding numbers of opposite sign. This is consistent with the general reasoning that the total winding number is a conserved quantity in the Lifshitz transition.

Update on Advection-Diffusion Purge Flow Model

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

Gaseous purge is commonly used in sensitive spacecraft optical or electronic instruments to prevent infiltration of contaminants and/or water vapor. Typically, purge is sized using simplistic zero-dimensional models that do not take into account instrument geometry, surface effects, and the dependence of diffusive flux on the concentration gradient. For this reason, an axisymmetric computational fluid dynamics (CFD) simulation was recently developed to model contaminant infiltration and removal by purge. The solver uses a combined Navier-Stokes and Advection-Diffusion approach. In this talk, we report on updates in the model, namely inclusion of a particulate transport model.

Pathology of nodal marginal zone lymphomas.

PubMed

Pileri, Stefano; Ponzoni, Maurilio

Nodal marginal zone B cell lymphomas (NMZLs) are a rare group of lymphoid disorders part of the spectrum of marginal zone B-cell lymphomas, which encompass splenic marginal one B-cell lymphoma (SMZL) and extra nodal marginal zone of B-cell lymphoma (EMZL), often of MALT-type. Two clinicopathological forms of NMZL are recognized: adult-type and pediatric-type, respectively. NMZLs show overlapping features with other types of MZ, but distinctive features as well. In this review, we will focus on the salient distinguishing features of NMZL mostly under morphological/immunophenotypical/molecular perspectives in views of the recent acquisitions and forthcoming updated 2016 WHO classification of lymphoid malignancies. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

A quantitative description of normal AV nodal conduction curve in man.

PubMed

Teague, S; Collins, S; Wu, D; Denes, P; Rosen, K; Arzbaecher, R

1976-01-01

The AV nodal conduction curve generated by the atrial extrastimulus technique has been described only qualitatively in man, making clinical comparison of known normal curves with those of suspected AV nodal dysfunction difficult. Also, the effects of physiological and pharmacological interventions have not been quantifiable. In 50 patients with normal AV conduction as defined by normal AH (less than 130 ms), normal AV nodal effective and functional refractory periods (less than 380 and less than 500 ms), and absence of demonstrable dual AV nodal pathways, we found that conduction curves (at sinus rhythm or longest paced cycle length) can be described by an exponential equation of the form delta = Ae-Bx. In this equation, delta is the increase in AV nodal conduction time of an extrastimulus compared to that of a regular beat and x is extrastimulus interval. The natural logarithm of this equation is linear in the semilogarithmic plane, thus permitting the constants A and B to be easily determined by a least-squares regression analysis with a hand calculator.

Targeting Nodal in Conjunction with Dacarbazine Induces Synergistic Anti-cancer Effects in Metastatic Melanoma

PubMed Central

Hardy, Katharine M.; Strizzi, Luigi; Margaryan, Naira V.; Gupta, Kanika; Murphy, George F.; Scolyer, Richard A.; Hendrix, Mary J.C.

2015-01-01

Metastatic melanoma is a highly aggressive skin cancer with a poor prognosis. Despite a complete response in fewer than 5% of patients, the chemotherapeutic agent Dacarbazine (DTIC) remains the reference drug after almost 40 years. More recently FDA approved drugs have shown promise but patient outcome remains modest, predominantly due to drug resistance. As such, combinatorial targeting has received increased attention, and will advance with the identification of new molecular targets. One attractive target for improving melanoma therapy is the growth factor Nodal, whose normal expression is largely restricted to embryonic development, but is reactivated in metastatic melanoma. In this study, we sought to determine how Nodal-positive human melanoma cells respond to DTIC treatment and to ascertain if targeting Nodal in combination with DTIC would be more effective than monotherapy. A single treatment with DTIC inhibited cell growth but did not induce apoptosis. Rather than reducing Nodal expression, DTIC increased the size of the Nodal-positive subpopulation, an observation coincident with increased cellular invasion. Importantly, clinical tissue specimens from patients with melanomas refractory to DTIC therapy stained positive for Nodal expression, both in pre- and post-DTIC tumors, underscoring the value of targeting Nodal. In vitro, anti-Nodal antibodies alone had some adverse effects on proliferation and apoptosis, but combining DTIC treatment with anti-Nodal antibodies decreased cell growth and increased apoptosis synergistically, at concentrations incapable of producing meaningful effects as monotherapy. Implications Targeting Nodal in combination with DTIC therapy holds promise for the treatment of metastatic melanoma. PMID:25767211

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.

Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling

PubMed Central

Norris, Megan L; Pauli, Andrea; Gagnon, James A; Lord, Nathan D; Rogers, Katherine W; Mosimann, Christian; Zon, Leonard I

2017-01-01

Toddler/Apela/Elabela is a conserved secreted peptide that regulates mesendoderm development during zebrafish gastrulation. Two non-exclusive models have been proposed to explain Toddler function. The ‘specification model’ postulates that Toddler signaling enhances Nodal signaling to properly specify endoderm, whereas the ‘migration model’ posits that Toddler signaling regulates mesendodermal cell migration downstream of Nodal signaling. Here, we test key predictions of both models. We find that in toddler mutants Nodal signaling is initially normal and increasing endoderm specification does not rescue mesendodermal cell migration. Mesodermal cell migration defects in toddler mutants result from a decrease in animal pole-directed migration and are independent of endoderm. Conversely, endodermal cell migration defects are dependent on a Cxcr4a-regulated tether of the endoderm to mesoderm. These results suggest that Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling and indirectly affects endodermal cell migration via Cxcr4a-signaling. PMID:29117894

Nodal patterning without Lefty inhibitory feedback is functional but fragile

PubMed Central

Gagnon, James A; Pauli, Andrea; Zimmerman, Steven; Aksel, Deniz C; Reyon, Deepak; Tsai, Shengdar Q; Joung, J Keith

2017-01-01

Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in lefty mutants can be rescued by ectopic expression of lefty far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile. PMID:29215332

Development of axisymmetric lattice Boltzmann flux solver for complex multiphase flows

NASA Astrophysics Data System (ADS)

Wang, Yan; Shu, Chang; Yang, Li-Ming; Yuan, Hai-Zhuan

2018-05-01

This paper presents an axisymmetric lattice Boltzmann flux solver (LBFS) for simulating axisymmetric multiphase flows. In the solver, the two-dimensional (2D) multiphase LBFS is applied to reconstruct macroscopic fluxes excluding axisymmetric effects. Source terms accounting for axisymmetric effects are introduced directly into the governing equations. As compared to conventional axisymmetric multiphase lattice Boltzmann (LB) method, the present solver has the kinetic feature for flux evaluation and avoids complex derivations of external forcing terms. In addition, the present solver also saves considerable computational efforts in comparison with three-dimensional (3D) computations. The capability of the proposed solver in simulating complex multiphase flows is demonstrated by studying single bubble rising in a circular tube. The obtained results compare well with the published data.

Occult Nodal Disease Prevalence and Distribution in Recurrent Laryngeal Cancer Requiring Salvage Laryngectomy.

PubMed

Birkeland, Andrew C; Rosko, Andrew J; Issa, Mohamad R; Shuman, Andrew G; Prince, Mark E; Wolf, Gregory T; Bradford, Carol R; McHugh, Jonathan B; Brenner, J Chad; Spector, Matthew E

2016-03-01

The indications for neck dissection concurrent with salvage laryngectomy in the clinically N0 setting remain unclear. Our goals were to determine the prevalence of occult nodal disease, analyze nodal disease distribution patterns, and identify predictors of occult nodal disease in a salvage laryngectomy cohort. Case series with planned data collection. Tertiary academic center. Patients with persistent or recurrent laryngeal squamous cell carcinoma (LSCC) after radiation/chemoradiation failure undergoing salvage laryngectomy with neck dissection. We analyzed a single-institution retrospective case series of patients between 1997 and 2014 and identified those who had clinically N0 (cN0) necks (n = 203). Clinical and pathologic data, including nodal prevalence and distribution, were collected and statistical analyses performed. Overall, cN0 necks had histologically positive occult nodes in 17% (n = 35) of cases. Univariate predictors of occult nodal positivity included recurrent T4 stage (34% T4 vs 12% non-T4; P = .0003) and supraglottic subsite (28% supraglottic vs 10% nonsupraglottic; P = .0006). Histologically positive nodes associated with supraglottic primaries were most frequently positive in ipsilateral levels II and III (17% and 16%). Positive nodes for glottic LSCC were most frequently positive in the ipsilateral and contralateral paratracheal nodes (11% and 9%). Histologically positive occult nodes are identified in 17% of cN0 patients undergoing salvage laryngectomy with neck dissection. Occult nodal disease varies in frequency and distribution based on tumor subsite. Predictors of high (>20%) occult nodal positivity include T4 tumors and supraglottic subsite. In glottic LSCC, the most frequent sites of occult nodal disease are the paratracheal nodal basins. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

Using SPARK as a Solver for Modelica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetter, Michael; Wetter, Michael; Haves, Philip

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 simulationmore » 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.« less

Mass-conserving advection-diffusion Lattice Boltzmann model for multi-species reacting flows

NASA Astrophysics Data System (ADS)

Hosseini, S. A.; Darabiha, N.; Thévenin, D.

2018-06-01

Given the complex geometries usually found in practical applications, the Lattice Boltzmann (LB) method is becoming increasingly attractive. In addition to the simple treatment of intricate geometrical configurations, LB solvers can be implemented on very large parallel clusters with excellent scalability. However, reacting flows and especially combustion lead to additional challenges and have seldom been studied by LB methods. Indeed, overall mass conservation is a pressing issue in modeling multi-component flows. The classical advection-diffusion LB model recovers the species transport equations with the generalized Fick approximation under the assumption of an incompressible flow. However, for flows involving multiple species with different diffusion coefficients and density fluctuations - as is the case with weakly compressible solvers like Lattice Boltzmann -, this approximation is known not to conserve overall mass. In classical CFD, as the Fick approximation does not satisfy the overall mass conservation constraint a diffusion correction velocity is usually introduced. In the present work, a local expression is first derived for this correction velocity in a LB framework. In a second step, the error due to the incompressibility assumption is also accounted for through a modified equilibrium distribution function. Theoretical analyses and simulations show that the proposed scheme performs much better than the conventional advection-diffusion Lattice Boltzmann model in terms of overall mass conservation.

47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... DEMS Nodal Station licenses should specify the maximum number of 10.6 GHz DEMS User Stations to be served by that nodal station. Any increase in that number must be applied for pursuant to § 1.913 of this... Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY...

47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... DEMS Nodal Station licenses should specify the maximum number of 10.6 GHz DEMS User Stations to be served by that nodal station. Any increase in that number must be applied for pursuant to § 1.913 of this... Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY...

47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... DEMS Nodal Station licenses should specify the maximum number of 10.6 GHz DEMS User Stations to be served by that nodal station. Any increase in that number must be applied for pursuant to § 1.913 of this... Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY...

47 CFR 101.503 - Digital Electronic Message Service Nodal Stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... DEMS Nodal Station licenses should specify the maximum number of 10.6 GHz DEMS User Stations to be served by that nodal station. Any increase in that number must be applied for pursuant to § 1.913 of this... Stations. 101.503 Section 101.503 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY...

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.

Tumor microvessel density–associated mast cells in canine nodal lymphoma

PubMed Central

Mann, Elizabeth; Whittington, Lisa

2014-01-01

Objective: Mast cells are associated in angiogenesis in various human and animal neoplasms. However, association of mast cells with tumor microvessel density in canine lymphoma was not previously documented. The objective of the study is to determine if mast cells are increased in canine nodal lymphomas and to evaluate their correlation with tumor microvessel density and grading of lymphomas. Methods: Nodal lymphomas from 33 dogs were studied and compared with nonneoplastic lymph nodes from 6 dogs as control. Mast cell count was made on Toluidine blue stained sections. Immunohistochemistry using antibody against Factor VIII was employed to visualize and determine microvessel density. Results: The mast cell count in lymphoma (2.95 ± 2.4) was significantly higher (p < 0.05) than that in the control (0.83 ± 0.3) and was positively correlated with tumor microvessel density (r = 0.44, p = 0.009). Significant difference was not observed in mast cell count and tumor microvessel density among different gradings of lymphomas. Conclusions: Mast cells are associated with tumor microvessel density in canine nodal lymphoma with no significant difference among gradings of lymphomas. Mast cells may play an important role in development of canine nodal lymphomas. Further detailed investigation on the role of mast cells as important part of tumor microenvironment in canine nodal lymphomas is recommended. PMID:26770752

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

PubMed Central

2014-01-01

Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

PubMed

Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

2014-04-11

Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming

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

PubMed Central

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

2013-01-01

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

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

Comparison of Modal to Nodal Approaches for Wavefront Correction,

DTIC Science & Technology

1986-02-01

the influence function of the wavefront corrector. (Implicit here is the assumption that the influence function is the same for every node, which is...To implement a nodal correction, the wavefront to be corrected is -. .. decomposed using a basis which is determined by the nodal (actuator) influence ... function of the wavefront corrector. This decomposition results in a set of coefficients which correspond to the drive signal required at the

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.

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.

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. D., Jr.

1992-01-01

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 od 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.

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.

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.

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.

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.

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 PbTaSe 2 with strong spin-orbit coupling. Remarkably, the spin-orbit nodal lines in PbTaSe 2 are not only protected by the reflection symmetry butmore » 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.« less

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

New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

NASA Astrophysics Data System (ADS)

Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

2012-02-01

Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Jing; Liu, Su-zhi; Lin, Yan

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 significantmore » 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.« less

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.

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)

Steady potential solver for unsteady aerodynamic analyses

NASA Technical Reports Server (NTRS)

Hoyniak, Dan

1994-01-01

Development of a steady flow solver for use with LINFLO was the objective of this report. The solver must be compatible with LINFLO, be composed of composite mesh, and have transonic capability. The approaches used were: (1) steady flow potential equations written in nonconservative form; (2) Newton's Method; (3) implicit, least-squares, interpolation method to obtain finite difference equations; and (4) matrix inversion routines from LINFLO. This report was given during the NASA LeRC Workshop on Forced Response in Turbomachinery in August of 1993.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Bin; Chen, Luoping; Hu, Xiaozhe

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 investigatemore » the performance of multigrid algorithms with either collective smoothers or distributive smoothers when solving the preconditioner systems.« less

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.

Barrier tunneling of the loop-nodal semimetal in the hyperhoneycomb lattice

NASA Astrophysics Data System (ADS)

Guan, Ji-Huan; Zhang, Yan-Yang; Lu, Wei-Er; Xia, Yang; Li, Shu-Shen

2018-05-01

We theoretically investigate the barrier tunneling in the 3D model of the hyperhoneycomb lattice, which is a nodal-line semimetal with a Dirac loop at zero energy. In the presence of a rectangular potential, the scattering amplitudes for different injecting states around the nodal loop are calculated, by using analytical treatments of the effective model, as well as numerical simulations of the tight binding model. In the low energy regime, states with remarkable transmissions are only concentrated in a small range around the loop plane. When the momentum of the injecting electron is coplanar with the nodal loop, nearly perfect transmissions can occur for a large range of injecting azimuthal angles if the potential is not high. For higher potential energies, the transmission shows a resonant oscillation with the potential, but still with peaks being perfect transmissions that do not decay with the potential width. These strikingly robust transports of the loop-nodal semimetal can be approximately explained by a momentum dependent Dirac Hamiltonian.

Quantum anomalies in nodal line semimetals

NASA Astrophysics Data System (ADS)

Burkov, A. A.

2018-04-01

Topological semimetals are a new class of condensed matter systems with nontrivial electronic structure topology. Their unusual observable properties may often be understood in terms of quantum anomalies. In particular, Weyl and Dirac semimetals, which have point band-touching nodes, are characterized by the chiral anomaly, which leads to the Fermi arc surface states, anomalous Hall effect, negative longitudinal magnetoresistance, and planar Hall effect. In this paper, we explore analogous phenomena in nodal line semimetals. We demonstrate that such semimetals realize a three-dimensional analog of the parity anomaly, which is a known property of two-dimensional Dirac semimetals arising, for example, on the surface of a three-dimensional topological insulator. We relate one of the characteristic properties of nodal line semimetals, namely, the drumhead surface states, to this anomaly, and derive the field theory, which encodes the corresponding anomalous response.

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.

Three-dimensional graphdiyne as a topological nodal-line semimetal

NASA Astrophysics Data System (ADS)

Nomura, Takafumi; Habe, Tetsuro; Sakamoto, Ryota; Koshino, Mikito

2018-05-01

We study the electronic band structure of three-dimensional ABC-stacked (rhombohedral) graphdiyne, which is a new planar carbon allotrope recently fabricated. Using first-principles calculation, we show that the system is a nodal-line semimetal, in which the conduction band and valence band cross at a closed ring in the momentum space. We derive the minimum tight-binding model and the low-energy effective Hamiltonian in a 4 ×4 matrix form. The nodal line is protected by a nontrivial winding number, and it ensures the existence of the topological surface state in a finite-thickness slab. The Fermi surface of the doped system exhibits a peculiar, self-intersecting hourglass structure, which is quite different from the torus or pipe shape in the previously proposed nodal semimetals. Despite its simple configuration, three-dimensional graphdiyne offers unique electronic properties distinct from any other carbon allotropes.

Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Justin; Karra, Satish; Nakshatrala, Kalyana B.

It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, usedmore » for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.« less

Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

DOE PAGES

Chang, Justin; Karra, Satish; Nakshatrala, Kalyana B.

2016-07-26

It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, usedmore » for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.« less

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.

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.

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

Topological nodal superconducting phases and topological phase transition in the hyperhoneycomb lattice

NASA Astrophysics Data System (ADS)

Bouhon, Adrien; Schmidt, Johann; Black-Schaffer, Annica M.

2018-03-01

We establish the topology of the spin-singlet superconducting states in the bare hyperhoneycomb lattice, and we derive analytically the full phase diagram using only symmetry and topology in combination with simple energy arguments. The phase diagram is dominated by two states preserving time-reversal symmetry. We find a line-nodal state dominating at low doping levels that is topologically nontrivial and exhibits surface Majorana flatbands, which we show perfectly match the bulk-boundary correspondence using the Berry phase approach. At higher doping levels, we find a fully gapped state with trivial topology. By analytically calculating the topological invariant of the nodal lines, we derive the critical point between the line-nodal and fully gapped states as a function of both pairing parameters and doping. We find that the line-nodal state is favored not only at lower doping levels but also if symmetry-allowed deformations of the lattice are present. Adding simple energy arguments, we establish that a fully gapped state with broken time-reversal symmetry likely appears covering the actual phase transition. We find this fully gapped state to be topologically trivial, while we find an additional point-nodal state at very low doing levels that also break time-reversal symmetry and has nontrivial topology with associated Fermi surface arcs. We eventually address the robustness of the phase diagram to generalized models also including adiabatic spin-orbit coupling, and we show how all but the point-nodal state are reasonably stable.

Unilateral dampening of Bmp activity by nodal generates cardiac left-right asymmetry.

PubMed

Veerkamp, Justus; Rudolph, Franziska; Cseresnyes, Zoltan; Priller, Florian; Otten, Cécile; Renz, Marc; Schaefer, Liliana; Abdelilah-Seyfried, Salim

2013-03-25

Signaling by Nodal and Bmp is essential for cardiac laterality. How activities of these pathways translate into left-right asymmetric organ morphogenesis is largely unknown. We show that, in zebrafish, Nodal locally reduces Bmp activity on the left side of the cardiac field. This effect is mediated by the extracellular matrix enzyme Hyaluronan synthase 2, expression of which is induced by Nodal. Unilateral reduction of Bmp signaling results in lower expression of nonmuscle myosin II and higher cell motility on the left, driving asymmetric displacement of the entire cardiac field. In silico modeling shows that left-right differences in cell motility are sufficient to induce a robust, directional migration of cardiac tissue. Thus, the mechanism underlying the formation of cardiac left-right asymmetry involves Nodal modulating an antimotogenic Bmp activity. Copyright © 2013 Elsevier Inc. All rights reserved.

Initial system design method for non-rotationally symmetric systems based on Gaussian brackets and Nodal aberration theory.

PubMed

Zhong, Yi; Gross, Herbert

2017-05-01

Freeform surfaces play important roles in improving the imaging performance of off-axis optical systems. However, for some systems with high requirements in specifications, the structure of the freeform surfaces could be very complicated and the number of freeform surfaces could be large. That brings challenges in fabrication and increases the cost. Therefore, to achieve a good initial system with minimum aberrations and reasonable structure before implementing freeform surfaces is essential for optical designers. The already existing initial system design methods are limited to certain types of systems. A universal tool or method to achieve a good initial system efficiently is very important. In this paper, based on the Nodal aberration theory and the system design method using Gaussian Brackets, the initial system design method is extended from rotationally symmetric systems to general non-rotationally symmetric systems. The design steps are introduced and on this basis, two off-axis three-mirror systems are pre-designed using spherical shape surfaces. The primary aberrations are minimized using the nonlinear least-squares solver. This work provides insight and guidance for initial system design of off-axis mirror systems.

An adaptive discontinuous Galerkin solver for aerodynamic flows

NASA Astrophysics Data System (ADS)

Burgess, Nicholas K.

This work considers the accuracy, efficiency, and robustness of an unstructured high-order accurate discontinuous Galerkin (DG) solver for computational fluid dynamics (CFD). Recently, there has been a drive to reduce the discretization error of CFD simulations using high-order methods on unstructured grids. However, high-order methods are often criticized for lacking robustness and having high computational cost. The goal of this work is to investigate methods that enhance the robustness of high-order discontinuous Galerkin (DG) methods on unstructured meshes, while maintaining low computational cost and high accuracy of the numerical solutions. This work investigates robustness enhancement of high-order methods by examining effective non-linear solvers, shock capturing methods, turbulence model discretizations and adaptive refinement techniques. The goal is to develop an all encompassing solver that can simulate a large range of physical phenomena, where all aspects of the solver work together to achieve a robust, efficient and accurate solution strategy. The components and framework for a robust high-order accurate solver that is capable of solving viscous, Reynolds Averaged Navier-Stokes (RANS) and shocked flows is presented. In particular, this work discusses robust discretizations of the turbulence model equation used to close the RANS equations, as well as stable shock capturing strategies that are applicable across a wide range of discretization orders and applicable to very strong shock waves. Furthermore, refinement techniques are considered as both efficiency and robustness enhancement strategies. Additionally, efficient non-linear solvers based on multigrid and Krylov subspace methods are presented. The accuracy, efficiency, and robustness of the solver is demonstrated using a variety of challenging aerodynamic test problems, which include turbulent high-lift and viscous hypersonic flows. Adaptive mesh refinement was found to play a critical role in

Face Centered Cubic SnSe as a Z2 Trivial Dirac Nodal Line Material

NASA Astrophysics Data System (ADS)

Tateishi, Ikuma; Matsuura, Hiroyasu

2018-07-01

The presence of a Dirac nodal line in a time-reversal and inversion symmetric system is dictated by the Z2 index when spin-orbit interaction is absent. In a first principles calculation, we show that a Dirac nodal line can emerge in Z2 trivial material by calculating the band structure of SnSe in a face centered cubic lattice as an example. We qualitatively show that it becomes a topological crystalline insulator when spin-orbit interaction is taken into account. We clarify the origin of the Dirac nodal line by obtaining irreducible representations corresponding to bands and explain the triviality of the Z2 index. We construct an effective model representing the Dirac nodal line using the k · p method, and discuss the Berry phase and a surface state expected from the Dirac nodal line.

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.

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.

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.

Symmorphic Intersecting Nodal Rings in Semiconducting Layers

NASA Astrophysics Data System (ADS)

Gong, Cheng; Xie, Yuee; Chen, Yuanping; Kim, Heung-Sik; Vanderbilt, David

2018-03-01

The unique properties of topological semimetals have strongly driven efforts to seek for new topological phases and related materials. Here, we identify a critical condition for the existence of intersecting nodal rings (INRs) in symmorphic crystals, and further classify all possible kinds of INRs which can be obtained in the layered semiconductors with Amm2 and Cmmm space group symmetries. Several honeycomb structures are suggested to be topological INR semimetals, including layered and "hidden" layered structures. Transitions between the three types of INRs, named as α , β , and γ type, can be driven by external strains in these structures. The resulting surface states and Landau-level structures, more complicated than those resulting from a simple nodal loop, are also discussed.

User's Manual for PCSMS (Parallel Complex Sparse Matrix Solver). Version 1.

NASA Technical Reports Server (NTRS)

Reddy, C. J.

2000-01-01

PCSMS (Parallel Complex Sparse Matrix Solver) is a computer code written to make use of the existing real sparse direct solvers to solve complex, sparse matrix linear equations. PCSMS converts complex matrices into real matrices and use real, sparse direct matrix solvers to factor and solve the real matrices. The solution vector is reconverted to complex numbers. Though, this utility is written for Silicon Graphics (SGI) real sparse matrix solution routines, it is general in nature and can be easily modified to work with any real sparse matrix solver. The User's Manual is written to make the user acquainted with the installation and operation of the code. Driver routines are given to aid the users to integrate PCSMS routines in their own codes.

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

PubMed Central

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

1996-01-01

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

PBEQ-Solver for online visualization of electrostatic potential of biomolecules.

PubMed

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil

2008-07-01

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.

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

Brady's Geothermal Field Nodal Seismometers Metadata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesley Parker

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.

Amplification and protein overexpression of cyclin D1: Predictor of occult nodal metastasis in early oral cancer.

PubMed

Noorlag, Rob; Boeve, Koos; Witjes, Max J H; Koole, Ronald; Peeters, Ton L M; Schuuring, Ed; Willems, Stefan M; van Es, Robert J J

2017-02-01

Accurate nodal staging is pivotal for treatment planning in early (stage I-II) oral cancer. Unfortunately, current imaging modalities lack sensitivity to detect occult nodal metastases. Chromosomal region 11q13, including genes CCND1, Fas-associated death domain (FADD), and CTTN, is often amplified in oral cancer with nodal metastases. However, evidence in predicting occult nodal metastases is limited. In 158 patients with early tongue and floor of mouth (FOM) squamous cell carcinomas, both CCND1 amplification and cyclin D1, FADD, and cortactin protein expression were correlated with occult nodal metastases. CCND1 amplification and cyclin D1 expression correlated with occult nodal metastases. Cyclin D1 expression was validated in an independent multicenter cohort, confirming the correlation with occult nodal metastases in early FOM cancers. Cyclin D1 is a predictive biomarker for occult nodal metastases in early FOM cancers. Prospective research on biopsy material should confirm these results before implementing its use in routine clinical practice. © 2016 Wiley Periodicals, Inc. Head Neck 39: 326-333, 2017. © 2016 Wiley Periodicals, Inc.

Persistence of RSV promotes proliferation and epithelial-mesenchymal transition of bronchial epithelial cells through Nodal signaling.

PubMed

Xiang, Zhao; Liang, Zhang; Yanfeng, Huang; Leitao, Kang

2017-10-01

Nodal may play an important role in the development of cancers. The present study was designed to determine the effects of Nodal induced by respiratory syncytial virus (RSV) infection on the occurrence and development of lung cancer and the underlying mechanisms. After verification of RSV infection by observation of cytopathic effect and indirect immunofluorescence, real-time PCR, Western blot and methylation assays were used to verify the influence of RSV on Nodal expression. Then, a Nodal overexpressed vector was constructed and the effects of Nodal on the proliferation and apoptosis of bronchial epithelial cells (BECs) and epithelial-mesenchymal transition (EMT) were assayed by flow cytometry and Western blot, respectively. Moreover, Lefty and pSmad2/3 were assayed by Western blot and Cyclin D1, CDK4, c-myc and Bcl-2 induced by Nodal overepression or RSV infection were also assayed by real-time PCR. The results showed that Nodal over expression and demethylation of the promoter were observed in BECs after RSV infection. Activation of Nodal promoted proliferation, colony formation and EMT and inhibited apoptosis of BECs. Nodal also promoted malignant change by promoting expression of cyclin D1 and related-dependent kinase and inhibiting apoptosis. Besides, RSV infection inhibited Lefty expression and promoted the activation of pSmad2/3. RSV also promoted Cyclin D1, CDK4, c-myc and Bcl-2 expression through the activation of pSmad2/3. Our data showed that persistence of RSV promoted the proliferation, epithelial-mesenchymal transition and expression of oncogenes through Nodal signaling, which may be associated with the occurrence and development of lung cancers.

Brady's Geothermal Field - Map of DAS, Nodal, Vibroseis and Reftek Station Deployment

DOE Data Explorer

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

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

PubMed Central

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

2013-01-01

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

A Lattice Kinetic Monte Carlo Solver for First-Principles Microkinetic Trend Studies

DOE PAGES

Hoffmann, Max J.; Bligaard, Thomas

2018-01-22

Here, mean-field microkinetic models in combination with Brønsted–Evans–Polanyi like scaling relations have proven highly successful in identifying catalyst materials with good or promising reactivity and selectivity. Analysis of the microkinetic model by means of lattice kinetic Monte Carlo promises a faithful description of a range of atomistic features involving short-range ordering of species in the vicinity of an active site. In this paper, we use the “fruit fly” example reaction of CO oxidation on fcc(111) transition and coinage metals to motivate and develop a lattice kinetic Monte Carlo solver suitable for the numerically challenging case of vastly disparate rate constants.more » As a result, we show that for the case of infinitely fast diffusion and absence of adsorbate-adsorbate interaction it is, in fact, possible to match the prediction of the mean-field-theory method and the lattice kinetic Monte Carlo method. As a corollary, we conclude that lattice kinetic Monte Carlo simulations of surface chemical reactions are most likely to provide additional insight over mean-field simulations if diffusion limitations or adsorbate–adsorbate interactions have a significant influence on the mixing of the adsorbates.« less

A Lattice Kinetic Monte Carlo Solver for First-Principles Microkinetic Trend Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffmann, Max J.; Bligaard, Thomas

Here, mean-field microkinetic models in combination with Brønsted–Evans–Polanyi like scaling relations have proven highly successful in identifying catalyst materials with good or promising reactivity and selectivity. Analysis of the microkinetic model by means of lattice kinetic Monte Carlo promises a faithful description of a range of atomistic features involving short-range ordering of species in the vicinity of an active site. In this paper, we use the “fruit fly” example reaction of CO oxidation on fcc(111) transition and coinage metals to motivate and develop a lattice kinetic Monte Carlo solver suitable for the numerically challenging case of vastly disparate rate constants.more » As a result, we show that for the case of infinitely fast diffusion and absence of adsorbate-adsorbate interaction it is, in fact, possible to match the prediction of the mean-field-theory method and the lattice kinetic Monte Carlo method. As a corollary, we conclude that lattice kinetic Monte Carlo simulations of surface chemical reactions are most likely to provide additional insight over mean-field simulations if diffusion limitations or adsorbate–adsorbate interactions have a significant influence on the mixing of the adsorbates.« less

Parallel performance investigations of an unstructured mesh Navier-Stokes solver

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.

2000-01-01

A Reynolds-averaged Navier-Stokes solver based on unstructured mesh techniques for analysis of high-lift configurations is described. The method makes use of an agglomeration multigrid solver for convergence acceleration. Implicit line-smoothing is employed to relieve the stiffness associated with highly stretched meshes. A GMRES technique is also implemented to speed convergence at the expense of additional memory usage. The solver is cache efficient and fully vectorizable, and is parallelized using a two-level hybrid MPI-OpenMP implementation suitable for shared and/or distributed memory architectures, as well as clusters of shared memory machines. Convergence and scalability results are illustrated for various high-lift cases.

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).

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.

An efficient spectral crystal plasticity solver for GPU architectures

NASA Astrophysics Data System (ADS)

Malahe, Michael

2018-03-01

We present a spectral crystal plasticity (CP) solver for graphics processing unit (GPU) architectures that achieves a tenfold increase in efficiency over prior GPU solvers. The approach makes use of a database containing a spectral decomposition of CP simulations performed using a conventional iterative solver over a parameter space of crystal orientations and applied velocity gradients. The key improvements in efficiency come from reducing global memory transactions, exposing more instruction-level parallelism, reducing integer instructions and performing fast range reductions on trigonometric arguments. The scheme also makes more efficient use of memory than prior work, allowing for larger problems to be solved on a single GPU. We illustrate these improvements with a simulation of 390 million crystal grains on a consumer-grade GPU, which executes at a rate of 2.72 s per strain step.

Modifications of steam condensation model implemented in commercial solver

NASA Astrophysics Data System (ADS)

Sova, Libor; Jun, Gukchol; ŠÅ¥astný, Miroslav

2017-09-01

Nucleation theory and droplet grow theory and methods how they are incorporated into numerical solvers are crucial factors for proper wet steam modelling. Unfortunately, they are still covered by cloud of uncertainty and therefore some calibration of these models according to reliable experimental results is important for practical analyses of steam turbines. This article demonstrates how is possible to calibrate wet steam model incorporated into commercial solver ANSYS CFX.

An incomplete assembly with thresholding algorithm for systems of reaction-diffusion equations in three space dimensions IAT for reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Moore, Peter K.

2003-07-01

Solving systems of reaction-diffusion equations in three space dimensions can be prohibitively expensive both in terms of storage and CPU time. Herein, I present a new incomplete assembly procedure that is designed to reduce storage requirements. Incomplete assembly is analogous to incomplete factorization in that only a fixed number of nonzero entries are stored per row and a drop tolerance is used to discard small values. The algorithm is incorporated in a finite element method-of-lines code and tested on a set of reaction-diffusion systems. The effect of incomplete assembly on CPU time and storage and on the performance of the temporal integrator DASPK, algebraic solver GMRES and preconditioner ILUT is studied.

Adaptive Implicit Non-Equilibrium Radiation Diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Philip, Bobby; Wang, Zhen; Berrill, Mark A

2013-01-01

We describe methods for accurate and efficient long term time integra- tion of non-equilibrium radiation diffusion systems: implicit time integration for effi- cient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while control- ling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

A new fast direct solver for the boundary element method

NASA Astrophysics Data System (ADS)

Huang, S.; Liu, Y. J.

2017-09-01

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.

Immunoarchitectural patterns in nodal marginal zone B-cell lymphoma: a study of 51 cases.

PubMed

Salama, Mohamed E; Lossos, Izidore S; Warnke, Roger A; Natkunam, Yasodha

2009-07-01

Nodal marginal zone lymphoma (NMZL) represents a rare and heterogeneous group that lacks markers specific for the diagnosis. We evaluated morphologic and immunoarchitectural features of 51 NMZLs, and the following immunostains were performed: CD20, CD21, CD23, CD5, CD3, CD43, CD10, Ki-67, BCL1, BCL2, BCL6, HGAL, and LMO2. Four immunoarchitectural patterns were evident: diffuse (38 [75%]), well-formed nodular/follicular (5 [10%]), interfollicular (7 [14%]), and perifollicular (1 [2%]). Additional features included a monocytoid component (36 [71%]), admixed large cells (20 [39%]), plasma cells (24 [47%]), compartmentalizing stromal sclerosis (13 [25%]), and prominent blood vessel sclerosis (10 [20%]). CD21 highlighted disrupted follicular dendritic cell meshwork in 35 (71%) of 49 cases, and CD43 coexpression was present in 10 (24%) of 42 cases. A panel of germinal center-associated markers was helpful in eliminating cases of diffuse follicle center lymphoma. Our results highlight the histologic and immunoarchitectural spectrum of NMZL and the usefulness of immunohistochemical analysis for CD43, CD23, CD21, BCL6, HGAL, and LMO2 in the diagnosis of NMZL.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lao, Louis; Department of Radiation Oncology, Auckland City Hospital, Auckland; Hope, Andrew J.

2014-09-01

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

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).

Local error estimates for adaptive simulation of the Reaction–Diffusion Master Equation via operator splitting

PubMed Central

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2015-01-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity. PMID:26865735

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

PubMed

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2014-06-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

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.

A CFD Heterogeneous Parallel Solver Based on Collaborating CPU and GPU

NASA Astrophysics Data System (ADS)

Lai, Jianqi; Tian, Zhengyu; Li, Hua; Pan, Sha

2018-03-01

Since Graphic Processing Unit (GPU) has a strong ability of floating-point computation and memory bandwidth for data parallelism, it has been widely used in the areas of common computing such as molecular dynamics (MD), computational fluid dynamics (CFD) and so on. The emergence of compute unified device architecture (CUDA), which reduces the complexity of compiling program, brings the great opportunities to CFD. There are three different modes for parallel solution of NS equations: parallel solver based on CPU, parallel solver based on GPU and heterogeneous parallel solver based on collaborating CPU and GPU. As we can see, GPUs are relatively rich in compute capacity but poor in memory capacity and the CPUs do the opposite. We need to make full use of the GPUs and CPUs, so a CFD heterogeneous parallel solver based on collaborating CPU and GPU has been established. Three cases are presented to analyse the solver’s computational accuracy and heterogeneous parallel efficiency. The numerical results agree well with experiment results, which demonstrate that the heterogeneous parallel solver has high computational precision. The speedup on a single GPU is more than 40 for laminar flow, it decreases for turbulent flow, but it still can reach more than 20. What’s more, the speedup increases as the grid size becomes larger.

The orphan receptor ALK7 and the Activin receptor ALK4 mediate signaling by Nodal proteins during vertebrate development.

PubMed

Reissmann, E; Jörnvall, H; Blokzijl, A; Andersson, O; Chang, C; Minchiotti, G; Persico, M G; Ibáñez, C F; Brivanlou, A H

2001-08-01

Nodal proteins have crucial roles in mesendoderm formation and left-right patterning during vertebrate development. The molecular mechanisms of signal transduction by Nodal and related ligands, however, are not fully understood. In this paper, we present biochemical and functional evidence that the orphan type I serine/threonine kinase receptor ALK7 acts as a receptor for mouse Nodal and Xenopus Nodal-related 1 (Xnr1). Receptor reconstitution experiments indicate that ALK7 collaborates with ActRIIB to confer responsiveness to Xnr1 and Nodal. Both receptors can independently bind Xnr1. In addition, Cripto, an extracellular protein genetically implicated in Nodal signaling, can independently interact with both Xnr1 and ALK7, and its expression greatly enhances the ability of ALK7 and ActRIIB to respond to Nodal ligands. The Activin receptor ALK4 is also able to mediate Nodal signaling but only in the presence of Cripto, with which it can also interact directly. A constitutively activated form of ALK7 mimics the mesendoderm-inducing activity of Xnr1 in Xenopus embryos, whereas a dominant-negative ALK7 specifically blocks the activities of Nodal and Xnr1 but has little effect on other related ligands. In contrast, a dominant-negative ALK4 blocks all mesoderm-inducing ligands tested, including Nodal, Xnr1, Xnr2, Xnr4, and Activin. In agreement with a role in Nodal signaling, ALK7 mRNA is localized to the ectodermal and organizer regions of Xenopus gastrula embryos and is expressed during early stages of mouse embryonic development. Therefore, our results indicate that both ALK4 and ALK7 can mediate signal transduction by Nodal proteins, although ALK7 appears to be a receptor more specifically dedicated to Nodal signaling.

The orphan receptor ALK7 and the Activin receptor ALK4 mediate signaling by Nodal proteins during vertebrate development

PubMed Central

Reissmann, Eva; Jörnvall, Henrik; Blokzijl, Andries; Andersson, Olov; Chang, Chenbei; Minchiotti, Gabriella; Persico, M. Graziella; Ibáñez, Carlos F.; Brivanlou, Ali H.

2001-01-01

Nodal proteins have crucial roles in mesendoderm formation and left–right patterning during vertebrate development. The molecular mechanisms of signal transduction by Nodal and related ligands, however, are not fully understood. In this paper, we present biochemical and functional evidence that the orphan type I serine/threonine kinase receptor ALK7 acts as a receptor for mouse Nodal and Xenopus Nodal-related 1 (Xnr1). Receptor reconstitution experiments indicate that ALK7 collaborates with ActRIIB to confer responsiveness to Xnr1 and Nodal. Both receptors can independently bind Xnr1. In addition, Cripto, an extracellular protein genetically implicated in Nodal signaling, can independently interact with both Xnr1 and ALK7, and its expression greatly enhances the ability of ALK7 and ActRIIB to respond to Nodal ligands. The Activin receptor ALK4 is also able to mediate Nodal signaling but only in the presence of Cripto, with which it can also interact directly. A constitutively activated form of ALK7 mimics the mesendoderm-inducing activity of Xnr1 in Xenopus embryos, whereas a dominant-negative ALK7 specifically blocks the activities of Nodal and Xnr1 but has little effect on other related ligands. In contrast, a dominant-negative ALK4 blocks all mesoderm-inducing ligands tested, including Nodal, Xnr1, Xnr2, Xnr4, and Activin. In agreement with a role in Nodal signaling, ALK7 mRNA is localized to the ectodermal and organizer regions of Xenopus gastrula embryos and is expressed during early stages of mouse embryonic development. Therefore, our results indicate that both ALK4 and ALK7 can mediate signal transduction by Nodal proteins, although ALK7 appears to be a receptor more specifically dedicated to Nodal signaling. PMID:11485994

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

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.

Fault tolerance in an inner-outer solver: A GVR-enabled case study

DOE PAGES

Zhang, Ziming; Chien, Andrew A.; Teranishi, Keita

2015-04-18

Resilience is a major challenge for large-scale systems. It is particularly important for iterative linear solvers, since they take much of the time of many scientific applications. We show that single bit flip errors in the Flexible GMRES iterative linear solver can lead to high computational overhead or even failure to converge to the right answer. Informed by these results, we design and evaluate several strategies for fault tolerance in both inner and outer solvers appropriate across a range of error rates. We implement them, extending Trilinos’ solver library with the Global View Resilience (GVR) programming model, which provides multi-streammore » snapshots, multi-version data structures with portable and rich error checking/recovery. Lastly, experimental results validate correct execution with low performance overhead under varied error conditions.« less

Greedy algorithms for diffuse optical tomography reconstruction

NASA Astrophysics Data System (ADS)

Dileep, B. P. V.; Das, Tapan; Dutta, Pranab K.

2018-03-01

Diffuse optical tomography (DOT) is a noninvasive imaging modality that reconstructs the optical parameters of a highly scattering medium. However, the inverse problem of DOT is ill-posed and highly nonlinear due to the zig-zag propagation of photons that diffuses through the cross section of tissue. The conventional DOT imaging methods iteratively compute the solution of forward diffusion equation solver which makes the problem computationally expensive. Also, these methods fail when the geometry is complex. Recently, the theory of compressive sensing (CS) has received considerable attention because of its efficient use in biomedical imaging applications. The objective of this paper is to solve a given DOT inverse problem by using compressive sensing framework and various Greedy algorithms such as orthogonal matching pursuit (OMP), compressive sampling matching pursuit (CoSaMP), and stagewise orthogonal matching pursuit (StOMP), regularized orthogonal matching pursuit (ROMP) and simultaneous orthogonal matching pursuit (S-OMP) have been studied to reconstruct the change in the absorption parameter i.e, Δα from the boundary data. Also, the Greedy algorithms have been validated experimentally on a paraffin wax rectangular phantom through a well designed experimental set up. We also have studied the conventional DOT methods like least square method and truncated singular value decomposition (TSVD) for comparison. One of the main features of this work is the usage of less number of source-detector pairs, which can facilitate the use of DOT in routine applications of screening. The performance metrics such as mean square error (MSE), normalized mean square error (NMSE), structural similarity index (SSIM), and peak signal to noise ratio (PSNR) have been used to evaluate the performance of the algorithms mentioned in this paper. Extensive simulation results confirm that CS based DOT reconstruction outperforms the conventional DOT imaging methods in terms of

Application of an unstructured grid flow solver to planes, trains and automobiles

NASA Technical Reports Server (NTRS)

Spragle, Gregory S.; Smith, Wayne A.; Yadlin, Yoram

1993-01-01

Rampant, an unstructured flow solver developed at Fluent Inc., is used to compute three-dimensional, viscous, turbulent, compressible flow fields within complex solution domains. Rampant is an explicit, finite-volume flow solver capable of computing flow fields using either triangular (2d) or tetrahedral (3d) unstructured grids. Local time stepping, implicit residual smoothing, and multigrid techniques are used to accelerate the convergence of the explicit scheme. The paper describes the Rampant flow solver and presents flow field solutions about a plane, train, and automobile.

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisicaro, G., E-mail: giuseppe.fisicaro@unibas.ch; Goedecker, S.; Genovese, L.

2016-01-07

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and themore » linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.« less

A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments.

PubMed

Fisicaro, G; Genovese, L; Andreussi, O; Marzari, N; Goedecker, S

2016-01-07

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.

A low diffusive Lagrange-remap scheme for the simulation of violent air-water free-surface flows

NASA Astrophysics Data System (ADS)

Bernard-Champmartin, Aude; De Vuyst, Florian

2014-10-01

In 2002, Després and Lagoutière [17] proposed a low-diffusive advection scheme for pure transport equation problems, which is particularly accurate for step-shaped solutions, and thus suited for interface tracking procedure by a color function. This has been extended by Kokh and Lagoutière [28] in the context of compressible multifluid flows using a five-equation model. In this paper, we explore a simplified variant approach for gas-liquid three-equation models. The Eulerian numerical scheme has two ingredients: a robust remapped Lagrange solver for the solution of the volume-averaged equations, and a low diffusive compressive scheme for the advection of the gas mass fraction. Numerical experiments show the performance of the computational approach on various flow reference problems: dam break, sloshing of a tank filled with water, water-water impact and finally a case of Rayleigh-Taylor instability. One of the advantages of the present interface capturing solver is its natural implementation on parallel processors or computers.

Using hybrid implicit Monte Carlo diffusion to simulate gray radiation hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleveland, Mathew A., E-mail: cleveland7@llnl.gov; Gentile, Nick

This work describes how to couple a hybrid Implicit Monte Carlo Diffusion (HIMCD) method with a Lagrangian hydrodynamics code to evaluate the coupled radiation hydrodynamics equations. This HIMCD method dynamically applies Implicit Monte Carlo Diffusion (IMD) [1] to regions of a problem that are opaque and diffusive while applying standard Implicit Monte Carlo (IMC) [2] to regions where the diffusion approximation is invalid. We show that this method significantly improves the computational efficiency as compared to a standard IMC/Hydrodynamics solver, when optically thick diffusive material is present, while maintaining accuracy. Two test cases are used to demonstrate the accuracy andmore » performance of HIMCD as compared to IMC and IMD. The first is the Lowrie semi-analytic diffusive shock [3]. The second is a simple test case where the source radiation streams through optically thin material and heats a thick diffusive region of material causing it to rapidly expand. We found that HIMCD proves to be accurate, robust, and computationally efficient for these test problems.« less

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).

Boosting Stochastic Problem Solvers Through Online Self-Analysis of Performance

DTIC Science & Technology

2003-07-21

Boosting Stochastic Problem Solvers Through Online Self-Analysis of Performance Vincent A. Cicirello CMU-RI-TR-03-27 Submitted in partial fulfillment...AND SUBTITLE Boosting Stochastic Problem Solvers Through Online Self-Analysis of Performance 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...lead to the development of a search control framework, called QD-BEACON that uses online -generated statistical models of search performance to

Application of NASA General-Purpose Solver to Large-Scale Computations in Aeroacoustics

NASA Technical Reports Server (NTRS)

Watson, Willie R.; Storaasli, Olaf O.

2004-01-01

Of several iterative and direct equation solvers evaluated previously for computations in aeroacoustics, the most promising was the NASA-developed General-Purpose Solver (winner of NASA's 1999 software of the year award). This paper presents detailed, single-processor statistics of the performance of this solver, which has been tailored and optimized for large-scale aeroacoustic computations. The statistics, compiled using an SGI ORIGIN 2000 computer with 12 Gb available memory (RAM) and eight available processors, are the central processing unit time, RAM requirements, and solution error. The equation solver is capable of solving 10 thousand complex unknowns in as little as 0.01 sec using 0.02 Gb RAM, and 8.4 million complex unknowns in slightly less than 3 hours using all 12 Gb. This latter solution is the largest aeroacoustics problem solved to date with this technique. The study was unable to detect any noticeable error in the solution, since noise levels predicted from these solution vectors are in excellent agreement with the noise levels computed from the exact solution. The equation solver provides a means for obtaining numerical solutions to aeroacoustics problems in three dimensions.

A nodal signaling pathway regulates the laterality of neuroanatomical asymmetries in the zebrafish forebrain.

PubMed

Concha, M L; Burdine, R D; Russell, C; Schier, A F; Wilson, S W

2000-11-01

Animals show behavioral asymmetries that are mediated by differences between the left and right sides of the brain. We report that the laterality of asymmetric development of the diencephalic habenular nuclei and the photoreceptive pineal complex is regulated by the Nodal signaling pathway and by midline tissue. Analysis of zebrafish embryos with compromised Nodal signaling reveals an early role for this pathway in the repression of asymmetrically expressed genes in the diencephalon. Later signaling mediated by the EGF-CFC protein One-eyed pinhead and the forkhead transcription factor Schmalspur is required to overcome this repression. When expression of Nodal pathway genes is either absent or symmetrical, neuroanatomical asymmetries are still established but are randomized. This indicates that Nodal signaling is not required for asymmetric development per se but is essential to determine the laterality of the asymmetry.

An approach to model reactor core nodalization for deterministic safety analysis

NASA Astrophysics Data System (ADS)

Salim, Mohd Faiz; Samsudin, Mohd Rafie; Mamat @ Ibrahim, Mohd Rizal; Roslan, Ridha; Sadri, Abd Aziz; Farid, Mohd Fairus Abd

2016-01-01

Adopting good nodalization strategy is essential to produce an accurate and high quality input model for Deterministic Safety Analysis (DSA) using System Thermal-Hydraulic (SYS-TH) computer code. The purpose of such analysis is to demonstrate the compliance against regulatory requirements and to verify the behavior of the reactor during normal and accident conditions as it was originally designed. Numerous studies in the past have been devoted to the development of the nodalization strategy for small research reactor (e.g. 250kW) up to the bigger research reactor (e.g. 30MW). As such, this paper aims to discuss the state-of-arts thermal hydraulics channel to be employed in the nodalization for RTP-TRIGA Research Reactor specifically for the reactor core. At present, the required thermal-hydraulic parameters for reactor core, such as core geometrical data (length, coolant flow area, hydraulic diameters, and axial power profile) and material properties (including the UZrH1.6, stainless steel clad, graphite reflector) have been collected, analyzed and consolidated in the Reference Database of RTP using standardized methodology, mainly derived from the available technical documentations. Based on the available information in the database, assumptions made on the nodalization approach and calculations performed will be discussed and presented. The development and identification of the thermal hydraulics channel for the reactor core will be implemented during the SYS-TH calculation using RELAP5-3D® computer code. This activity presented in this paper is part of the development of overall nodalization description for RTP-TRIGA Research Reactor under the IAEA Norwegian Extra-Budgetary Programme (NOKEBP) mentoring project on Expertise Development through the Analysis of Reactor Thermal-Hydraulics for Malaysia, denoted as EARTH-M.

An approach to model reactor core nodalization for deterministic safety analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salim, Mohd Faiz, E-mail: mohdfaizs@tnb.com.my; Samsudin, Mohd Rafie, E-mail: rafies@tnb.com.my; Mamat Ibrahim, Mohd Rizal, E-mail: m-rizal@nuclearmalaysia.gov.my

Adopting good nodalization strategy is essential to produce an accurate and high quality input model for Deterministic Safety Analysis (DSA) using System Thermal-Hydraulic (SYS-TH) computer code. The purpose of such analysis is to demonstrate the compliance against regulatory requirements and to verify the behavior of the reactor during normal and accident conditions as it was originally designed. Numerous studies in the past have been devoted to the development of the nodalization strategy for small research reactor (e.g. 250kW) up to the bigger research reactor (e.g. 30MW). As such, this paper aims to discuss the state-of-arts thermal hydraulics channel to bemore » employed in the nodalization for RTP-TRIGA Research Reactor specifically for the reactor core. At present, the required thermal-hydraulic parameters for reactor core, such as core geometrical data (length, coolant flow area, hydraulic diameters, and axial power profile) and material properties (including the UZrH{sub 1.6}, stainless steel clad, graphite reflector) have been collected, analyzed and consolidated in the Reference Database of RTP using standardized methodology, mainly derived from the available technical documentations. Based on the available information in the database, assumptions made on the nodalization approach and calculations performed will be discussed and presented. The development and identification of the thermal hydraulics channel for the reactor core will be implemented during the SYS-TH calculation using RELAP5-3D{sup ®} computer code. This activity presented in this paper is part of the development of overall nodalization description for RTP-TRIGA Research Reactor under the IAEA Norwegian Extra-Budgetary Programme (NOKEBP) mentoring project on Expertise Development through the Analysis of Reactor Thermal-Hydraulics for Malaysia, denoted as EARTH-M.« less

Validation of the Chemistry Module for the Euler Solver in Unified Flow Solver

DTIC Science & Technology

2012-03-01

traveling through the atmosphere there are three types of flow regimes that exist; the first is the continuum regime, second is the rarified regime and...The second method has been used in a program called Unified Flow Solver (UFS). UFS is currently being developed under collaborative efforts the Air...thermal non-equilibrium case and finally to a thermo-chemical non- equilibrium case. The data from the simulations will be compared to a second code

Structural insights into the interaction of a monoclonal antibody and Nodal peptides by STD-NMR spectroscopy.

PubMed

Calvanese, Luisa; Focà, Annalia; Sandomenico, Annamaria; Focà, Giuseppina; Caporale, Andrea; Doti, Nunzianna; Iaccarino, Emanuela; Leonardi, Antonio; D'Auria, Gabriella; Ruvo, Menotti; Falcigno, Lucia

2017-12-15

Nodal is a growth factor expressed during early embryonic development, but reactivated in several advanced-stage cancers. Targeting of Nodal signaling, which occurs via the binding to Cripto-1 co-receptor, results in inhibition of cell aggressiveness and reduced tumor growth. The Nodal binding region to Cripto-1 was identified and targeted with a high affinity monoclonal antibody (3D1). By STD-NMR technique, we investigated the interaction of Nodal fragments with 3D1 with the aim to elucidate at atomic level the interaction surface. Data indicate with high accuracy the antibody-antigen contact atoms and confirm the information previously obtained by immune-enzymatic methods. Main residues contacted by 3D1 are P46, V47, E49 and E50, which belong to the Nodal loop involved in the interaction with the co-receptor. Copyright © 2017 Elsevier Ltd. All rights reserved.

Performance of uncertainty quantification methodologies and linear solvers in cardiovascular simulations

NASA Astrophysics Data System (ADS)

Seo, Jongmin; Schiavazzi, Daniele; Marsden, Alison

2017-11-01

Cardiovascular simulations are increasingly used in clinical decision making, surgical planning, and disease diagnostics. Patient-specific modeling and simulation typically proceeds through a pipeline from anatomic model construction using medical image data to blood flow simulation and analysis. To provide confidence intervals on simulation predictions, we use an uncertainty quantification (UQ) framework to analyze the effects of numerous uncertainties that stem from clinical data acquisition, modeling, material properties, and boundary condition selection. However, UQ poses a computational challenge requiring multiple evaluations of the Navier-Stokes equations in complex 3-D models. To achieve efficiency in UQ problems with many function evaluations, we implement and compare a range of iterative linear solver and preconditioning techniques in our flow solver. We then discuss applications to patient-specific cardiovascular simulation and how the problem/boundary condition formulation in the solver affects the selection of the most efficient linear solver. Finally, we discuss performance improvements in the context of uncertainty propagation. Support from National Institute of Health (R01 EB018302) is greatly appreciated.

Analysis of nodal aberration properties in off-axis freeform system design.

PubMed

Shi, Haodong; Jiang, Huilin; Zhang, Xin; Wang, Chao; Liu, Tao

2016-08-20

Freeform surfaces have the advantage of balancing off-axis aberration. In this paper, based on the framework of nodal aberration theory (NAT) applied to the coaxial system, the third-order astigmatism and coma wave aberration expressions of an off-axis system with Zernike polynomial surfaces are derived. The relationship between the off-axis and surface shape acting on the nodal distributions is revealed. The nodal aberration properties of the off-axis freeform system are analyzed and validated by using full-field displays (FFDs). It has been demonstrated that adding Zernike terms, up to nine, to the off-axis system modifies the nodal locations, but the field dependence of the third-order aberration does not change. On this basis, an off-axis two-mirror freeform system with 500 mm effective focal length (EFL) and 300 mm entrance pupil diameter (EPD) working in long-wave infrared is designed. The field constant aberrations induced by surface tilting are corrected by selecting specific Zernike terms. The design results show that the nodes of third-order astigmatism and coma move back into the field of view (FOV). The modulation transfer function (MTF) curves are above 0.4 at 20 line pairs per millimeter (lp/mm) which meets the infrared reconnaissance requirement. This work provides essential insight and guidance for aberration correction in off-axis freeform system design.

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

PubMed

Seol, Ki Ho; Lee, Jeong Eun

2016-03-01

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

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

PubMed Central

Seol, Ki Ho

2016-01-01

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

Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Yu-Hang, E-mail: yuhang_tang@brown.edu; Kudo, Shuhei, E-mail: shuhei-kudo@outlook.jp; Bian, Xin, E-mail: xin_bian@brown.edu

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 anmore » 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)« less

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

AQUASOL: An efficient solver for the dipolar Poisson–Boltzmann–Langevin equation

PubMed Central

Koehl, Patrice; Delarue, Marc

2010-01-01

The Poisson–Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson–Boltzmann–Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.

PubMed

Koehl, Patrice; Delarue, Marc

2010-02-14

The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE

AN EXTENSION OF THE ATHENA++ CODE FRAMEWORK FOR GRMHD BASED ON ADVANCED RIEMANN SOLVERS AND STAGGERED-MESH CONSTRAINED TRANSPORT

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Segregated nodal domains of two-dimensional multispecies Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Chang, Shu-Ming; Lin, Chang-Shou; Lin, Tai-Chia; Lin, Wen-Wei

2004-09-01

In this paper, we study the distribution of m segregated nodal domains of the m-mixture of Bose-Einstein condensates under positive and large repulsive scattering lengths. It is shown that components of positive bound states may repel each other and form segregated nodal domains as the repulsive scattering lengths go to infinity. Efficient numerical schemes are created to confirm our theoretical results and discover a new phenomenon called verticillate multiplying, i.e., the generation of multiple verticillate structures. In addition, our proposed Gauss-Seidel-type iteration method is very effective in that it converges linearly in 10-20 steps.

A high performance linear equation solver on the VPP500 parallel supercomputer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakanishi, Makoto; Ina, Hiroshi; Miura, Kenichi

1994-12-31

This paper describes the implementation of two high performance linear equation solvers developed for the Fujitsu VPP500, a distributed memory parallel supercomputer system. The solvers take advantage of the key architectural features of VPP500--(1) scalability for an arbitrary number of processors up to 222 processors, (2) flexible data transfer among processors provided by a crossbar interconnection network, (3) vector processing capability on each processor, and (4) overlapped computation and transfer. The general linear equation solver based on the blocked LU decomposition method achieves 120.0 GFLOPS performance with 100 processors in the LIN-PACK Highly Parallel Computing benchmark.

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.

LAPACKrc: Fast linear algebra kernels/solvers for FPGA accelerators

NASA Astrophysics Data System (ADS)

Gonzalez, Juan; Núñez, Rafael C.

2009-07-01

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

Adaptive Nodal Transport Methods for Reactor Transient Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Implementation of density-based solver for all speeds in the framework of OpenFOAM

NASA Astrophysics Data System (ADS)

Shen, Chun; Sun, Fengxian; Xia, Xinlin

2014-10-01

In the framework of open source CFD code OpenFOAM, a density-based solver for all speeds flow field is developed. In this solver the preconditioned all speeds AUSM+(P) scheme is adopted and the dual time scheme is implemented to complete the unsteady process. Parallel computation could be implemented to accelerate the solving process. Different interface reconstruction algorithms are implemented, and their accuracy with respect to convection is compared. Three benchmark tests of lid-driven cavity flow, flow crossing over a bump, and flow over a forward-facing step are presented to show the accuracy of the AUSM+(P) solver for low-speed incompressible flow, transonic flow, and supersonic/hypersonic flow. Firstly, for the lid driven cavity flow, the computational results obtained by different interface reconstruction algorithms are compared. It is indicated that the one dimensional reconstruction scheme adopted in this solver possesses high accuracy and the solver developed in this paper can effectively catch the features of low incompressible flow. Then via the test cases regarding the flow crossing over bump and over forward step, the ability to capture characteristics of the transonic and supersonic/hypersonic flows are confirmed. The forward-facing step proves to be the most challenging for the preconditioned solvers with and without the dual time scheme. Nonetheless, the solvers described in this paper reproduce the main features of this flow, including the evolution of the initial transient.

Preconditioned implicit solvers for the Navier-Stokes equations on distributed-memory machines

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Liou, Meng-Sing; Dyson, Rodger W.

1994-01-01

The GMRES method is parallelized, and combined with local preconditioning to construct an implicit parallel solver to obtain steady-state solutions for the Navier-Stokes equations of fluid flow on distributed-memory machines. The new implicit parallel solver is designed to preserve the convergence rate of the equivalent 'serial' solver. A static domain-decomposition is used to partition the computational domain amongst the available processing nodes of the parallel machine. The SPMD (Single-Program Multiple-Data) programming model is combined with message-passing tools to develop the parallel code on a 32-node Intel Hypercube and a 512-node Intel Delta machine. The implicit parallel solver is validated for internal and external flow problems, and is found to compare identically with flow solutions obtained on a Cray Y-MP/8. A peak computational speed of 2300 MFlops/sec has been achieved on 512 nodes of the Intel Delta machine,k for a problem size of 1024 K equations (256 K grid points).

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.

Multigrid approaches to non-linear diffusion problems on unstructured meshes

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

The efficiency of three multigrid methods for solving highly non-linear diffusion problems on two-dimensional unstructured meshes is examined. The three multigrid methods differ mainly in the manner in which the nonlinearities of the governing equations are handled. These comprise a non-linear full approximation storage (FAS) multigrid method which is used to solve the non-linear equations directly, a linear multigrid method which is used to solve the linear system arising from a Newton linearization of the non-linear system, and a hybrid scheme which is based on a non-linear FAS multigrid scheme, but employs a linear solver on each level as a smoother. Results indicate that all methods are equally effective at converging the non-linear residual in a given number of grid sweeps, but that the linear solver is more efficient in cpu time due to the lower cost of linear versus non-linear grid sweeps.

Multigrid treatment of implicit continuum diffusion

NASA Astrophysics Data System (ADS)

Francisquez, Manaure; Zhu, Ben; Rogers, Barrett

2017-10-01

Implicit treatment of diffusive terms of various differential orders common in continuum mechanics modeling, such as computational fluid dynamics, is investigated with spectral and multigrid algorithms in non-periodic 2D domains. In doubly periodic time dependent problems these terms can be efficiently and implicitly handled by spectral methods, but in non-periodic systems solved with distributed memory parallel computing and 2D domain decomposition, this efficiency is lost for large numbers of processors. We built and present here a multigrid algorithm for these types of problems which outperforms a spectral solution that employs the highly optimized FFTW library. This multigrid algorithm is not only suitable for high performance computing but may also be able to efficiently treat implicit diffusion of arbitrary order by introducing auxiliary equations of lower order. We test these solvers for fourth and sixth order diffusion with idealized harmonic test functions as well as a turbulent 2D magnetohydrodynamic simulation. It is also shown that an anisotropic operator without cross-terms can improve model accuracy and speed, and we examine the impact that the various diffusion operators have on the energy, the enstrophy, and the qualitative aspect of a simulation. This work was supported by DOE-SC-0010508. This research used resources of the National Energy Research Scientific Computing Center (NERSC).

Efficiency optimization of a fast Poisson solver in beam dynamics simulation

NASA Astrophysics Data System (ADS)

Zheng, Dawei; Pöplau, Gisela; van Rienen, Ursula

2016-01-01

Calculating the solution of Poisson's equation relating to space charge force is still the major time consumption in beam dynamics simulations and calls for further improvement. In this paper, we summarize a classical fast Poisson solver in beam dynamics simulations: the integrated Green's function method. We introduce three optimization steps of the classical Poisson solver routine: using the reduced integrated Green's function instead of the integrated Green's function; using the discrete cosine transform instead of discrete Fourier transform for the Green's function; using a novel fast convolution routine instead of an explicitly zero-padded convolution. The new Poisson solver routine preserves the advantages of fast computation and high accuracy. This provides a fast routine for high performance calculation of the space charge effect in accelerators.

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.

A mixed fluid-kinetic solver for the Vlasov-Poisson equations

NASA Astrophysics Data System (ADS)

Cheng, Yongtao

Plasmas are ionized gases that appear in a wide range of applications including astrophysics and space physics, as well as in laboratory settings such as in magnetically confined fusion. There are two prevailing types of modeling strategies to describe a plasma system: kinetic models and fluid models. Kinetic models evolve particle probability density distributions (PDFs) in phase space, which are accurate but computationally expensive. Fluid models evolve a small number of moments of the distribution function and reduce the dimension of the solution. However, some approximation is necessary to close the system, and finding an accurate moment closure that correctly captures the dynamics away from thermodynamic equilibrium is a difficult and still open problem. The main contributions of the present work can be divided into two main parts: (1) a new class of moment closures, based on a modification of existing quadrature-based moment-closure methods, is developed using bi-B-spline and bi-bubble representations; and (2) a novel mixed solver that combines a fluid and a kinetic solver is proposed, which uses the new class of moment-closure methods described in the first part. For the newly developed quadrature-based moment-closure based on bi-B-spline and bi-bubble representation, the explicit form of flux terms and the moment-realizability conditions are given. It is shown that while the bi-delta system is weakly hyperbolic, the newly proposed fluid models are strongly hyperbolic. Using a high-order Runge-Kutta discontinuous Galerkin method together with Strang operator splitting, the resulting models are applied to the Vlasov-Poisson-Fokker-Planck system in the high field limit. In the second part of this work, results from kinetic solver are used to provide a corrected closure to the fluid model. This correction keeps the fluid model hyperbolic and gives fluid results that match the moments as computed from the kinetic solution. Furthermore, a prolongation operation

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.

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.

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.

Gpu Implementation of a Viscous Flow Solver on Unstructured Grids

NASA Astrophysics Data System (ADS)

Xu, Tianhao; Chen, Long

2016-06-01

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

Computation of three-dimensional multiphase flow dynamics by Fully-Coupled Immersed Flow (FCIF) solver

NASA Astrophysics Data System (ADS)

Miao, Sha; Hendrickson, Kelli; Liu, Yuming

2017-12-01

This work presents a Fully-Coupled Immersed Flow (FCIF) solver for the three-dimensional simulation of fluid-fluid interaction by coupling two distinct flow solvers using an Immersed Boundary (IB) method. The FCIF solver captures dynamic interactions between two fluids with disparate flow properties, while retaining the desirable simplicity of non-boundary-conforming grids. For illustration, we couple an IB-based unsteady Reynolds Averaged Navier Stokes (uRANS) simulator with a depth-integrated (long-wave) solver for the application of slug development with turbulent gas and laminar liquid. We perform a series of validations including turbulent/laminar flows over prescribed wavy boundaries and freely-evolving viscous fluids. These confirm the effectiveness and accuracy of both one-way and two-way coupling in the FCIF solver. Finally, we present a simulation example of the evolution from a stratified turbulent/laminar flow through the initiation of a slug that nearly bridges the channel. The results show both the interfacial wave dynamics excited by the turbulent gas forcing and the influence of the liquid on the gas turbulence. These results demonstrate that the FCIF solver effectively captures the essential physics of gas-liquid interaction and can serve as a useful tool for the mechanistic study of slug generation in two-phase gas/liquid flows in channels and pipes.

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.

Fast Laplace solver approach to pore-scale permeability

NASA Astrophysics Data System (ADS)

Arns, C. H.; Adler, P. M.

2018-02-01

We introduce a powerful and easily implemented method to calculate the permeability of porous media at the pore scale using an approximation based on the Poiseulle equation to calculate permeability to fluid flow with a Laplace solver. The method consists of calculating the Euclidean distance map of the fluid phase to assign local conductivities and lends itself naturally to the treatment of multiscale problems. We compare with analytical solutions as well as experimental measurements and lattice Boltzmann calculations of permeability for Fontainebleau sandstone. The solver is significantly more stable than the lattice Boltzmann approach, uses less memory, and is significantly faster. Permeabilities are in excellent agreement over a wide range of porosities.

A fast mass spring model solver for high-resolution elastic objects

NASA Astrophysics Data System (ADS)

Zheng, Mianlun; Yuan, Zhiyong; Zhu, Weixu; Zhang, Guian

2017-03-01

Real-time simulation of elastic objects is of great importance for computer graphics and virtual reality applications. The fast mass spring model solver can achieve visually realistic simulation in an efficient way. Unfortunately, this method suffers from resolution limitations and lack of mechanical realism for a surface geometry model, which greatly restricts its application. To tackle these problems, in this paper we propose a fast mass spring model solver for high-resolution elastic objects. First, we project the complex surface geometry model into a set of uniform grid cells as cages through *cages mean value coordinate method to reflect its internal structure and mechanics properties. Then, we replace the original Cholesky decomposition method in the fast mass spring model solver with a conjugate gradient method, which can make the fast mass spring model solver more efficient for detailed surface geometry models. Finally, we propose a graphics processing unit accelerated parallel algorithm for the conjugate gradient method. Experimental results show that our method can realize efficient deformation simulation of 3D elastic objects with visual reality and physical fidelity, which has a great potential for applications in computer animation.

An approximate Riemann solver for real gas parabolized Navier-Stokes equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urbano, Annafederica, E-mail: annafederica.urbano@uniroma1.it; Nasuti, Francesco, E-mail: francesco.nasuti@uniroma1.it

2013-01-15

Under specific assumptions, parabolized Navier-Stokes equations are a suitable mean to study channel flows. A special case is that of high pressure flow of real gases in cooling channels where large crosswise gradients of thermophysical properties occur. To solve the parabolized Navier-Stokes equations by a space marching approach, the hyperbolicity of the system of governing equations is obtained, even for very low Mach number flow, by recasting equations such that the streamwise pressure gradient is considered as a source term. For this system of equations an approximate Roe's Riemann solver is developed as the core of a Godunov type finitemore » volume algorithm. The properties of the approximated Riemann solver, which is a modification of Roe's Riemann solver for the parabolized Navier-Stokes equations, are presented and discussed with emphasis given to its original features introduced to handle fluids governed by a generic real gas EoS. Sample solutions are obtained for low Mach number high compressible flows of transcritical methane, heated in straight long channels, to prove the solver ability to describe flows dominated by complex thermodynamic phenomena.« less

Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

DOE PAGES

Zhang, Bo; Lu, Benzhuo; Cheng, Xiaolin; ...

2013-01-01

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. Lastly, the potential of the solver is demonstrated with preliminary numericalmore » results.« less

IRMHD: an implicit radiative and magnetohydrodynamical solver for self-gravitating systems

NASA Astrophysics Data System (ADS)

Hujeirat, A.

1998-07-01

The 2D implicit hydrodynamical solver developed by Hujeirat & Rannacher is now modified to include the effects of radiation, magnetic fields and self-gravity in different geometries. The underlying numerical concept is based on the operator splitting approach, and the resulting 2D matrices are inverted using different efficient preconditionings such as ADI (alternating direction implicit), the approximate factorization method and Line-Gauss-Seidel or similar iteration procedures. Second-order finite volume with third-order upwinding and second-order time discretization is used. To speed up convergence and enhance efficiency we have incorporated an adaptive time-step control and monotonic multilevel grid distributions as well as vectorizing the code. Test calculations had shown that it requires only 38 per cent more computational effort than its explicit counterpart, whereas its range of application to astrophysical problems is much larger. For example, strongly time-dependent, quasi-stationary and steady-state solutions for the set of Euler and Navier-Stokes equations can now be sought on a non-linearly distributed and strongly stretched mesh. As most of the numerical techniques used to build up this algorithm have been described by Hujeirat & Rannacher in an earlier paper, we focus in this paper on the inclusion of self-gravity, radiation and magnetic fields. Strategies for satisfying the condition ∇.B=0 in the implicit evolution of MHD flows are given. A new discretization strategy for the vector potential which allows alternating use of the direct method is prescribed. We investigate the efficiencies of several 2D solvers for a Poisson-like equation and compare their convergence rates. We provide a splitting approach for the radiative flux within the FLD (flux-limited diffusion) approximation to enhance consistency and accuracy between regions of different optical depths. The results of some test problems are presented to demonstrate the accuracy and

An enriched finite element method to fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

2017-08-01

In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

Maternal Gdf3 is an obligatory cofactor in Nodal signaling for embryonic axis formation in zebrafish

PubMed Central

Bisgrove, Brent W; Su, Yi-Chu

2017-01-01

Zebrafish Gdf3 (Dvr1) is a member of the TGFβ superfamily of cell signaling ligands that includes Xenopus Vg1 and mammalian Gdf1/3. Surprisingly, engineered homozygous mutants in zebrafish have no apparent phenotype. Elimination of Gdf3 in oocytes of maternal-zygotic mutants results in embryonic lethality that can be fully rescued with gdf3 RNA, demonstrating that Gdf3 is required only early in development, beyond which mutants are viable and fertile. Gdf3 mutants are refractory to Nodal ligands and Nodal repressor Lefty1. Signaling driven by TGFβ ligand Activin and constitutively active receptors Alk4 and Alk2 remain intact in gdf3 mutants, indicating that Gdf3 functions at the same pathway step as Nodal. Targeting gdf3 and ndr2 RNA to specific lineages indicates that exogenous gdf3 is able to fully rescue mutants only when co-expressed with endogenous Nodal. Together, these findings demonstrate that Gdf3 is an essential cofactor of Nodal signaling during establishment of the embryonic axis. PMID:29140249

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.

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...

Pressure-induced organic topological nodal-line semimetal in the three-dimensional molecular crystal Pd (dddt) 2

NASA Astrophysics Data System (ADS)

Liu, Zhao; Wang, Haidi; Wang, Z. F.; Yang, Jinlong; Liu, Feng

2018-04-01

The nodal-line semimetal represents a class of topological materials characterized with highest band degeneracy. It is usually found in inorganic materials of high crystal symmetry or a minimum symmetry of inversion aided with accidental band degeneracy [Phys. Rev. Lett. 118, 176402 (2017), 10.1103/PhysRevLett.118.176402]. Based on first-principles band structure, Wannier charge center, and topological surface state calculations, here we predict a pressure-induced topological nodal-line semimetal in the absence of spin-orbit coupling (SOC) in the synthesized single-component 3D molecular crystal Pd (dddt) 2 . We show a Γ -centered single nodal line undulating within a narrow energy window across the Fermi level. This intriguing nodal line is generated by pressure-induced accidental band degeneracy, without protection from any crystal symmetry. When SOC is included, the fourfold degenerated nodal line is gapped and Pd (dddt) 2 becomes a strong 3D topological metal with an Z2 index of (1;000). However, the tiny SOC gap makes it still possible to detect the nodal-line properties experimentally. Our findings afford an attractive route for designing and realizing topological states in 3D molecular crystals, as they are weakly bonded through van der Waals forces with a low crystal symmetry so that their electronic structures can be easily tuned by pressure.

Radiotherapy for esthesioneuroblastoma: is elective nodal irradiation warranted in the multimodality treatment approach?

PubMed

Noh, O Kyu; Lee, Sang-wook; Yoon, Sang Min; Kim, Sung Bae; Kim, Sang Yoon; Kim, Chang Jin; Jo, Kyung Ja; Choi, Eun Kyung; Song, Si Yeol; Kim, Jong Hoon; Ahn, Seung Do

2011-02-01

The role of elective nodal irradiation (ENI) in radiotherapy for esthesioneuroblastoma (ENB) has not been clearly defined. We analyzed treatment outcomes of patients with ENB and the frequency of cervical nodal failure in the absence of ENI. Between August 1996 and December 2007, we consulted with 19 patients with ENB regarding radiotherapy. Initial treatment consisted of surgery alone in 2 patients; surgery and postoperative radiotherapy in 4; surgery and adjuvant chemotherapy in 1; surgery, postoperative radiotherapy, and chemotherapy in 3; and chemotherapy followed by radiotherapy or concurrent chemoradiotherapy in 5. Five patients did not receive planned radiotherapy because of disease progression. Including 2 patients who received salvage radiotherapy, 14 patients were treated with radiotherapy. Elective nodal irradiation was performed in 4 patients with high-risk factors, including 3 with cervical lymph node metastasis at presentation. Fourteen patients were analyzable, with a median follow-up of 27 months (range, 7-64 months). The overall 3-year survival rate was 73.4%. Local failure occurred in 3 patients (21.4%), regional cervical failure in 3 (21.4%), and distant failure in 2 (14.3%). No cervical nodal failure occurred in patients treated with combined systemic chemotherapy regardless of ENI. Three cervical failures occurred in the 4 patients treated with ENI or neck dissection (75%), none of whom received systemic chemotherapy. ENI during radiotherapy for ENB seems to play a limited role in preventing cervical nodal failure. Omitting ENI may be an option if patients are treated with a combination of radiotherapy and chemotherapy. Copyright © 2011 Elsevier Inc. All rights reserved.

A fast direct solver for a class of two-dimensional separable elliptic equations on the sphere

NASA Technical Reports Server (NTRS)

Moorthi, Shrinivas; Higgins, R. Wayne

1992-01-01

An efficient, direct, second-order solver for the discrete solution of two-dimensional separable elliptic equations on the sphere is presented. The method involves a Fourier transformation in longitude and a direct solution of the resulting coupled second-order finite difference equations in latitude. The solver is made efficient by vectorizing over longitudinal wavenumber and by using a vectorized fast Fourier transform routine. It is evaluated using a prescribed solution method and compared with a multigrid solver and the standard direct solver from FISHPAK.

Risk of isolated nodal failure for non-small cell lung cancer (NSCLC) treated with the elective nodal irradiation (ENI) using 3D-conformal radiotherapy (3D-CRT) techniques--a retrospective analysis.

PubMed

Kepka, Lucyna; Bujko, Krzysztof; Zolciak-Siwinska, Agnieszka

2008-01-01

To estimate retrospectively the rate of isolated nodal failures (INF) in NSCLC patients treated with the elective nodal irradiation (ENI) using 3D-conformal radiotherapy (3D-CRT). One hundred and eighty-five patients with I-IIIB stage treated with 3D-CRT in consecutive clinical trials differing in an extent of the ENI were analyzed. According to the extent of the ENI, two groups were distinguished: extended (n = 124) and limited (n = 61) ENI. INF was defined as regional nodal failure occurring without local progression. Cumulative Incidence of INF (CIINF) was evaluated by univariate and multivariate analysis with regard to prognostic factors. With a median follow up of 30 months, the two-year actuarial overall survival was 35%. The two-year CIINF rate was 12%. There were 16 (9%) INF, eight (6%) for extended and eight (13%) for limited ENI. In the univariate analysis bulky mediastinal disease (BMD), left side, higher N stage, and partial response to RT had a significant negative impact on the CIINF. BMD was the only independent predictor of the risk of incidence of the INF (p = 0.001). INF is more likely to occur in case of more advanced nodal status.

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

PubMed

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

2017-10-01

This paper describes a fast-forward electromagnetic solver (FFS) for the image reconstruction algorithm of our microwave tomography 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 (EM) inverse problem and takes into account the real EM 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 EM 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 EM model of a numerical breast phantom.

Observation of nodal line in non-symmorphic topological semimetal InBi

DOE PAGES

Ekahana, Sandy Adhitia; Wu, Shu-Chun; Jiang, Juan; ...

2017-05-30

Topological nodal semimetal (TNS), characterized by its touching conduction and valence bands, is a newly discovered state of quantum matter which exhibits various exotic physical phenomena. Recently, a new type of TNS called topological nodal line semimetal (TNLS) is predicted where its conduction and valence band form a degenerate one-dimension line which is further protected by its crystal symmetry. In this work, we systematically investigated the bulk and surface electronic structure of the non-symmorphic, TNLS in InBi (which is also a type II Dirac semimetal) with strong spin–orbit coupling by using angle resolved photoemission spectroscopy. By tracking the crossing points of the bulk bands at the Brillouin zone boundary, we discovered the nodal-line feature along themore » $${{k}}_{{z}}$$ direction, in agreement with the ab initio calculations and confirmed it to be a new compound in the TNLS family. Our discovery provides a new material platform for the study of these exotic topological quantum phases and paves the way for possible future applications.« less

Implementation of a parallel unstructured Euler solver on the CM-5

NASA Technical Reports Server (NTRS)

Morano, Eric; Mavriplis, D. J.

1995-01-01

An efficient unstructured 3D Euler solver is parallelized on a Thinking Machine Corporation Connection Machine 5, distributed memory computer with vectoring capability. In this paper, the single instruction multiple data (SIMD) strategy is employed through the use of the CM Fortran language and the CMSSL scientific library. The performance of the CMSSL mesh partitioner is evaluated and the overall efficiency of the parallel flow solver is discussed.

Encapsulation of nodal cuttings and shoot tips for storage and exchange of cassava germplasm.

PubMed

Danso, K E; Ford-Lloyd, B V

2003-04-01

We report the encapsulation of in vitro-derived nodal cuttings or shoot tips of cassava in 3% calcium alginate for storage and germplasm exchange purposes. Shoot regrowth was not significantly affected by the concentration of sucrose in the alginate matrix while root formation was. In contrast, increasing the sucrose concentration in the calcium chloride polymerisation medium significantly reduced regrowth from encapsulated nodal cuttings of accession TME 60444. Supplementing the alginate matrix with increased concentrations of 6-benzylaminopurine and alpha-naphthaleneacetic acid enhanced complete plant regrowth within 2 weeks. Furthermore, plant regrowth by encapsulated nodal cuttings and shoot tips was significantly affected by the duration of the storage period as shoot recovery decreased from almost 100% to 73.3% for encapsulated nodal cuttings and 94.4% to 60% for shoot tips after 28 days of storage. The high frequency of plant regrowth from alginate-coated micropropagules coupled with high viability percentage after 28 days of storage is highly encouraging for the exchange of cassava genetic resources. Such encapsulated micropropagules could be used as an alternative to synthetic seeds derived from somatic embryos.

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.

Parallel-vector out-of-core equation solver for computational mechanics

NASA Technical Reports Server (NTRS)

Qin, J.; Agarwal, T. K.; Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.

1993-01-01

A parallel/vector out-of-core equation solver is developed for shared-memory computers, such as the Cray Y-MP machine. The input/ output (I/O) time is reduced by using the a synchronous BUFFER IN and BUFFER OUT, which can be executed simultaneously with the CPU instructions. The parallel and vector capability provided by the supercomputers is also exploited to enhance the performance. Numerical applications in large-scale structural analysis are given to demonstrate the efficiency of the present out-of-core solver.

Role of Ultrasonography of Regional Nodal Basins in Staging Triple-Negative Breast Cancer and Implications For Local-Regional Treatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaitelman, Simona F., E-mail: sfshaitelman@mdanderson.org; Tereffe, Welela; Dogan, Basak E.

2015-09-01

Purpose: We sought to determine the rate at which regional nodal ultrasonography would increase the nodal disease stage in patients with triple-negative breast cancer (TNBC) beyond the clinical stage determined by physical examination and mammography alone, and significantly affect the treatments delivered to these patients. Methods and Materials: We retrospectively reviewed the charts of women with stages I to III TNBC who underwent physical examination, mammography, breast and regional nodal ultrasonography with needle biopsy of abnormal nodes, and definitive local-regional treatment at our institution between 2004 and 2011. The stages of these patients' disease with and without ultrasonography of the regionalmore » nodal basins were compared using the Pearson χ{sup 2} test. Definitive treatments of patients whose nodal disease was upstaged on the basis of ultrasonographic findings were compared to those of patients whose disease stage remained the same. Results: A total of 572 women met the study requirements. In 111 (19.4%) of these patients, regional nodal ultrasonography with needle biopsy resulted in an increase in disease stage from the original stage by physical examination and mammography alone. Significantly higher percentages of patients whose nodal disease was upstaged by ultrasonographic findings compared to that in patients whose disease was not upstaged underwent neoadjuvant systemic therapy (91.9% and 51.2%, respectively; P<.0001), axillary lymph node dissection (99.1% and 34.5%, respectively; P<.0001), and radiation to the regional nodal basins (88.2% and 29.1%, respectively; P<.0001). Conclusions: Regional nodal ultrasonography in TNBC frequently changes the initial clinical stage and plays an important role in treatment planning.« less

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

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.

Computational aeroelasticity using a pressure-based solver

NASA Astrophysics Data System (ADS)

Kamakoti, Ramji

A computational methodology for performing fluid-structure interaction computations for three-dimensional elastic wing geometries is presented. The flow solver used is based on an unsteady Reynolds-Averaged Navier-Stokes (RANS) model. A well validated k-ε turbulence model with wall function treatment for near wall region was used to perform turbulent flow calculations. Relative merits of alternative flow solvers were investigated. The predictor-corrector-based Pressure Implicit Splitting of Operators (PISO) algorithm was found to be computationally economic for unsteady flow computations. Wing structure was modeled using Bernoulli-Euler beam theory. A fully implicit time-marching scheme (using the Newmark integration method) was used to integrate the equations of motion for structure. Bilinear interpolation and linear extrapolation techniques were used to transfer necessary information between fluid and structure solvers. Geometry deformation was accounted for by using a moving boundary module. The moving grid capability was based on a master/slave concept and transfinite interpolation techniques. Since computations were performed on a moving mesh system, the geometric conservation law must be preserved. This is achieved by appropriately evaluating the Jacobian values associated with each cell. Accurate computation of contravariant velocities for unsteady flows using the momentum interpolation method on collocated, curvilinear grids was also addressed. Flutter computations were performed for the AGARD 445.6 wing at subsonic, transonic and supersonic Mach numbers. Unsteady computations were performed at various dynamic pressures to predict the flutter boundary. Results showed favorable agreement of experiment and previous numerical results. The computational methodology exhibited capabilities to predict both qualitative and quantitative features of aeroelasticity.

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.

Nodal liquids in extended t-J models and dynamical supersymmetry

NASA Astrophysics Data System (ADS)

Mavromatos, Nick E.; Sarkar, Sarben

2000-08-01

In the context of extended t-J models, with intersite Coulomb interactions of the form -V∑ninj, with ni denoting the electron number operator at site i, nodal liquids are discussed. We use the spin-charge separation ansatz as applied to the nodes of a d-wave superconducting gap. Such a situation may be of relevance to the physics of high-temperature superconductivity. We point out the possibility of existence of certain points in the parameter space of the model characterized by dynamical supersymmetries between the spinon and holon degrees of freedom, which are quite different from the symmetries in conventional supersymmetric t-J models. Such symmetries pertain to the continuum effective-field theory of the nodal liquid, and one's hope is that the ancestor lattice model may differ from the continuum theory only by renormalization-group irrelevant operators in the infrared. We give plausible arguments that nodal liquids at such supersymmetric points are characterized by superconductivity of Kosterlitz-Thouless type. The fact that quantum fluctuations around such points can be studied in a controlled way, probably makes such systems of special importance for an eventual nonperturbative understanding of the complex phase diagram of the associated high-temperature superconducting materials.

Elimination of numerical diffusion in 1 - phase and 2 - phase flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajamaeki, M.

1997-07-01

The new hydraulics solution method PLIM (Piecewise Linear Interpolation Method) is capable of avoiding the excessive errors, numerical diffusion and also numerical dispersion. The hydraulics solver CFDPLIM uses PLIM and solves the time-dependent one-dimensional flow equations in network geometry. An example is given for 1-phase flow in the case when thermal-hydraulics and reactor kinetics are strongly coupled. Another example concerns oscillations in 2-phase flow. Both the example computations are not possible with conventional methods.

A fast direct solver for boundary value problems on locally perturbed geometries

NASA Astrophysics Data System (ADS)

Zhang, Yabin; Gillman, Adrianna

2018-03-01

Many applications including optimal design and adaptive discretization techniques involve solving several boundary value problems on geometries that are local perturbations of an original geometry. This manuscript presents a fast direct solver for boundary value problems that are recast as boundary integral equations. The idea is to write the discretized boundary integral equation on a new geometry as a low rank update to the discretized problem on the original geometry. Using the Sherman-Morrison formula, the inverse can be expressed in terms of the inverse of the original system applied to the low rank factors and the right hand side. Numerical results illustrate for problems where perturbation is localized the fast direct solver is three times faster than building a new solver from scratch.

Analysis of nodal coverage utilizing image guided radiation therapy for primary gynecologic tumor volumes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, Faisal; Loma Linda University Medical Center, Department of Radiation Oncology, Loma Linda, CA; Sarkar, Vikren

Purpose: To evaluate radiation dose delivered to pelvic lymph nodes, if daily Image Guided Radiation Therapy (IGRT) was implemented with treatment shifts based on the primary site (primary clinical target volume [CTV]). Our secondary goal was to compare dosimetric coverage with patient outcomes. Materials and methods: A total of 10 female patients with gynecologic malignancies were evaluated retrospectively after completion of definitive intensity-modulated radiation therapy (IMRT) to their pelvic lymph nodes and primary tumor site. IGRT consisted of daily kilovoltage computed tomography (CT)-on-rails imaging fused with initial planning scans for position verification. The initial plan was created using Varian's Eclipsemore » treatment planning software. Patients were treated with a median radiation dose of 45 Gy (range: 37.5 to 50 Gy) to the primary volume and 45 Gy (range: 45 to 64.8 Gy) to nodal structures. One IGRT scan per week was randomly selected from each patient's treatment course and re-planned on the Eclipse treatment planning station. CTVs were recreated by fusion on the IGRT image series, and the patient's treatment plan was applied to the new image set to calculate delivered dose. We evaluated the minimum, maximum, and 95% dose coverage for primary and nodal structures. Reconstructed primary tumor volumes were recreated within 4.7% of initial planning volume (0.9% to 8.6%), and reconstructed nodal volumes were recreated to within 2.9% of initial planning volume (0.01% to 5.5%). Results: Dosimetric parameters averaged less than 10% (range: 1% to 9%) of the original planned dose (45 Gy) for primary and nodal volumes on all patients (n = 10). For all patients, ≥99.3% of the primary tumor volume received ≥ 95% the prescribed dose (V95%) and the average minimum dose was 96.1% of the prescribed dose. In evaluating nodal CTV coverage, ≥ 99.8% of the volume received ≥ 95% the prescribed dose and the average minimum dose was 93%. In evaluating

Tree-based solvers for adaptive mesh refinement code FLASH - I: gravity and optical depths

NASA Astrophysics Data System (ADS)

Wünsch, R.; Walch, S.; Dinnbier, F.; Whitworth, A.

2018-04-01

We describe an OctTree algorithm for the MPI parallel, adaptive mesh refinement code FLASH, which can be used to calculate the gas self-gravity, and also the angle-averaged local optical depth, for treating ambient diffuse radiation. The algorithm communicates to the different processors only those parts of the tree that are needed to perform the tree-walk locally. The advantage of this approach is a relatively low memory requirement, important in particular for the optical depth calculation, which needs to process information from many different directions. This feature also enables a general tree-based radiation transport algorithm that will be described in a subsequent paper, and delivers excellent scaling up to at least 1500 cores. Boundary conditions for gravity can be either isolated or periodic, and they can be specified in each direction independently, using a newly developed generalization of the Ewald method. The gravity calculation can be accelerated with the adaptive block update technique by partially re-using the solution from the previous time-step. Comparison with the FLASH internal multigrid gravity solver shows that tree-based methods provide a competitive alternative, particularly for problems with isolated or mixed boundary conditions. We evaluate several multipole acceptance criteria (MACs) and identify a relatively simple approximate partial error MAC which provides high accuracy at low computational cost. The optical depth estimates are found to agree very well with those of the RADMC-3D radiation transport code, with the tree-solver being much faster. Our algorithm is available in the standard release of the FLASH code in version 4.0 and later.

Topological and trivial magnetic oscillations in nodal loop semimetals

NASA Astrophysics Data System (ADS)

Oroszlány, László; Dóra, Balázs; Cserti, József; Cortijo, Alberto

2018-05-01

Nodal loop semimetals are close descendants of Weyl semimetals and possess a topologically dressed band structure. We argue by combining the conventional theory of magnetic oscillation with topological arguments that nodal loop semimetals host coexisting topological and trivial magnetic oscillations. These originate from mapping the topological properties of the extremal Fermi surface cross sections onto the physics of two dimensional semi-Dirac systems, stemming from merging two massless Dirac cones. By tuning the chemical potential and the direction of magnetic field, a sharp transition is identified from purely trivial oscillations, arising from the Landau levels of a normal two dimensional (2D) electron gas, to a phase where oscillations of topological and trivial origin coexist, originating from 2D massless Dirac and semi-Dirac points, respectively. These could in principle be directly identified in current experiments.

Rapid enhancement of nodal quasiparticle mass with heavily underdoping in Bi2212

NASA Astrophysics Data System (ADS)

Anzai, Hiroaki; Arita, Masashi; Namatame, Hirofumi; Taniguchi, Masaki; Ishikado, Motoyuki; Fujita, Kazuhiro; Ishida, Shigeyuki; Uchida, Shin-ichi; Ino, Akihiro

2018-05-01

We report substantial advance of our low-energy angle-resolved photoemission study of nodal quasiparticles in Bi2Sr2CaCu2O8+δ. The new data cover the samples from underdoped down to heavily underdoped levels. We also present the nodal Fermi velocities that determined by using an excitation-photon energy of hν = 7.0 eV over a wide doping range. The consistency between the results with hν = 8.1 and 7.0 eV allows us to rule out the effect of photoemission matrix elements. In comparison with the data previously reported, the nodal effective mass increases by a factor of ∼ 1.5 in going from optimally doped to heavily underdoped levels. We find a rapid enhancement of the nodal quasiparticle mass at low doping levels near the superconductor-to-insulator transition. The effective coupling spectrum, λ (ω) , is extracted directly from the energy derivatives of the quasiparticle dispersion and scattering rate, as a causal function of the mass enhancement factor. A steplike increase in Reλ (ω) around ∼ 65 meV is demonstrated clearly by the Kramers-Kronig transform of Imλ (ω) . To extract the low-energy renormalization effect, we calculated a simple model for the electron-boson interaction. This model reveals that the contribution of the renormalization at | ω | ≤ 15 meV to the quasiparticle mass is larger than that around 65 meV in underdoped samples.

Parallelization of the preconditioned IDR solver for modern multicore computer systems

NASA Astrophysics Data System (ADS)

Bessonov, O. A.; Fedoseyev, A. I.

2012-10-01

This paper present the analysis, parallelization and optimization approach for the large sparse matrix solver CNSPACK for modern multicore microprocessors. CNSPACK is an advanced solver successfully used for coupled solution of stiff problems arising in multiphysics applications such as CFD, semiconductor transport, kinetic and quantum problems. It employs iterative IDR algorithm with ILU preconditioning (user chosen ILU preconditioning order). CNSPACK has been successfully used during last decade for solving problems in several application areas, including fluid dynamics and semiconductor device simulation. However, there was a dramatic change in processor architectures and computer system organization in recent years. Due to this, performance criteria and methods have been revisited, together with involving the parallelization of the solver and preconditioner using Open MP environment. Results of the successful implementation for efficient parallelization are presented for the most advances computer system (Intel Core i7-9xx or two-processor Xeon 55xx/56xx).

A Parallel Multigrid Solver for Viscous Flows on Anisotropic Structured Grids

NASA Technical Reports Server (NTRS)

Prieto, Manuel; Montero, Ruben S.; Llorente, Ignacio M.; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

This paper presents an efficient parallel multigrid solver for speeding up the computation of a 3-D model that treats the flow of a viscous fluid over a flat plate. The main interest of this simulation lies in exhibiting some basic difficulties that prevent optimal multigrid efficiencies from being achieved. As the computing platform, we have used Coral, a Beowulf-class system based on Intel Pentium processors and equipped with GigaNet cLAN and switched Fast Ethernet networks. Our study not only examines the scalability of the solver but also includes a performance evaluation of Coral where the investigated solver has been used to compare several of its design choices, namely, the interconnection network (GigaNet versus switched Fast-Ethernet) and the node configuration (dual nodes versus single nodes). As a reference, the performance results have been compared with those obtained with the NAS-MG benchmark.

FoSSI: the family of simplified solver interfaces for the rapid development of parallel numerical atmosphere and ocean models

NASA Astrophysics Data System (ADS)

Frickenhaus, Stephan; Hiller, Wolfgang; Best, Meike

The portable software FoSSI is introduced that—in combination with additional free solver software packages—allows for an efficient and scalable parallel solution of large sparse linear equations systems arising in finite element model codes. FoSSI is intended to support rapid model code development, completely hiding the complexity of the underlying solver packages. In particular, the model developer need not be an expert in parallelization and is yet free to switch between different solver packages by simple modifications of the interface call. FoSSI offers an efficient and easy, yet flexible interface to several parallel solvers, most of them available on the web, such as PETSC, AZTEC, MUMPS, PILUT and HYPRE. FoSSI makes use of the concept of handles for vectors, matrices, preconditioners and solvers, that is frequently used in solver libraries. Hence, FoSSI allows for a flexible treatment of several linear equations systems and associated preconditioners at the same time, even in parallel on separate MPI-communicators. The second special feature in FoSSI is the task specifier, being a combination of keywords, each configuring a certain phase in the solver setup. This enables the user to control a solver over one unique subroutine. Furthermore, FoSSI has rather similar features for all solvers, making a fast solver intercomparison or exchange an easy task. FoSSI is a community software, proven in an adaptive 2D-atmosphere model and a 3D-primitive equation ocean model, both formulated in finite elements. The present paper discusses perspectives of an OpenMP-implementation of parallel iterative solvers based on domain decomposition methods. This approach to OpenMP solvers is rather attractive, as the code for domain-local operations of factorization, preconditioning and matrix-vector product can be readily taken from a sequential implementation that is also suitable to be used in an MPI-variant. Code development in this direction is in an advanced state under

A comparison of viscous-plastic sea ice solvers with and without replacement pressure

NASA Astrophysics Data System (ADS)

Kimmritz, Madlen; Losch, Martin; Danilov, Sergey

2017-07-01

Recent developments of the explicit elastic-viscous-plastic (EVP) solvers call for a new comparison with implicit solvers for the equations of viscous-plastic sea ice dynamics. In Arctic sea ice simulations, the modified and the adaptive EVP solvers, and the implicit Jacobian-free Newton-Krylov (JFNK) solver are compared against each other. The adaptive EVP method shows convergence rates that are generally similar or even better than those of the modified EVP method, but the convergence of the EVP methods is found to depend dramatically on the use of the replacement pressure (RP). Apparently, using the RP can affect the pseudo-elastic waves in the EVP methods by introducing extra non-physical oscillations so that, in the extreme case, convergence to the VP solution can be lost altogether. The JFNK solver also suffers from higher failure rates with RP implying that with RP the momentum equations are stiffer and more difficult to solve. For practical purposes, both EVP methods can be used efficiently with an unexpectedly low number of sub-cycling steps without compromising the solutions. The differences between the RP solutions and the NoRP solutions (when the RP is not being used) can be reduced with lower thresholds of viscous regularization at the cost of increasing stiffness of the equations, and hence the computational costs of solving them.

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.

Three-Dimensional Inverse Transport Solver Based on Compressive Sensing Technique

NASA Astrophysics Data System (ADS)

Cheng, Yuxiong; Wu, Hongchun; Cao, Liangzhi; Zheng, Youqi

2013-09-01

According to the direct exposure measurements from flash radiographic image, a compressive sensing-based method for three-dimensional inverse transport problem is presented. The linear absorption coefficients and interface locations of objects are reconstructed directly at the same time. It is always very expensive to obtain enough measurements. With limited measurements, compressive sensing sparse reconstruction technique orthogonal matching pursuit is applied to obtain the sparse coefficients by solving an optimization problem. A three-dimensional inverse transport solver is developed based on a compressive sensing-based technique. There are three features in this solver: (1) AutoCAD is employed as a geometry preprocessor due to its powerful capacity in graphic. (2) The forward projection matrix rather than Gauss matrix is constructed by the visualization tool generator. (3) Fourier transform and Daubechies wavelet transform are adopted to convert an underdetermined system to a well-posed system in the algorithm. Simulations are performed and numerical results in pseudo-sine absorption problem, two-cube problem and two-cylinder problem when using compressive sensing-based solver agree well with the reference value.

Finite difference method accelerated with sparse solvers for structural analysis of the metal-organic complexes

NASA Astrophysics Data System (ADS)

Guda, A. A.; Guda, S. A.; Soldatov, M. A.; Lomachenko, K. A.; Bugaev, A. L.; Lamberti, C.; Gawelda, W.; Bressler, C.; Smolentsev, G.; Soldatov, A. V.; Joly, Y.

2016-05-01

Finite difference method (FDM) implemented in the FDMNES software [Phys. Rev. B, 2001, 63, 125120] was revised. Thorough analysis shows, that the calculated diagonal in the FDM matrix consists of about 96% zero elements. Thus a sparse solver would be more suitable for the problem instead of traditional Gaussian elimination for the diagonal neighbourhood. We have tried several iterative sparse solvers and the direct one MUMPS solver with METIS ordering turned out to be the best. Compared to the Gaussian solver present method is up to 40 times faster and allows XANES simulations for complex systems already on personal computers. We show applicability of the software for metal-organic [Fe(bpy)3]2+ complex both for low spin and high spin states populated after laser excitation.

SU-E-J-179: Prediction of Pelvic Nodal Coverage Using Mutual Information Between Cone-Beam and Planning CTs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jani, S; Kishan, A; O'Connell, D

2014-06-01

Purpose: To investigate if pelvic nodal coverage for prostate patients undergoing intensity modulated radiotherapy (IMRT) can be predicted using mutual image information computed between planning and cone-beam CTs (CBCTs). Methods: Four patients with high-risk prostate adenocarcinoma were treated with IMRT on a Varian TrueBeam. Plans were designed such that 95% of the nodal planning target volume (PTV) received the prescription dose of 45 Gy (N=1) or 50.4 Gy (N=3). Weekly CBCTs (N=25) were acquired and the nodal clinical target volumes and organs at risk were contoured by a physician. The percent nodal volume receiving prescription dose was recorded as amore » ground truth. Using the recorded shifts performed by the radiation therapists at the time of image acquisition, CBCTs were aligned with the planning kVCT. Mutual image information (MI) was calculated between the CBCT and the aligned planning CT within the contour of the nodal PTV. Due to variable CBCT fields-of-view, CBCT images covering less than 90% of the nodal volume were excluded from the analysis, resulting in the removal of eight CBCTs. Results: A correlation coefficient of 0.40 was observed between the MI metric and the percent of the nodal target volume receiving the prescription dose. One patient's CBCTs had clear outliers from the rest of the patients. Upon further investigation, we discovered image artifacts that were present only in that patient's images. When those four images were excluded, the correlation improved to 0.81. Conclusion: This pilot study shows the potential of predicting pelvic nodal dosimetry by computing the mutual image information between planning CTs and patient setup CBCTs. Importantly, this technique does not involve manual or automatic contouring of the CBCT images. Additional patients and more robust exclusion criteria will help validate our findings.« less

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

PubMed Central

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

2015-01-01

Purpose: To evaluate the accuracy of axillary ultrasound (AUS) in detecting nodal metastasis in patients with early-stage breast cancer and to identify AUS features with high predictive power. Materials and Methods: Prospective single-center preliminary study in 105 patients with a primary diagnosis of breast cancer and clinically negative axilla. AUS was performed using a 12 MHz linear-array transducer before ultrasound-guided needle biopsy. Nodal characteristics (shape, longitudinal-transverse [LT] axis ratio, margins, cortical thickness, hyperechoic hilum) were correlated with histopathological nodal status after SLNB or axillary lymph node dissection (ALND). Results: Nodal metastases were present in 42/105 patients (40.0%). Univariate analyses showed that absence of hyperechoic hilum, round shape, LT axis ratio<2, sharp margins and cortical thickness>3 mm were associated with lymph node metastasis. Multivariate logistic regression analysis revealed cortical thickness > 3 mm as an independent predictive parameter for nodal involvement. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 66.7, 74.6, 63.6, 77.0% and 71.4% respectively when cortical thickness > 3 mm was applied as the criterion for AUS positivity. Axillary tumor volume was low in patients with pT1/2 tumors and negative AUS, since only 3.2% of patients had > 2 metastatic lymph nodes. Conclusion: Cortical thickness>3 mm is a reliable predictor of nodal metastatic involvement. Negative AUS does not exclude lymph node metastases, but extensive axillary tumor volume is rare. PMID:27689144

A Flexible CUDA LU-based Solver for Small, Batched Linear Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumeo, Antonino; Gawande, Nitin A.; Villa, Oreste

This chapter presents the implementation of a batched CUDA solver based on LU factorization for small linear systems. This solver may be used in applications such as reactive flow transport models, which apply the Newton-Raphson technique to linearize and iteratively solve the sets of non linear equations that represent the reactions for ten of thousands to millions of physical locations. The implementation exploits somewhat counterintuitive GPGPU programming techniques: it assigns the solution of a matrix (representing a system) to a single CUDA thread, does not exploit shared memory and employs dynamic memory allocation on the GPUs. These techniques enable ourmore » implementation to simultaneously solve sets of systems with over 100 equations and to employ LU decomposition with complete pivoting, providing the higher numerical accuracy required by certain applications. Other currently available solutions for batched linear solvers are limited by size and only support partial pivoting, although they may result faster in certain conditions. We discuss the code of our implementation and present a comparison with the other implementations, discussing the various tradeoffs in terms of performance and flexibility. This work will enable developers that need batched linear solvers to choose whichever implementation is more appropriate to the features and the requirements of their applications, and even to implement dynamic switching approaches that can choose the best implementation depending on the input data.« less

LEOPARD: A grid-based dispersion relation solver for arbitrary gyrotropic distributions

NASA Astrophysics Data System (ADS)

Astfalk, Patrick; Jenko, Frank

2017-01-01

Particle velocity distributions measured in collisionless space plasmas often show strong deviations from idealized model distributions. Despite this observational evidence, linear wave analysis in space plasma environments such as the solar wind or Earth's magnetosphere is still mainly carried out using dispersion relation solvers based on Maxwellians or other parametric models. To enable a more realistic analysis, we present the new grid-based kinetic dispersion relation solver LEOPARD (Linear Electromagnetic Oscillations in Plasmas with Arbitrary Rotationally-symmetric Distributions) which no longer requires prescribed model distributions but allows for arbitrary gyrotropic distribution functions. In this work, we discuss the underlying numerical scheme of the code and we show a few exemplary benchmarks. Furthermore, we demonstrate a first application of LEOPARD to ion distribution data obtained from hybrid simulations. In particular, we show that in the saturation stage of the parallel fire hose instability, the deformation of the initial bi-Maxwellian distribution invalidates the use of standard dispersion relation solvers. A linear solver based on bi-Maxwellians predicts further growth even after saturation, while LEOPARD correctly indicates vanishing growth rates. We also discuss how this complies with former studies on the validity of quasilinear theory for the resonant fire hose. In the end, we briefly comment on the role of LEOPARD in directly analyzing spacecraft data, and we refer to an upcoming paper which demonstrates a first application of that kind.

Brady's Geothermal Field Nodal Seismometer Earthquake Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurt Feigl

90-second records of data from 238 three-component nodal seismometer deployed at Bradys geothermal field. The time window catches an earthquake arrival. Earthquake data from USGS online catalog: Magnitude: 4.3 ml +/- 0.4 Location: 38.479 deg N 118.366 deg W +/- 0.7 km Depth: 9.9 km +/- 0.7 Date and Time: 2016-03-21 07:37:10.535 UTC

Matlab Geochemistry: An open source geochemistry solver based on MRST

NASA Astrophysics Data System (ADS)

McNeece, C. J.; Raynaud, X.; Nilsen, H.; Hesse, M. A.

2017-12-01

The study of geological systems often requires the solution of complex geochemical relations. To address this need we present an open source geochemical solver based on the Matlab Reservoir Simulation Toolbox (MRST) developed by SINTEF. The implementation supports non-isothermal multicomponent aqueous complexation, surface complexation, ion exchange, and dissolution/precipitation reactions. The suite of tools available in MRST allows for rapid model development, in particular the incorporation of geochemical calculations into transport simulations of multiple phases, complex domain geometry and geomechanics. Different numerical schemes and additional physics can be easily incorporated into the existing tools through the object-oriented framework employed by MRST. The solver leverages the automatic differentiation tools available in MRST to solve arbitrarily complex geochemical systems with any choice of species or element concentration as input. Four mathematical approaches enable the solver to be quite robust: 1) the choice of chemical elements as the basis components makes all entries in the composition matrix positive thus preserving convexity, 2) a log variable transformation is used which transfers the nonlinearity to the convex composition matrix, 3) a priori bounds on variables are calculated from the structure of the problem, constraining Netwon's path and 4) an initial guess is calculated implicitly by sequentially adding model complexity. As a benchmark we compare the model to experimental and semi-analytic solutions of the coupled salinity-acidity transport system. Together with the reservoir simulation capabilities of MRST the solver offers a promising tool for geochemical simulations in reservoir domains for applications in a diversity of fields from enhanced oil recovery to radionuclide storage.

Isospectral discrete and quantum graphs with the same flip counts and nodal counts

NASA Astrophysics Data System (ADS)

Juul, Jonas S.; Joyner, Christopher H.

2018-06-01

The existence of non-isomorphic graphs which share the same Laplace spectrum (to be referred to as isospectral graphs) leads naturally to the following question: what additional information is required in order to resolve isospectral graphs? It was suggested by Band, Shapira and Smilansky that this might be achieved by either counting the number of nodal domains or the number of times the eigenfunctions change sign (the so-called flip count) (Band et al 2006 J. Phys. A: Math. Gen. 39 13999–4014 Band and Smilansky 2007 Eur. Phys. J. Spec. Top. 145 171–9). Recent examples of (discrete) isospectral graphs with the same flip count and nodal count have been constructed by Ammann by utilising Godsil–McKay switching (Ammann private communication). Here, we provide a simple alternative mechanism that produces systematic examples of both discrete and quantum isospectral graphs with the same flip and nodal counts.

Using a multifrontal sparse solver in a high performance, finite element code

NASA Technical Reports Server (NTRS)

King, Scott D.; Lucas, Robert; Raefsky, Arthur

1990-01-01

We consider the performance of the finite element method on a vector supercomputer. The computationally intensive parts of the finite element method are typically the individual element forms and the solution of the global stiffness matrix both of which are vectorized in high performance codes. To further increase throughput, new algorithms are needed. We compare a multifrontal sparse solver to a traditional skyline solver in a finite element code on a vector supercomputer. The multifrontal solver uses the Multiple-Minimum Degree reordering heuristic to reduce the number of operations required to factor a sparse matrix and full matrix computational kernels (e.g., BLAS3) to enhance vector performance. The net result in an order-of-magnitude reduction in run time for a finite element application on one processor of a Cray X-MP.

On Riemann solvers and kinetic relations for isothermal two-phase flows with surface tension

NASA Astrophysics Data System (ADS)

Rohde, Christian; Zeiler, Christoph

2018-06-01

We consider a sharp interface approach for the inviscid isothermal dynamics of compressible two-phase flow that accounts for phase transition and surface tension effects. Kinetic relations are frequently used to fix the mass exchange and entropy dissipation rate across the interface. The complete unidirectional dynamics can then be understood by solving generalized two-phase Riemann problems. We present new well-posedness theorems for the Riemann problem and corresponding computable Riemann solvers that cover quite general equations of state, metastable input data and curvature effects. The new Riemann solver is used to validate different kinetic relations on physically relevant problems including a comparison with experimental data. Riemann solvers are building blocks for many numerical schemes that are used to track interfaces in two-phase flow. It is shown that the new Riemann solver enables reliable and efficient computations for physical situations that could not be treated before.

An Implicit Solver on A Parallel Block-Structured Adaptive Mesh Grid for FLASH

NASA Astrophysics Data System (ADS)

Lee, D.; Gopal, S.; Mohapatra, P.

2012-07-01

We introduce a fully implicit solver for FLASH based on a Jacobian-Free Newton-Krylov (JFNK) approach with an appropriate preconditioner. The main goal of developing this JFNK-type implicit solver is to provide efficient high-order numerical algorithms and methodology for simulating stiff systems of differential equations on large-scale parallel computer architectures. A large number of natural problems in nonlinear physics involve a wide range of spatial and time scales of interest. A system that encompasses such a wide magnitude of scales is described as "stiff." A stiff system can arise in many different fields of physics, including fluid dynamics/aerodynamics, laboratory/space plasma physics, low Mach number flows, reactive flows, radiation hydrodynamics, and geophysical flows. One of the big challenges in solving such a stiff system using current-day computational resources lies in resolving time and length scales varying by several orders of magnitude. We introduce FLASH's preliminary implementation of a time-accurate JFNK-based implicit solver in the framework of FLASH's unsplit hydro solver.

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.

A comparison of SuperLU solvers on the intel MIC architecture

NASA Astrophysics Data System (ADS)

Tuncel, Mehmet; Duran, Ahmet; Celebi, M. Serdar; Akaydin, Bora; Topkaya, Figen O.

2016-10-01

In many science and engineering applications, problems may result in solving a sparse linear system AX=B. For example, SuperLU_MCDT, a linear solver, was used for the large penta-diagonal matrices for 2D problems and hepta-diagonal matrices for 3D problems, coming from the incompressible blood flow simulation (see [1]). It is important to test the status and potential improvements of state-of-the-art solvers on new technologies. In this work, sequential, multithreaded and distributed versions of SuperLU solvers (see [2]) are examined on the Intel Xeon Phi coprocessors using offload programming model at the EURORA cluster of CINECA in Italy. We consider a portfolio of test matrices containing patterned matrices from UFMM ([3]) and randomly located matrices. This architecture can benefit from high parallelism and large vectors. We find that the sequential SuperLU benefited up to 45 % performance improvement from the offload programming depending on the sparse matrix type and the size of transferred and processed data.

A nodal domain theorem for integrable billiards in two dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samajdar, Rhine; Jain, Sudhir R., E-mail: srjain@barc.gov.in

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 familymore » 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.« less

A fast semi-discrete Kansa method to solve the two-dimensional spatiotemporal fractional diffusion equation

NASA Astrophysics Data System (ADS)

Sun, HongGuang; Liu, Xiaoting; Zhang, Yong; Pang, Guofei; Garrard, Rhiannon

2017-09-01

Fractional-order diffusion equations (FDEs) extend classical diffusion equations by quantifying anomalous diffusion frequently observed in heterogeneous media. Real-world diffusion can be multi-dimensional, requiring efficient numerical solvers that can handle long-term memory embedded in mass transport. To address this challenge, a semi-discrete Kansa method is developed to approximate the two-dimensional spatiotemporal FDE, where the Kansa approach first discretizes the FDE, then the Gauss-Jacobi quadrature rule solves the corresponding matrix, and finally the Mittag-Leffler function provides an analytical solution for the resultant time-fractional ordinary differential equation. Numerical experiments are then conducted to check how the accuracy and convergence rate of the numerical solution are affected by the distribution mode and number of spatial discretization nodes. Applications further show that the numerical method can efficiently solve two-dimensional spatiotemporal FDE models with either a continuous or discrete mixing measure. Hence this study provides an efficient and fast computational method for modeling super-diffusive, sub-diffusive, and mixed diffusive processes in large, two-dimensional domains with irregular shapes.

Preoperative predictors of occult nodal disease in cT1N0 oral cavity squamous cell carcinoma: Review of 2623 cases.

PubMed

Zhan, Kevin Y; Morgan, Patrick F; Neskey, David M; Kim, Joanne J; Huang, Andrew T; Garrett-Mayer, Elizabeth; Day, Terry A

2018-05-14

Nodal disease predicts survival in oral cavity squamous cell carcinoma (SCC). Currently, no large studies on predictors of occult nodal disease in cT1N0 oral cavity SCC exist. The National Cancer Database (NCDB) review for cT1N0 oral cavity SCC with surgical resection and elective neck dissection (END). The number of patients found with occult nodal disease was 2623 (15.1%). In multivariable regression, female sex and tumor differentiation predict occult nodal disease. Occult nodal disease incidence was 5.9% in well-differentiated tumors, 17.4% in moderately differentiated tumors, and 28.5% in poorly differentiated tumor (P < .001). Women with oral tongue tumors had higher occult nodal disease (19.1%) than men (12%; P = .001). Adjusted odds ratios (aORs) for occult nodal disease in women were: aOR 1.26; 95% confidence interval (CI) 1.01-1.59; P = .045; moderately differentiated aOR 3.52; 95% CI 2.47-5.01; P < .001; and poorly differentiated aOR 6.25; 95% CI 4.17-9.38; P < .001. Sex and tumor differentiation significantly predict occult nodal disease. END is recommended for all moderately and poorly differentiated cT1N0 oral cavity SCC, regardless of the depth of invasion. One can consider not performing END in well-differentiated tumors. © 2018 Wiley Periodicals, Inc.

Cryopreservation of in vitro grown nodal segments of Rauvolfia serpentina by PVS2 vitrification.

PubMed

Ray, Avik; Bhattacharya, Sabita

2008-01-01

This paper describes the cryopreservation by PVS2 vitrification of Rauvolfia serpentina (L.) Benth ex kurz, an important tropical medicinal plant. The effects of type and size of explants, sucrose preculture (duration and concentration) and vitrification treatment were tested. Preliminary experiments with PVS1, 2 and 3 produced shoot growth only for PVS2. When optimizing the PVS2 vitrification of nodal segments, those of 0.31 - 0.39 cm in size were better than other nodal sizes and or apices. Sucrose preculture had a positive role in survival and subsequent regrowth of the cryopreserved explants. Seven days on 0.5 M sucrose solution significantly improved the viability of nodal segments. PVS2 incubation for 45 minutes combined with a 7-day preculture gave the optimum result of 66 percent. Plantlets derived after cryopreservation resumed growth and regenerated normally.

A Tensor-Train accelerated solver for integral equations in complex geometries

NASA Astrophysics Data System (ADS)

Corona, Eduardo; Rahimian, Abtin; Zorin, Denis

2017-04-01

We present a framework using the Quantized Tensor Train (QTT) decomposition to accurately and efficiently solve volume and boundary integral equations in three dimensions. We describe how the QTT decomposition can be used as a hierarchical compression and inversion scheme for matrices arising from the discretization of integral equations. For a broad range of problems, computational and storage costs of the inversion scheme are extremely modest O (log ⁡ N) and once the inverse is computed, it can be applied in O (Nlog ⁡ N) . We analyze the QTT ranks for hierarchically low rank matrices and discuss its relationship to commonly used hierarchical compression techniques such as FMM and HSS. We prove that the QTT ranks are bounded for translation-invariant systems and argue that this behavior extends to non-translation invariant volume and boundary integrals. For volume integrals, the QTT decomposition provides an efficient direct solver requiring significantly less memory compared to other fast direct solvers. We present results demonstrating the remarkable performance of the QTT-based solver when applied to both translation and non-translation invariant volume integrals in 3D. For boundary integral equations, we demonstrate that using a QTT decomposition to construct preconditioners for a Krylov subspace method leads to an efficient and robust solver with a small memory footprint. We test the QTT preconditioners in the iterative solution of an exterior elliptic boundary value problem (Laplace) formulated as a boundary integral equation in complex, multiply connected geometries.

Prognostic impact of the level of nodal involvement: retrospective analysis of patients with advanced oral squamous cell carcinoma.

PubMed

Murakami, R; Nakayama, H; Semba, A; Hiraki, A; Nagata, M; Kawahara, K; Shiraishi, S; Hirai, T; Uozumi, H; Yamashita, Y

2017-01-01

We retrospectively evaluated the prognostic impact of the level of nodal involvement in patients with advanced oral squamous cell carcinoma (SCC). Between 2005 and 2010, 105 patients with clinical stage III or IV oral SCC had chemoradiotherapy preoperatively. Clinical (cN) and pathological nodal (pN) involvement was primarily at levels Ib and II. We defined nodal involvement at levels Ia and III-V as anterior and inferior extensions, respectively, and recorded such findings as extensive. With respect to pretreatment variables (age, clinical stage, clinical findings of the primary tumour, and nodal findings), univariate analysis showed that extensive cN was the only significant factor for overall survival (hazard ratio [HR], 3.27; 95% CI 1.50 to 7.13; p=0.001). Univariate analysis showed that all pN findings, including the nodal classification (invaded nodes, multiple, and contralateral) and extensive involvement were significant, and multivariate analysis confirmed that extensive pN (HR 4.71; 95% CI 1.85 to 11.97; p=0.001) and multiple pN (HR 2.59; 95% CI 1.10 to 6.09; p=0.029) were independent predictors of overall survival. Assessment based on the level of invaded neck nodes may be a better predictor of survival than the current nodal classification. Copyright © 2016 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Point-particle method to compute diffusion-limited cellular uptake.

PubMed

Sozza, A; Piazza, F; Cencini, M; De Lillo, F; Boffetta, G

2018-02-01

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study the configurations of multiple absorbers of increasing complexity to examine the performance of the method by comparing our simulations with available exact analytical or numerical results. We demonstrate the potential of the method to resolve the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudospectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry, and related sciences.

EUPDF: An Eulerian-Based Monte Carlo Probability Density Function (PDF) Solver. User's Manual

NASA Technical Reports Server (NTRS)

Raju, M. S.

1998-01-01

EUPDF is an Eulerian-based Monte Carlo PDF solver developed for application with sprays, combustion, parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with the coding required to couple the PDF code to any given flow code and a basic understanding of the EUPDF code structure as well as the models involved in the PDF formulation. The source code of EUPDF will be available with the release of the National Combustion Code (NCC) as a complete package.

Fast Euler solver for transonic airfoils. I - Theory. II - Applications

NASA Technical Reports Server (NTRS)

Dadone, Andrea; Moretti, Gino

1988-01-01

Equations written in terms of generalized Riemann variables are presently integrated by inverting six bidiagonal matrices and two tridiagonal matrices, using an implicit Euler solver that is based on the lambda-formulation. The solution is found on a C-grid whose boundaries are very close to the airfoil. The fast solver is then applied to the computation of several flowfields on a NACA 0012 airfoil at various Mach number and alpha values, yielding results that are primarily concerned with transonic flows. The effects of grid fineness and boundary distances are analyzed; the code is found to be robust and accurate, as well as fast.

Characterization of Lifshitz transitions in topological nodal line semimetals

NASA Astrophysics Data System (ADS)

Jiang, Hui; Li, Linhu; Gong, Jiangbin; Chen, Shu

2018-04-01

We introduce a two-band model of three-dimensional nodal line semimetals (NLSMs), the Fermi surface of which at half-filling may form various one-dimensional configurations of different topology. We study the symmetries and "drumhead" surface states of the model, and find that the transitions between different configurations, namely, the Lifshitz transitions, can be identified solely by the number of gap-closing points on some high-symmetry planes in the Brillouin zone. A global phase diagram of this model is also obtained accordingly. We then investigate the effect of some extra terms analogous to a two-dimensional Rashba-type spin-orbit coupling. The introduced extra terms open a gap for the NLSMs and can be useful in engineering different topological insulating phases. We demonstrate that the behavior of surface Dirac cones in the resulting insulating system has a clear correspondence with the different configurations of the original nodal lines in the absence of the gap terms.

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.

Cervical nodal metastases in squamous cell carcinoma of the head and neck: what to expect.

PubMed

Mukherji, S K; Armao, D; Joshi, V M

2001-11-01

The treatment and management of malignancies of the head and neck is directly altered by the presence of metastatic cervical adenopathy. The treatment of nodal metastases in squamous cell carcinoma of the head and neck (HNSCCA) is determined by the lymphatic drainage of the upper aerodigestive tract. The lymphatic drainage is site-specific and occurs in a predictable manner. The purpose of this text is to provide an overview of the normal routes of lymphatic drainage in the head and neck and correlate this with the current nodal classification system. The specific aims of this manuscript are to 1) illustrate the expected lymphatic drainage patterns of HNSCCA arising in the different subsites (nasopharynx, oropharynx, oral cavity, larynx, and hypopharynx) and 2) review the expected frequency of metastases within nodal groups for HNSCCA that arise in these locations. An understanding of the topographical distribution and incidence of cervical lymph node metastases plays an integral role in the physical examination and radiological evaluation of patients with HNSCCA. For the neuroradiologist, this information may increases the ability to identify those nodal groups at risk for metastatic involvement. Copyright 2001 John Wiley & Sons, Inc. Head Neck 23: 995-1005, 2001.

Theory of nodal s ±-wave pairing symmetry in the Pu-based 115 superconductor family

DOE PAGES

Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

2015-02-27

The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-T c superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scatteringmore » channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

Execution of a parallel edge-based Navier-Stokes solver on commodity graphics processor units

NASA Astrophysics Data System (ADS)

Corral, Roque; Gisbert, Fernando; Pueblas, Jesus

2017-02-01

The implementation of an edge-based three-dimensional Reynolds Average Navier-Stokes solver for unstructured grids able to run on multiple graphics processing units (GPUs) is presented. Loops over edges, which are the most time-consuming part of the solver, have been written to exploit the massively parallel capabilities of GPUs. Non-blocking communications between parallel processes and between the GPU and the central processor unit (CPU) have been used to enhance code scalability. The code is written using a mixture of C++ and OpenCL, to allow the execution of the source code on GPUs. The Message Passage Interface (MPI) library is used to allow the parallel execution of the solver on multiple GPUs. A comparative study of the solver parallel performance is carried out using a cluster of CPUs and another of GPUs. It is shown that a single GPU is up to 64 times faster than a single CPU core. The parallel scalability of the solver is mainly degraded due to the loss of computing efficiency of the GPU when the size of the case decreases. However, for large enough grid sizes, the scalability is strongly improved. A cluster featuring commodity GPUs and a high bandwidth network is ten times less costly and consumes 33% less energy than a CPU-based cluster with an equivalent computational power.

A systematic approach to numerical dispersion in Maxwell solvers

NASA Astrophysics Data System (ADS)

Blinne, Alexander; Schinkel, David; Kuschel, Stephan; Elkina, Nina; Rykovanov, Sergey G.; Zepf, Matt

2018-03-01

The finite-difference time-domain (FDTD) method is a well established method for solving the time evolution of Maxwell's equations. Unfortunately the scheme introduces numerical dispersion and therefore phase and group velocities which deviate from the correct values. The solution to Maxwell's equations in more than one dimension results in non-physical predictions such as numerical dispersion or numerical Cherenkov radiation emitted by a relativistic electron beam propagating in vacuum. Improved solvers, which keep the staggered Yee-type grid for electric and magnetic fields, generally modify the spatial derivative operator in the Maxwell-Faraday equation by increasing the computational stencil. These modified solvers can be characterized by different sets of coefficients, leading to different dispersion properties. In this work we introduce a norm function to rewrite the choice of coefficients into a minimization problem. We solve this problem numerically and show that the minimization procedure leads to phase and group velocities that are considerably closer to c as compared to schemes with manually set coefficients available in the literature. Depending on a specific problem at hand (e.g. electron beam propagation in plasma, high-order harmonic generation from plasma surfaces, etc.), the norm function can be chosen accordingly, for example, to minimize the numerical dispersion in a certain given propagation direction. Particle-in-cell simulations of an electron beam propagating in vacuum using our solver are provided.

MODFLOW-2000, The U.S. Geological Survey Modular Ground-Water Model -- GMG Linear Equation Solver Package Documentation

USGS Publications Warehouse

Wilson, John D.; Naff, Richard L.

2004-01-01

A geometric multigrid solver (GMG), based in the preconditioned conjugate gradient algorithm, has been developed for solving systems of equations resulting from applying the cell-centered finite difference algorithm to flow in porous media. This solver has been adapted to the U.S. Geological Survey ground-water flow model MODFLOW-2000. The documentation herein is a description of the solver and the adaptation to MODFLOW-2000.

Galerkin CFD solvers for use in a multi-disciplinary suite for modeling advanced flight vehicles

NASA Astrophysics Data System (ADS)

Moffitt, Nicholas J.

This work extends existing Galerkin CFD solvers for use in a multi-disciplinary suite. The suite is proposed as a means of modeling advanced flight vehicles, which exhibit strong coupling between aerodynamics, structural dynamics, controls, rigid body motion, propulsion, and heat transfer. Such applications include aeroelastics, aeroacoustics, stability and control, and other highly coupled applications. The suite uses NASA STARS for modeling structural dynamics and heat transfer. Aerodynamics, propulsion, and rigid body dynamics are modeled in one of the five CFD solvers below. Euler2D and Euler3D are Galerkin CFD solvers created at OSU by Cowan (2003). These solvers are capable of modeling compressible inviscid aerodynamics with modal elastics and rigid body motion. This work reorganized these solvers to improve efficiency during editing and at run time. Simple and efficient propulsion models were added, including rocket, turbojet, and scramjet engines. Viscous terms were added to the previous solvers to create NS2D and NS3D. The viscous contributions were demonstrated in the inertial and non-inertial frames. Variable viscosity (Sutherland's equation) and heat transfer boundary conditions were added to both solvers but not verified in this work. Two turbulence models were implemented in NS2D and NS3D: Spalart-Allmarus (SA) model of Deck, et al. (2002) and Menter's SST model (1994). A rotation correction term (Shur, et al., 2000) was added to the production of turbulence. Local time stepping and artificial dissipation were adapted to each model. CFDsol is a Taylor-Galerkin solver with an SA turbulence model. This work improved the time accuracy, far field stability, viscous terms, Sutherland?s equation, and SA model with NS3D as a guideline and added the propulsion models from Euler3D to CFDsol. Simple geometries were demonstrated to utilize current meshing and processing capabilities. Air-breathing hypersonic flight vehicles (AHFVs) represent the ultimate

Atlas-Based Segmentation Improves Consistency and Decreases Time Required for Contouring Postoperative Endometrial Cancer Nodal Volumes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Amy V.; Department of Radiation Oncology, St. Luke's-Roosevelt Hospital, New York, NY; Wortham, Angela

2011-03-01

Purpose: Accurate target delineation of the nodal volumes is essential for three-dimensional conformal and intensity-modulated radiotherapy planning for endometrial cancer adjuvant therapy. We hypothesized that atlas-based segmentation ('autocontouring') would lead to time savings and more consistent contours among physicians. Methods and Materials: A reference anatomy atlas was constructed using the data from 15 postoperative endometrial cancer patients by contouring the pelvic nodal clinical target volume on the simulation computed tomography scan according to the Radiation Therapy Oncology Group 0418 trial using commercially available software. On the simulation computed tomography scans from 10 additional endometrial cancer patients, the nodal clinical targetmore » volume autocontours were generated. Three radiation oncologists corrected the autocontours and delineated the manual nodal contours under timed conditions while unaware of the other contours. The time difference was determined, and the overlap of the contours was calculated using Dice's coefficient. Results: For all physicians, manual contouring of the pelvic nodal target volumes and editing the autocontours required a mean {+-} standard deviation of 32 {+-} 9 vs. 23 {+-} 7 minutes, respectively (p = .000001), a 26% time savings. For each physician, the time required to delineate the manual contours vs. correcting the autocontours was 30 {+-} 3 vs. 21 {+-} 5 min (p = .003), 39 {+-} 12 vs. 30 {+-} 5 min (p = .055), and 29 {+-} 5 vs. 20 {+-} 5 min (p = .0002). The mean overlap increased from manual contouring (0.77) to correcting the autocontours (0.79; p = .038). Conclusion: The results of our study have shown that autocontouring leads to increased consistency and time savings when contouring the nodal target volumes for adjuvant treatment of endometrial cancer, although the autocontours still required careful editing to ensure that the lymph nodes at risk of recurrence are properly included in the

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

DOE PAGES

Li, Xinya; Deng, Z. Daniel; USA, Richland Washington; ...

2014-11-27

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developedmore » using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.« less

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

NASA Astrophysics Data System (ADS)

Li, Xinya; Deng, Z. Daniel; Sun, Yannan; Martinez, Jayson J.; Fu, Tao; McMichael, Geoffrey A.; Carlson, Thomas J.

2014-11-01

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

PubMed Central

Li, Xinya; Deng, Z. Daniel; Sun, Yannan; Martinez, Jayson J.; Fu, Tao; McMichael, Geoffrey A.; Carlson, Thomas J.

2014-01-01

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature. PMID:25427517

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters.

PubMed

Li, Xinya; Deng, Z Daniel; Sun, Yannan; Martinez, Jayson J; Fu, Tao; McMichael, Geoffrey A; Carlson, Thomas J

2014-11-27

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developed using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.

A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xinya; Deng, Z. Daniel; USA, Richland Washington

Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to observe the out-migratory behavior of juvenile salmonids tagged by surgical implantation of acoustic micro-transmitters and to estimate the survival when passing through dams on the Snake and Columbia Rivers. A robust three-dimensional solver was needed to accurately and efficiently estimate the time sequence of locations of fish tagged with JSATS acoustic transmitters, to describe in sufficient detail the information needed to assess the function of dam-passage design alternatives. An approximate maximum likelihood solver was developedmore » using measurements of time difference of arrival from all hydrophones in receiving arrays on which a transmission was detected. Field experiments demonstrated that the developed solver performed significantly better in tracking efficiency and accuracy than other solvers described in the literature.« less

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

New preconditioning strategy for Jacobian-free solvers for variably saturated flows with Richards’ equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipnikov, Konstantin; Moulton, David; Svyatskiy, Daniil

2016-04-29

We develop a new approach for solving the nonlinear Richards’ equation arising in variably saturated flow modeling. The growing complexity of geometric models for simulation of subsurface flows leads to the necessity of using unstructured meshes and advanced discretization methods. Typically, a numerical solution is obtained by first discretizing PDEs and then solving the resulting system of nonlinear discrete equations with a Newton-Raphson-type method. Efficiency and robustness of the existing solvers rely on many factors, including an empiric quality control of intermediate iterates, complexity of the employed discretization method and a customized preconditioner. We propose and analyze a new preconditioningmore » strategy that is based on a stable discretization of the continuum Jacobian. We will show with numerical experiments for challenging problems in subsurface hydrology that this new preconditioner improves convergence of the existing Jacobian-free solvers 3-20 times. Furthermore, we show that the Picard method with this preconditioner becomes a more efficient nonlinear solver than a few widely used Jacobian-free solvers.« less

Human papillomavirus reduces the prognostic value of nodal involvement in tonsillar squamous cell carcinomas.

PubMed

Straetmans, Jos M J A A; Olthof, Nadine; Mooren, Jeroen J; de Jong, Jos; Speel, Ernst-Jan M; Kremer, Bernd

2009-10-01

Assessment of the prognostic value of nodal status in relation to human papillomavirus (HPV) status and the various treatment modalities in tonsillar squamous cell carcinomas (TSCC). Retrospective 5-year survival analysis. A 5-year follow-up of disease-free, disease-specific, and overall survival in a group of 81 patients with TSCC was conducted. The nodal status and integration of HPV-DNA in the genome (detected with fluorescence in situ hybridization) as prognostic indicators were examined while correcting for other clinical parameters (smoking habits, alcohol consumption, treatment modality, differentiation, TNM classification). Of TSCCs, 41% were positive for HPV type 16. In these TSCCs, the primary tumor was significantly smaller when compared to HVP-negative TSCCs (P = .04), whereas the percentage of cases with cervical metastases was identical. In the total population, it was not nodal involvement, but rather HPV manifestation, which was related to patient prognosis. Within the treatment modalities (surgery combined with radiotherapy and radiotherapy alone), neither nodal status nor HPV were prognostic indicators. Since a substantial percentage of TSCCs are HPV-positive and metastasizes to cervical lymph nodes in less advanced primary tumors, the N status is an unreliable prognostic indicator in TSCCs. HPV is only prognostically relevant in the total tumor population, but loses its value within patient groups receiving a single treatment modality. The value of HPV for prognosis of patients with TSCC requires further study.

Convergence Acceleration of a Navier-Stokes Solver for Efficient Static Aeroelastic Computations

NASA Technical Reports Server (NTRS)

Obayashi, Shigeru; Guruswamy, Guru P.

1995-01-01

New capabilities have been developed for a Navier-Stokes solver to perform steady-state simulations more efficiently. The flow solver for solving the Navier-Stokes equations is based on a combination of the lower-upper factored symmetric Gauss-Seidel implicit method and the modified Harten-Lax-van Leer-Einfeldt upwind scheme. A numerically stable and efficient pseudo-time-marching method is also developed for computing steady flows over flexible wings. Results are demonstrated for transonic flows over rigid and flexible wings.

Transonic Drag Prediction on a DLR-F6 Transport Configuration Using Unstructured Grid Solvers

NASA Technical Reports Server (NTRS)

Lee-Rausch, E. M.; Frink, N. T.; Mavriplis, D. J.; Rausch, R. D.; Milholen, W. E.

2004-01-01

A second international AIAA Drag Prediction Workshop (DPW-II) was organized and held in Orlando Florida on June 21-22, 2003. The primary purpose was to inves- tigate the code-to-code uncertainty. address the sensitivity of the drag prediction to grid size and quantify the uncertainty in predicting nacelle/pylon drag increments at a transonic cruise condition. This paper presents an in-depth analysis of the DPW-II computational results from three state-of-the-art unstructured grid Navier-Stokes flow solvers exercised on similar families of tetrahedral grids. The flow solvers are USM3D - a tetrahedral cell-centered upwind solver. FUN3D - a tetrahedral node-centered upwind solver, and NSU3D - a general element node-centered central-differenced solver. For the wingbody, the total drag predicted for a constant-lift transonic cruise condition showed a decrease in code-to-code variation with grid refinement as expected. For the same flight condition, the wing/body/nacelle/pylon total drag and the nacelle/pylon drag increment predicted showed an increase in code-to-code variation with grid refinement. Although the range in total drag for the wingbody fine grids was only 5 counts, a code-to-code comparison of surface pressures and surface restricted streamlines indicated that the three solvers were not all converging to the same flow solutions- different shock locations and separation patterns were evident. Similarly, the wing/body/nacelle/pylon solutions did not appear to be converging to the same flow solutions. Overall, grid refinement did not consistently improve the correlation with experimental data for either the wingbody or the wing/body/nacelle pylon configuration. Although the absolute values of total drag predicted by two of the solvers for the medium and fine grids did not compare well with the experiment, the incremental drag predictions were within plus or minus 3 counts of the experimental data. The correlation with experimental incremental drag was not

Avoiding Communication in the Lanczos Bidiagonalization Routine and Associated Least Squares QR Solver

DTIC Science & Technology

2015-04-12

Avoiding communication in the Lanczos bidiagonalization routine and associated Least Squares QR solver Erin Carson Electrical Engineering and...Bidiagonalization Routine and Associated Least Squares QR Solver 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...throughout scienti c codes , are often the bottlenecks in application perfor- mance due to a low computation/communication ratio. In this paper we develop

Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Nkonga, Boniface

2017-10-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

Final Report: Subcontract B623868 Algebraic Multigrid solvers for coupled PDE systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brannick, J.

The Pennsylvania State University (“Subcontractor”) continued to work on the design of algebraic multigrid solvers for coupled systems of partial differential equations (PDEs) arising in numerical modeling of various applications, with a main focus on solving the Dirac equation arising in Quantum Chromodynamics (QCD). The goal of the proposed work was to develop combined geometric and algebraic multilevel solvers that are robust and lend themselves to efficient implementation on massively parallel heterogeneous computers for these QCD systems. The research in these areas built on previous works, focusing on the following three topics: (1) the development of parallel full-multigrid (PFMG) andmore » non-Galerkin coarsening techniques in this frame work for solving the Wilson Dirac system; (2) the use of these same Wilson MG solvers for preconditioning the Overlap and Domain Wall formulations of the Dirac equation; and (3) the design and analysis of algebraic coarsening algorithms for coupled PDE systems including Stokes equation, Maxwell equation and linear elasticity.« less

A new solver for granular avalanche simulation: Indoor experiment verification and field scale case study

NASA Astrophysics Data System (ADS)

Wang, XiaoLiang; Li, JiaChun

2017-12-01

A new solver based on the high-resolution scheme with novel treatments of source terms and interface capture for the Savage-Hutter model is developed to simulate granular avalanche flows. The capability to simulate flow spread and deposit processes is verified through indoor experiments of a two-dimensional granular avalanche. Parameter studies show that reduction in bed friction enhances runout efficiency, and that lower earth pressure restraints enlarge the deposit spread. The April 9, 2000, Yigong avalanche in Tibet, China, is simulated as a case study by this new solver. The predicted results, including evolution process, deposit spread, and hazard impacts, generally agree with site observations. It is concluded that the new solver for the Savage-Hutter equation provides a comprehensive software platform for granular avalanche simulation at both experimental and field scales. In particular, the solver can be a valuable tool for providing necessary information for hazard forecasts, disaster mitigation, and countermeasure decisions in mountainous areas.

Tumour thickness as a predictor of nodal metastases in oral cancer: comparison between tongue and floor of mouth subsites.

PubMed

Balasubramanian, Deepak; Ebrahimi, Ardalan; Gupta, Ruta; Gao, Kan; Elliott, Michael; Palme, Carsten E; Clark, Jonathan R

2014-12-01

To identify whether tumour thickness as a predictor of nodal metastases in oral squamous cell carcinoma differs between tongue and floor of mouth (FOM) subsites. Retrospective review of 343 patients treated between 1987 and 2012. The neck was considered positive in the presence of pathologically proven nodal metastases on neck dissection or during follow-up. There were 222 oral tongue and 121 FOM tumours. In patients with FOM tumours 2.1-4mm thick, the rate of nodal metastases was 41.7%. In contrast, for tongue cancers of a similar thickness the rate was only 11.2%. This increased to 38.5% in patients with tongue cancers that were 4.1-6mm thick. Comparing these two subsites, FOM cancers cross the critical 20% threshold of probability for nodal metastases between 1 and 2mm whereas tongue cancers cross the 20% threshold just under 4mm thickness. On logistic regression adjusting for relevant covariates, there was a significant difference in the propensity for nodal metastases based on tumour thickness according to subsite (p=0.028). Thin FOM tumours (2.1-4mm) have a high rate of nodal metastases. Elective neck dissection is appropriate in FOM tumours ⩾2mm thick and in tongue tumours ⩾4mm thick. Copyright © 2014 Elsevier Ltd. All rights reserved.

A robust and contact resolving Riemann solver on unstructured mesh, Part I, Euler method

NASA Astrophysics Data System (ADS)

Shen, Zhijun; Yan, Wei; Yuan, Guangwei

2014-07-01

This article presents a new cell-centered numerical method for compressible flows on arbitrary unstructured meshes. A multi-dimensional Riemann solver based on the HLLC method (denoted by HLLC-2D solver) is established. The work is an extension from the cell-centered Lagrangian scheme of Maire et al. [27] to the Eulerian framework. Similarly to the work in [27], a two-dimensional contact velocity defined on a grid node is introduced, and the motivation is to keep an edge flux consistency with the node velocity connected to the edge intrinsically. The main new feature of the algorithm is to relax the condition that the contact pressures must be same in the traditional HLLC solver. The discontinuous fluxes are constructed across each wave sampling direction rather than only along the contact wave direction. The two-dimensional contact velocity of the grid node is determined via enforcing conservation of mass, momentum and total energy, and thus the new method satisfies these conservation properties at nodes rather than on grid edges. Other good properties of the HLLC-2d solver, such as the positivity and the contact preserving, are described, and the two-dimensional high-order extension is constructed employing MUSCL type reconstruction procedure. Numerical results based on both quadrilateral and triangular grids are presented to demonstrate the robustness and the accuracy of this new solver, which shows it has better performance than the existing HLLC method.

NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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, ourmore » 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.« less

Disappearance of nodal gap across the insulator-superconductor transition in a copper-oxide superconductor.

PubMed

Peng, Yingying; Meng, Jianqiao; Mou, Daixiang; He, Junfeng; Zhao, Lin; Wu, Yue; Liu, Guodong; Dong, Xiaoli; He, Shaolong; Zhang, Jun; Wang, Xiaoyang; Peng, Qinjun; Wang, Zhimin; Zhang, Shenjin; Yang, Feng; Chen, Chuangtian; Xu, Zuyan; Lee, T K; Zhou, X J

2013-01-01

The parent compound of the copper-oxide high-temperature superconductors is a Mott insulator. Superconductivity is realized by doping an appropriate amount of charge carriers. How a Mott insulator transforms into a superconductor is crucial in understanding the unusual physical properties of high-temperature superconductors and the superconductivity mechanism. Here we report high-resolution angle-resolved photoemission measurement on heavily underdoped Bi₂Sr₂-xLaxCuO(₆+δ) system. The electronic structure of the lightly doped samples exhibit a number of characteristics: existence of an energy gap along the nodal direction, d-wave-like anisotropic energy gap along the underlying Fermi surface, and coexistence of a coherence peak and a broad hump in the photoemission spectra. Our results reveal a clear insulator-superconductor transition at a critical doping level of ~0.10 where the nodal energy gap approaches zero, the three-dimensional antiferromagnetic order disappears, and superconductivity starts to emerge. These observations clearly signal a close connection between the nodal gap, antiferromagnetism and superconductivity.

SMITHERS: An object-oriented modular mapping methodology for MCNP-based neutronic–thermal hydraulic multiphysics

DOE PAGES

Richard, Joshua; Galloway, Jack; Fensin, Michael; ...

2015-04-04

A novel object-oriented modular mapping methodology for externally coupled neutronics–thermal hydraulics multiphysics simulations was developed. The Simulator using MCNP with Integrated Thermal-Hydraulics for Exploratory Reactor Studies (SMITHERS) code performs on-the-fly mapping of material-wise power distribution tallies implemented by MCNP-based neutron transport/depletion solvers for use in estimating coolant temperature and density distributions with a separate thermal-hydraulic solver. The key development of SMITHERS is that it reconstructs the hierarchical geometry structure of the material-wise power generation tallies from the depletion solver automatically, with only a modicum of additional information required from the user. In addition, it performs the basis mapping from themore » combinatorial geometry of the depletion solver to the required geometry of the thermal-hydraulic solver in a generalizable manner, such that it can transparently accommodate varying levels of thermal-hydraulic solver geometric fidelity, from the nodal geometry of multi-channel analysis solvers to the pin-cell level of discretization for sub-channel analysis solvers.« less

Flowfield Comparisons from Three Navier-Stokes Solvers for an Axisymmetric Separate Flow Jet

NASA Technical Reports Server (NTRS)

Koch, L. Danielle; Bridges, James; Khavaran, Abbas

2002-01-01

To meet new noise reduction goals, many concepts to enhance mixing in the exhaust jets of turbofan engines are being studied. Accurate steady state flowfield predictions from state-of-the-art computational fluid dynamics (CFD) solvers are needed as input to the latest noise prediction codes. The main intent of this paper was to ascertain that similar Navier-Stokes solvers run at different sites would yield comparable results for an axisymmetric two-stream nozzle case. Predictions from the WIND and the NPARC codes are compared to previously reported experimental data and results from the CRAFT Navier-Stokes solver. Similar k-epsilon turbulence models were employed in each solver, and identical computational grids were used. Agreement between experimental data and predictions from each code was generally good for mean values. All three codes underpredict the maximum value of turbulent kinetic energy. The predicted locations of the maximum turbulent kinetic energy were farther downstream than seen in the data. A grid study was conducted using the WIND code, and comments about convergence criteria and grid requirements for CFD solutions to be used as input for noise prediction computations are given. Additionally, noise predictions from the MGBK code, using the CFD results from the CRAFT code, NPARC, and WIND as input are compared to data.

A Stable Finite-Difference Scheme for Population Growth and Diffusion on a Map

PubMed Central

Callegari, S.; Lake, G. R.; Tkachenko, N.; Weissmann, J. D.; Zollikofer, Ch. P. E.

2017-01-01

We describe a general Godunov-type splitting for numerical simulations of the Fisher–Kolmogorov–Petrovski–Piskunov growth and diffusion equation on a world map with Neumann boundary conditions. The procedure is semi-implicit, hence quite stable. Our principal application for this solver is modeling human population dispersal over geographical maps with changing paleovegetation and paleoclimate in the late Pleistocene. As a proxy for carrying capacity we use Net Primary Productivity (NPP) to predict times for human arrival in the Americas. PMID:28085882

A Stable Finite-Difference Scheme for Population Growth and Diffusion on a Map.

PubMed

Petersen, W P; Callegari, S; Lake, G R; Tkachenko, N; Weissmann, J D; Zollikofer, Ch P E

2017-01-01

We describe a general Godunov-type splitting for numerical simulations of the Fisher-Kolmogorov-Petrovski-Piskunov growth and diffusion equation on a world map with Neumann boundary conditions. The procedure is semi-implicit, hence quite stable. Our principal application for this solver is modeling human population dispersal over geographical maps with changing paleovegetation and paleoclimate in the late Pleistocene. As a proxy for carrying capacity we use Net Primary Productivity (NPP) to predict times for human arrival in the Americas.

Comparison of Einstein-Boltzmann solvers for testing general relativity

NASA Astrophysics Data System (ADS)

Bellini, E.; Barreira, A.; Frusciante, N.; Hu, B.; Peirone, S.; Raveri, M.; Zumalacárregui, M.; Avilez-Lopez, A.; Ballardini, M.; Battye, R. A.; Bolliet, B.; Calabrese, E.; Dirian, Y.; Ferreira, P. G.; Finelli, F.; Huang, Z.; Ivanov, M. M.; Lesgourgues, J.; Li, B.; Lima, N. A.; Pace, F.; Paoletti, D.; Sawicki, I.; Silvestri, A.; Skordis, C.; Umiltà, C.; Vernizzi, F.

2018-01-01

We compare Einstein-Boltzmann solvers that include modifications to general relativity and find that, for a wide range of models and parameters, they agree to a high level of precision. We look at three general purpose codes that primarily model general scalar-tensor theories, three codes that model Jordan-Brans-Dicke (JBD) gravity, a code that models f (R ) gravity, a code that models covariant Galileons, a code that models Hořava-Lifschitz gravity, and two codes that model nonlocal models of gravity. Comparing predictions of the angular power spectrum of the cosmic microwave background and the power spectrum of dark matter for a suite of different models, we find agreement at the subpercent level. This means that this suite of Einstein-Boltzmann solvers is now sufficiently accurate for precision constraints on cosmological and gravitational parameters.

Diffusion of external magnetic fields into the cone-in-shell target in the fast ignition

NASA Astrophysics Data System (ADS)

Sunahara, Atsushi; Morita, Hiroki; Johzaki, Tomoyuki; Nagatomo, Hideo; Fujioka, Shinsuke; Hassanein, Ahmed; Firex Project Team

2017-10-01

We simulated the diffusion of externally applied magnetic fields into cone-in-shell target in the fast ignition. Recently, in the fast ignition scheme, the externally magnetic fields up to kilo-Tesla is used to guide fast electrons to the high-dense imploded core. In order to study the profile of the magnetic field, we have developed 2D cylindrical Maxwell equation solver with Ohm's law, and carried out simulations of diffusion of externally applied magnetic fields into a cone-in-shell target. We estimated the conductivity of the cone and shell target based on the assumption of Saha-ionization equilibrium. Also, we calculated the temporal evolution of the target temperature heated by the eddy current driven by temporal variation of magnetic fields, based on the accurate equation of state. Both, the diffusion of magnetic field and the increase of target temperature interact with each other. We present our results of temporal evolution of the magnetic field and its diffusion into the cone and shell target.

Are Your Students Problem Performers or Problem Solvers?

ERIC Educational Resources Information Center

Barlow, Angela T.; Duncan, Matthew; Lischka, Alyson E.; Hartland, Kristin S.; Willingham, J. Christopher

2017-01-01

When presented with a problem in mathematics class, students often function as problem performers rather than problem solvers (Rigelman 2007). That is, rather than understanding the problem, students focus on using an operation to complete it. Students' tendencies to act as problem performers can prevent them from suggesting problem-solving…

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.

Treating convection in sequential solvers

NASA Technical Reports Server (NTRS)

Shyy, Wei; Thakur, Siddharth

1992-01-01

The treatment of the convection terms in the sequential solver, a standard procedure found in virtually all pressure based algorithms, to compute the flow problems with sharp gradients and source terms is investigated. Both scalar model problems and one-dimensional gas dynamics equations have been used to study the various issues involved. Different approaches including the use of nonlinear filtering techniques and adoption of TVD type schemes have been investigated. Special treatments of the source terms such as pressure gradients and heat release have also been devised, yielding insight and improved accuracy of the numerical procedure adopted.

Modification of atrioventricular nodal electrophysiology by selective radiofrequency delivery on the anterior or posterior approaches.

PubMed

Chorro, F J; Sanchis, J; Such, L; Artal, L; Llavador, J J; Llavador, E; Monmeneu, J V; López-Merino, V

1997-05-01

An analysis was made in 14 isolated and perfused rabbit hearts of the electrophysiological effects of selective radiofrequency (RF) delivery in the anterior (group I, n = 7) or posterior zone (group II, n = 7) of the Koch triangle, with the aim of modifying atrioventricular nodal (AVN) conduction without suppressing 1:1 transmission. After opening the right atrium, RF was delivered (0.5 W) with a 1-mm diameter unipolar electrode positioned in the selected zone until a prolongation of no less than 15% was obtained in the Wenckebach cycle length (WCL). Before and after (30 min) RF, anterograde and retrograde AVN refractoriness and conduction were evaluated, stimulating from the crista terminalis (CT), the interatrial septum (IAS), and from the RV epicardium. After RF, the following percentage increments were observed in group I: AH(CT) = 36% +/- 9%, AH(IAS) = 38% +/- 11%, WCL(CT) = 28% +/- 8%, WCL(IAS) = 22% +/- 6%, functional refractory period (FRP) of the AVN(CT) = 13% +/- 11%, FRP-AVN(IAS) = 13% +/- 8%, retrograde WCL = 20% +/- 19%, and retrograde FRPVA = 13% +/- 16%. The increments observed in group II and the significances of the differences with respect to group I were: AH(CT) = 11% +/- 14% (P < 0.01), AH(IAS) = 19% +/- 32% (NS), WCL(CT) = 42% +/- 14% (P < 0.05), WCL(IAS) = 42% +/- 16% (P < 0.01), FRP-AVN(CT) = 28% +/- 28% (NS), FRP-AVN(LAS) = 21% +/- 19% (NS), retrograde WCL = 35% +/- 24% (NS), and retrograde FRP = 16% +/- 13% (NS). In both groups, the AH interval variations were not correlated with those of the rest of the parameters analyzed. Truncated nodal function curves suggestive of a dual AV nodal pathway were obtained in three experiments, though in only one of them was this observed under basal conditions. In the other two experiments, with dual AV nodal physiology only after RF (one from each group), AV nodal reentrant tachycardias were triggered with atrial extrastimulus at coupling intervals equal to or shorter than at those that cause a sudden

Electrodynamics of the nodal metal state in weakly doped high- Tc cuprates

NASA Astrophysics Data System (ADS)

Lee, Y. S.; Segawa, Kouji; Li, Z. Q.; Padilla, W. J.; Dumm, M.; Dordevic, S. V.; Homes, C. C.; Ando, Yoichi; Basov, D. N.

2005-08-01

We report on the detailed analysis of the infrared (IR) conductivity of two prototypical high- Tc systems YBa2Cu3Oy and La2-xSrxCuO4 throughout the complex phase diagram of these compounds. Our focus in this work is to thoroughly document the electromagnetic response of the nodal metal state which is initiated with only a few holes doped in parent antiferromagnetic systems and extends up to the pseudogap boundary in the phase diagram. The key signature of the nodal metal is the two-component conductivity: the Drude mode at low energies followed by a resonance in mid-IR. The Drude component can be attributed to the response of coherent quasiparticles residing on the Fermi arcs detected in photoemission experiments. The microscopic origin of the mid-IR band is yet to be understood. A combination of transport and IR data uncovers fingerprints of the Fermi liquid behavior in the response of the nodal metal. The comprehensive nature of the data sets presented in this work allows us to critically re-evaluate common approaches to the interpretation of the optical data. Specifically we re-examine the role of magnetic excitations in generating electronic self-energy effects through the analysis of the IR data in a high magnetic field.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE PAGES

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto; ...

2017-09-15

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

ELSI: A unified software interface for Kohn-Sham electronic structure solvers

NASA Astrophysics Data System (ADS)

Yu, Victor Wen-zhe; Corsetti, Fabiano; García, Alberto; Huhn, William P.; Jacquelin, Mathias; Jia, Weile; Lange, Björn; Lin, Lin; Lu, Jianfeng; Mi, Wenhui; Seifitokaldani, Ali; Vázquez-Mayagoitia, Álvaro; Yang, Chao; Yang, Haizhao; Blum, Volker

2018-01-01

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

An Interesting Case of Retropharyngeal Lymph Nodal Metastases in a Case of Iodine-Refractory Thyroid Cancer.

PubMed

Harisankar, Chidambaram Natrajan Balasubramanian; Vijayabhaskar, Ramakrishnan

2018-01-01

Metastases to cervical lymph node are fairly common in differentiated thyroid cancer. In iodine-refractory disease, the disease may persist in the thyroid bed, cervical lymph nodes, lungs, or the bones commonly. Retropharyngeal lymph nodal involvement in thyroid cancer is unusual and may even be the presenting complaint. We represent a case of iodine-refractory thyroid cancer with retropharyngeal lymph nodal involvement in addition to lung metastases.

Courant Number and Mach Number Insensitive CE/SE Euler Solvers

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung

2005-01-01

It has been known that the space-time CE/SE method can be used to obtain ID, 2D, and 3D steady and unsteady flow solutions with Mach numbers ranging from 0.0028 to 10. However, it is also known that a CE/SE solution may become overly dissipative when the Mach number is very small. As an initial attempt to remedy this weakness, new 1D Courant number and Mach number insensitive CE/SE Euler solvers are developed using several key concepts underlying the recent successful development of Courant number insensitive CE/SE schemes. Numerical results indicate that the new solvers are capable of resolving crisply a contact discontinuity embedded in a flow with the maximum Mach number = 0.01.

Efficient Implementation of Multigrid Solvers on Message-Passing Parrallel Systems

NASA Technical Reports Server (NTRS)

Lou, John

1994-01-01

We discuss our implementation strategies for finite difference multigrid partial differential equation (PDE) solvers on message-passing systems. Our target parallel architecture is Intel parallel computers: the Delta and Paragon system.

Two highly-related regulatory subunits of PP2A exert opposite effects on TGF-β/Activin/Nodal signalling

PubMed Central

Batut, Julie; Schmierer, Bernhard; Cao, Jing; Raftery, Laurel A.; Hill, Caroline S.; Howell, Michael

2016-01-01

Summary We identify Bα (PPP2R2A) and Bδ (PPP2R2D), two highly-related members of the B family of regulatory subunits of the protein phosphatase PP2A, as important modulators of TGF-β/Activin/Nodal signalling, which affect the pathway in opposite ways. Knockdown of Bα in Xenopus embryos or mammalian tissue culture cells suppresses TGF-β/Activin/Nodal-dependent responses, whereas knockdown of Bδ enhances these responses. Moreover, in Drosophila, overexpression of Smad2 rescues a severe wing phenotype caused by overexpression of the single Drosophila PP2A B subunit, Twins. We show that in vertebrates Bα enhances TGF-β/Activin/Nodal signalling by stabilising the basal levels of type I receptor, whereas Bδ negatively modulates these pathways by restricting receptor activity. Thus, these highly-related members of the same subfamily of PP2A regulatory subunits differentially regulate TGF-β/Activin/Nodal signalling to elicit opposing biological outcomes. PMID:18697906

Whole-tumour diffusion kurtosis MR imaging histogram analysis of rectal adenocarcinoma: Correlation with clinical pathologic prognostic factors.

PubMed

Cui, Yanfen; Yang, Xiaotang; Du, Xiaosong; Zhuo, Zhizheng; Xin, Lei; Cheng, Xintao

2018-04-01

To investigate potential relationships between diffusion kurtosis imaging (DKI)-derived parameters using whole-tumour volume histogram analysis and clinicopathological prognostic factors in patients with rectal adenocarcinoma. 79 consecutive patients who underwent MRI examination with rectal adenocarcinoma were retrospectively evaluated. Parameters D, K and conventional ADC were measured using whole-tumour volume histogram analysis. Student's t-test or Mann-Whitney U-test, receiver operating characteristic curves and Spearman's correlation were used for statistical analysis. Almost all the percentile metrics of K were correlated positively with nodal involvement, higher histological grades, the presence of lymphangiovascular invasion (LVI) and circumferential margin (CRM) (p<0.05), with the exception of between K 10th , K 90th and histological grades. In contrast, significant negative correlations were observed between 25th, 50th percentiles and mean values of ADC and D, as well as ADC 10th , with tumour T stages (p< 0.05). Meanwhile, lower 75th and 90th percentiles of ADC and D values were also correlated inversely with nodal involvement (p< 0.05). K mean showed a relatively higher area under the curve (AUC) and higher specificity than other percentiles for differentiation of lesions with nodal involvement. DKI metrics with whole-tumour volume histogram analysis, especially K parameters, were associated with important prognostic factors of rectal cancer. • K correlated positively with some important prognostic factors of rectal cancer. • K mean showed higher AUC and specificity for differentiation of nodal involvement. • DKI metrics with whole-tumour volume histogram analysis depicted tumour heterogeneity.

Recovering tubewise power from three-dimensional nodal kinetics calculation during material relocation in an HWR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalimullah; Morris, E.E.; Yang, W.S.

1994-12-31

To analyze severe accidents in some special-purpose heavy-water reactors made of assemblies consisting of a number of coaxial tubes of aluminum-clad U-Al fuel and aluminum-clad neutron-capturing material, a mechanistic model, MARTINS, for tube beatup, melting, and molten material relocation has been developed and integrated with the DIF3D nodal hexagonal-z reactor kinetics and other phenomenological modules. The DIF3D kinetics homogenizes all materials located and computes the total power produced in an axial segment of a fuel assembly. This paper presents an approximate method, used in MARTINS, to calculate the distribution of this total nodal power into the intact fuel and capturingmore » material tubes and the meat-cladding mixtures relocating during tube disruption. The method accounts for the change in intraassembly radial power profile due to assembly geometry change with the progress of segment-by-segment disruption of different tubes. Earlier methods to recover pinwise power from nodal calculation for liquid-metal-cooled reactors and light water reactors (X-Y and hexagonal unit cells) are not practical for a disrupting assembly having material relocation. Figure 1 shows the assembly`s end view, divided into rings for modeling and analysis. A ring is a coolant subchannel plus the outer surrounding tube. The present method for distributing the nodal power consists of two parts: (a) calculation of the relative values of ring-by-ring power per unit uranium mass and power per unit mass of neutron-capturing material in a given assembly segment, and (b) normalization of these relative values such that the total power of all rings (intact tubes and U-Al-Cp meat-cladding mixtures, where Cp implies the neutron-capturing material) equals the DIF3D-calculated nodal power for the assembly axial segment.« less

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 CrX 3 (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.

Theoretical and experimental evidence for a nodal energy gap in MgB2

NASA Astrophysics Data System (ADS)

Agassi, Y. Dan; Oates, Daniel E.

2017-11-01

We present a phenomenological model that strongly suggests that the smaller of the two energy gaps in MgB2, the so-called π gap, contains nodal lines with a six-fold symmetry (i-wave). The model also indicates that the larger gap, the so-called σ gap, is conventional s-wave. The model is an extension of the BCS gap equation that accounts for the elastic anisotropy in MgB2 and the Coulomb repulsion. It is based on a phononic pairing mechanism and assumes no coupling between the two energy gaps in MgB2 at zero temperature. All of the parameters of the model, such as sound velocities and masses, are independently determined material constants. The results agree with a previous ad-hoc hypothesis that the π energy gap has six nodal lines. That hypothesis was motivated by low-temperature measurements of the surface impedance and intermodulation distortion in high-quality thin films. We briefly review experimental evidence in the literature that is relevant to the energy-gap symmetry. We find that the evidence from the literature for s-wave is inconclusive. Our finding is that the π gap has six nodal lines.

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.

Riemann Solvers in Relativistic Hydrodynamics: Basics and Astrophysical Applications

NASA Astrophysics Data System (ADS)

Ibanez, Jose M.

2001-12-01

My contribution to these proceedings summarizes a general overview on t High Resolution Shock Capturing methods (HRSC) in the field of relativistic hydrodynamics with special emphasis on Riemann solvers. HRSC techniques achieve highly accurate numerical approximations (formally second order or better) in smooth regions of the flow, and capture the motion of unresolved steep gradients without creating spurious oscillations. In the first part I will show how these techniques have been extended to relativistic hydrodynamics, making it possible to explore some challenging astrophysical scenarios. I will review recent literature concerning the main properties of different special relativistic Riemann solvers, and discuss several 1D and 2D test problems which are commonly used to evaluate the performance of numerical methods in relativistic hydrodynamics. In the second part I will illustrate the use of HRSC methods in several astrophysical applications where special and general relativistic hydrodynamical processes play a crucial role.

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.

Detailed modeling analysis for soot formation and radiation in microgravity gas jet diffusion flames

NASA Technical Reports Server (NTRS)

Ku, Jerry C.; Tong, LI; Greenberg, Paul S.

1995-01-01

Radiation heat transfer in combustion systems has been receiving increasing interest. In the case of hydrocarbon fuels, a significant portion of the radiation comes from soot particles, justifying the need for detailed soot formation model and radiation transfer calculations. For laminar gas jet diffusion flames, results from this project (4/1/91 8/22/95) and another NASA study show that flame shape, soot concentration, and radiation heat fluxes are substantially different under microgravity conditions. Our emphasis is on including detailed soot transport models and a detailed solution for radiation heat transfer, and on coupling them with the flame structure calculations. In this paper, we will discuss the following three specific areas: (1) Comparing two existing soot formation models, and identifying possible improvements; (2) A simple yet reasonably accurate approach to calculating total radiative properties and/or fluxes over the spectral range; and (3) Investigating the convergence of iterations between the flame structure solver and the radiation heat transfer solver.

Reactivity Coefficient Calculation for AP1000 Reactor Using the NODAL3 Code

NASA Astrophysics Data System (ADS)

Pinem, Surian; Malem Sembiring, Tagor; Tukiran; Deswandri; Sunaryo, Geni Rina

2018-02-01

The reactivity coefficient is a very important parameter for inherent safety and stability of nuclear reactors operation. To provide the safety analysis of the reactor, the calculation of changes in reactivity caused by temperature is necessary because it is related to the reactor operation. In this paper, the temperature reactivity coefficients of fuel and moderator of the AP1000 core are calculated, as well as the moderator density and boron concentration. All of these coefficients are calculated at the hot full power condition (HFP). All neutron diffusion constant as a function of temperature, water density and boron concentration were generated by the SRAC2006 code. The core calculations for determination of the reactivity coefficient parameter are done by using NODAL3 code. The calculation results show that the fuel temperature, moderator temperature and boron reactivity coefficients are in the range between -2.613 pcm/°C to -4.657pcm/°C, -1.00518 pcm/°C to 1.00649 pcm/°C and -9.11361 pcm/ppm to -8.0751 pcm/ppm, respectively. For the water density reactivity coefficients, the positive reactivity occurs at the water temperature less than 190 °C. The calculation results show that the reactivity coefficients are accurate because the results have a very good agreement with the design value.

Solvers' Making of Drawings in Mathematical Problem Solving and Their Understanding of the Problem Situations

ERIC Educational Resources Information Center

Nunokawa, Kazuhiko

2004-01-01

The purpose of this paper was to investigate how it becomes possible for solvers to make drawings to advance their problem solving processes, in order to understand the use of drawings in mathematical problem solving more deeply. For this purpose, three examples in which drawings made by the solver played a critical role in the solutions have been…

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.

Prescribed Velocity Gradients for Highly Viscous SPH Fluids with Vorticity Diffusion.

PubMed

Peer, Andreas; Teschner, Matthias

2017-12-01

Working with prescribed velocity gradients is a promising approach to efficiently and robustly simulate highly viscous SPH fluids. Such approaches allow to explicitly and independently process shear rate, spin, and expansion rate. This can be used to, e.g., avoid interferences between pressure and viscosity solvers. Another interesting aspect is the possibility to explicitly process the vorticity, e.g., to preserve the vorticity. In this context, this paper proposes a novel variant of the prescribed-gradient idea that handles vorticity in a physically motivated way. In contrast to a less appropriate vorticity preservation that has been used in a previous approach, vorticity is diffused. The paper illustrates the utility of the vorticity diffusion. Therefore, comparisons of the proposed vorticity diffusion with vorticity preservation and additionally with vorticity damping are presented. The paper further discusses the relation between prescribed velocity gradients and prescribed velocity Laplacians which improves the intuition behind the prescribed-gradient method for highly viscous SPH fluids. Finally, the paper discusses the relation of the proposed method to a physically correct implicit viscosity formulation.

Left Septal Slow Pathway Ablation for Atrioventricular Nodal Reentrant Tachycardia.

PubMed

Katritsis, Demosthenes G; John, Roy M; Latchamsetty, Rakesh; Muthalaly, Rahul G; Zografos, Theodoros; Katritsis, George D; Stevenson, William G; Efimov, Igor R; Morady, Fred

2018-03-01

Immunohistochemistry studies suggest that the anatomic substrate of the slow pathway in atrioventricular nodal reentrant tachycardia (AVNRT) is the left inferior nodal extension. We hypothesized that slow pathway ablation from the left septum is an effective alternative to right-sided ablation. We analyzed our databases of AVNRT in search of cases that had used slow pathway ablation from the left septum because of failure of right septal ablation, and then prospectively subjected consenting patients to a left septal-only procedure. Of 1342 patients subjected to right septal slow pathway ablation for AVNRT, 15 patients, 11 with typical and 4 with atypical AVNRT, had a left septal approach after unsuccessful right-sided ablation (R+L group). Eleven patients were subjected to a left septal-only approach for slow pathway ablation without a previous right septal attempt (L group). Fluoroscopy times in the R+L and L groups were 30.5 (21.0-44.0) and 20.0 (17.0-25.0) minutes, respectively ( P =0.061), and radiofrequency current delivery times were 11.3 (5.0-19.1) and 10.0 (7.0-12.0) minutes, respectively ( P =0.897). There was no need for additional ablation lesions at other anatomic sites in either group, and no cases of atrioventricular block were encountered. Recurrence rates of the arrhythmia for the R+L and L groups were 6.7% and 0%, respectively, in the 3 months after ablation ( P =1.000). Left septal ablation at the anatomic site of the left inferior nodal extension is an alternative for ablation of both typical and atypical AVNRT when ablation at the right posterior septum is ineffective. © 2018 American Heart Association, Inc.

Extending substructure based iterative solvers to multiple load and repeated analyses

NASA Technical Reports Server (NTRS)

Farhat, Charbel

1993-01-01

Direct solvers currently dominate commercial finite element structural software, but do not scale well in the fine granularity regime targeted by emerging parallel processors. Substructure based iterative solvers--often called also domain decomposition algorithms--lend themselves better to parallel processing, but must overcome several obstacles before earning their place in general purpose structural analysis programs. One such obstacle is the solution of systems with many or repeated right hand sides. Such systems arise, for example, in multiple load static analyses and in implicit linear dynamics computations. Direct solvers are well-suited for these problems because after the system matrix has been factored, the multiple or repeated solutions can be obtained through relatively inexpensive forward and backward substitutions. On the other hand, iterative solvers in general are ill-suited for these problems because they often must restart from scratch for every different right hand side. In this paper, we present a methodology for extending the range of applications of domain decomposition methods to problems with multiple or repeated right hand sides. Basically, we formulate the overall problem as a series of minimization problems over K-orthogonal and supplementary subspaces, and tailor the preconditioned conjugate gradient algorithm to solve them efficiently. The resulting solution method is scalable, whereas direct factorization schemes and forward and backward substitution algorithms are not. We illustrate the proposed methodology with the solution of static and dynamic structural problems, and highlight its potential to outperform forward and backward substitutions on parallel computers. As an example, we show that for a linear structural dynamics problem with 11640 degrees of freedom, every time-step beyond time-step 15 is solved in a single iteration and consumes 1.0 second on a 32 processor iPSC-860 system; for the same problem and the same parallel

Ramses-GPU: Second order MUSCL-Handcock finite volume fluid solver

NASA Astrophysics Data System (ADS)

Kestener, Pierre

2017-10-01

RamsesGPU is a reimplementation of RAMSES (ascl:1011.007) which drops the adaptive mesh refinement (AMR) features to optimize 3D uniform grid algorithms for modern graphics processor units (GPU) to provide an efficient software package for astrophysics applications that do not need AMR features but do require a very large number of integration time steps. RamsesGPU provides an very efficient C++/CUDA/MPI software implementation of a second order MUSCL-Handcock finite volume fluid solver for compressible hydrodynamics as a magnetohydrodynamics solver based on the constraint transport technique. Other useful modules includes static gravity, dissipative terms (viscosity, resistivity), and forcing source term for turbulence studies, and special care was taken to enhance parallel input/output performance by using state-of-the-art libraries such as HDF5 and parallel-netcdf.

Nodal signalling in Xenopus: the role of Xnr5 in left/right asymmetry and heart development.

PubMed

Tadjuidje, Emmanuel; Kofron, Matthew; Mir, Adnan; Wylie, Christopher; Heasman, Janet; Cha, Sang-Wook

2016-08-01

Nodal class TGF-β signalling molecules play essential roles in establishing the vertebrate body plan. In all vertebrates, nodal family members have specific waves of expression required for tissue specification and axis formation. In Xenopus laevis, six nodal genes are expressed before gastrulation, raising the question of whether they have specific roles or act redundantly with each other. Here, we examine the role of Xnr5. We find it acts at the late blastula stage as a mesoderm inducer and repressor of ectodermal gene expression, a role it shares with Vg1. However, unlike Vg1, Xnr5 depletion reduces the expression of the nodal family member xnr1 at the gastrula stage. It is also required for left/right laterality by controlling the expression of the laterality genes xnr1, antivin (lefty) and pitx2 at the tailbud stage. In Xnr5-depleted embryos, the heart field is established normally, but symmetrical reduction in Xnr5 levels causes a severely stunted midline heart, first evidenced by a reduction in cardiac troponin mRNA levels, while left-sided reduction leads to randomization of the left/right axis. This work identifies Xnr5 as the earliest step in the signalling pathway establishing normal heart laterality in Xenopus. © 2016 The Authors.

GDF3 is a BMP inhibitor that can activate Nodal signaling only at very high doses

PubMed Central

Levine, Ariel J.; Levine, Zachary J.; Brivanlou, Ali H.

2013-01-01

Within the TGF-β superfamily, there are approximately forty ligands divided into two major branches: the TGF-β/Activin/Nodal ligands and the BMP/GDF ligands. We studied the ligand GDF3 and found that it inhibits signaling by its co-family members, the BMPs; however, GDF3 has been described by others to have Nodal-like activity. Here, we show that GDF3 can activate Nodal signaling, but only at very high doses and only upon mRNA over-expression. In contrast, GDF3 inhibits BMP signaling upon over-expression of GDF3 mRNA, as recombinant protein, and regardless of its dose. We therefore further characterized the mechanism through which GDF3 protein acts as a specific BMP inhibitor and found that the BMP inhibitory activity of GDF3 resides redundantly in the unprocessed, predominant form and in the mature form of the protein. These results confirm and extend the activity that we described for GDF3 and illuminate the experimental basis for the different observations of others. We suggest that GDF3 is either a bi-functional TGF-β ligand, or, more likely, that it is a BMP inhibitor that can artificially activate Nodal signaling under non-physiological conditions. PMID:18823971

PUFoam : A novel open-source CFD solver for the simulation of polyurethane foams

NASA Astrophysics Data System (ADS)

Karimi, M.; Droghetti, H.; Marchisio, D. L.

2017-08-01

In this work a transient three-dimensional mathematical model is formulated and validated for the simulation of polyurethane (PU) foams. The model is based on computational fluid dynamics (CFD) and is coupled with a population balance equation (PBE) to describe the evolution of the gas bubbles/cells within the PU foam. The front face of the expanding foam is monitored on the basis of the volume-of-fluid (VOF) method using a compressible solver available in OpenFOAM version 3.0.1. The solver is additionally supplemented to include the PBE, solved with the quadrature method of moments (QMOM), the polymerization kinetics, an adequate rheological model and a simple model for the foam thermal conductivity. The new solver is labelled as PUFoam and is, for the first time in this work, validated for 12 different mixing-cup experiments. Comparison of the time evolution of the predicted and experimentally measured density and temperature of the PU foam shows the potentials and limitations of the approach.

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.

Multitasking domain decomposition fast Poisson solvers on the Cray Y-MP

NASA Technical Reports Server (NTRS)

Chan, Tony F.; Fatoohi, Rod A.

1990-01-01

The results of multitasking implementation of a domain decomposition fast Poisson solver on eight processors of the Cray Y-MP are presented. The object of this research is to study the performance of domain decomposition methods on a Cray supercomputer and to analyze the performance of different multitasking techniques using highly parallel algorithms. Two implementations of multitasking are considered: macrotasking (parallelism at the subroutine level) and microtasking (parallelism at the do-loop level). A conventional FFT-based fast Poisson solver is also multitasked. The results of different implementations are compared and analyzed. A speedup of over 7.4 on the Cray Y-MP running in a dedicated environment is achieved for all cases.

Modularization and Validation of FUN3D as a CREATE-AV Helios Near-Body Solver

NASA Technical Reports Server (NTRS)

Jain, Rohit; Biedron, Robert T.; Jones, William T.; Lee-Rausch, Elizabeth M.

2016-01-01

Under a recent collaborative effort between the US Army Aeroflightdynamics Directorate (AFDD) and NASA Langley, NASA's general unstructured CFD solver, FUN3D, was modularized as a CREATE-AV Helios near-body unstructured grid solver. The strategies adopted in Helios/FUN3D integration effort are described. A validation study of the new capability is performed for rotorcraft cases spanning hover prediction, airloads prediction, coupling with computational structural dynamics, counter-rotating dual-rotor configurations, and free-flight trim. The integration of FUN3D, along with the previously integrated NASA OVERFLOW solver, lays the ground for future interaction opportunities where capabilities of one component could be leveraged with those of others in a relatively seamless fashion within CREATE-AV Helios.

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.…

A GPU-based incompressible Navier-Stokes solver on moving overset grids

NASA Astrophysics Data System (ADS)

Chandar, Dominic D. J.; Sitaraman, Jayanarayanan; Mavriplis, Dimitri J.

2013-07-01

In pursuit of obtaining high fidelity solutions to the fluid flow equations in a short span of time, graphics processing units (GPUs) which were originally intended for gaming applications are currently being used to accelerate computational fluid dynamics (CFD) codes. With a high peak throughput of about 1 TFLOPS on a PC, GPUs seem to be favourable for many high-resolution computations. One such computation that involves a lot of number crunching is computing time accurate flow solutions past moving bodies. The aim of the present paper is thus to discuss the development of a flow solver on unstructured and overset grids and its implementation on GPUs. In its present form, the flow solver solves the incompressible fluid flow equations on unstructured/hybrid/overset grids using a fully implicit projection method. The resulting discretised equations are solved using a matrix-free Krylov solver using several GPU kernels such as gradient, Laplacian and reduction. Some of the simple arithmetic vector calculations are implemented using the CU++: An Object Oriented Framework for Computational Fluid Dynamics Applications using Graphics Processing Units, Journal of Supercomputing, 2013, doi:10.1007/s11227-013-0985-9 approach where GPU kernels are automatically generated at compile time. Results are presented for two- and three-dimensional computations on static and moving grids.

Omitting elective nodal irradiation during thoracic irradiation in limited-stage small cell lung cancer--evidence from a phase II trial.

PubMed

Colaco, Rovel; Sheikh, Hamid; Lorigan, Paul; Blackhall, Fiona; Hulse, Paul; Califano, Raffaele; Ashcroft, Linda; Taylor, Paul; Thatcher, Nicholas; Faivre-Finn, Corinne

2012-04-01

Omitting elective nodal irradiation (ENI) in limited-stage disease small cell lung cancer (LD-SCLC) is expected to result in smaller radiation fields. We report on data from a randomised phase II trial that omitted ENI in patients receiving concurrent chemo-radiotherapy for LD-SCLC. 38 patients with LD-SCLC were randomised to receive once-daily (66 Gy in 33 fractions) or twice-daily (45 Gy in 30 fractions) radiotherapy (RT). 3D-conformal RT was given concurrently with cisplatin and etoposide starting with the second cycle of a total of four cycles. The gross tumour volume was defined as primary tumour with involved lymph nodes (nodes ≥1 cm in short axis) identifiable with CT imaging. ENI was not used. Six recurrence patterns were identified: recurrence within planning target volume (PTV) only, recurrence within PTV+regional nodal recurrence and/or distant recurrence, isolated nodal recurrence outside PTV, nodal recurrence outside PTV+distant recurrence, distant metastases only and no recurrence. At median follow-up 16.9 months, 31/38 patients were evaluable and 14/31 patients had relapsed. There were no isolated nodal recurrences. Eight patients relapsed with intra-thoracic disease: 2 within PTV only, 4 within PTV and distantly and 2 with nodal recurrence outside PTV plus distant metastases. Rates of grade 3+ acute oesophagitis and pneumonitis in the 31 evaluable patients were 23 and 3% respectively. In our study of LD-SCLC, omitting ENI based on CT imaging was not associated with a high risk of isolated nodal recurrence, although further prospective studies are needed to confirm this. Routine ENI omission will be further evaluated prospectively in the ongoing phase III CONVERT trial (NCT00433563). Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

1997-06-01

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

Anisotropic resonator analysis using the Fourier-Bessel mode solver

NASA Astrophysics Data System (ADS)

Gauthier, Robert C.

2018-03-01

A numerical mode solver for optical structures that conform to cylindrical symmetry using Faraday's and Ampere's laws as starting expressions is developed when electric or magnetic anisotropy is present. The technique builds on the existing Fourier-Bessel mode solver which allows resonator states to be computed exploiting the symmetry properties of the resonator and states to reduce the matrix system. The introduction of anisotropy into the theoretical frame work facilitates the inclusion of PML borders permitting the computation of open ended structures and a better estimation of the resonator state quality factor. Matrix populating expressions are provided that can accommodate any material anisotropy with arbitrary orientation in the computation domain. Several example of electrical anisotropic computations are provided for rationally symmetric structures such as standard optical fibers, axial Bragg-ring fibers and bottle resonators. The anisotropy present in the materials introduces off diagonal matrix elements in the permittivity tensor when expressed in cylindrical coordinates. The effects of the anisotropy of computed states are presented and discussed.

Towards a Coupled Vortex Particle and Acoustic Boundary Element Solver to Predict the Noise Production of Bio-Inspired Propulsion

NASA Astrophysics Data System (ADS)

Wagenhoffer, Nathan; Moored, Keith; Jaworski, Justin

2016-11-01

The design of quiet and efficient bio-inspired propulsive concepts requires a rapid, unified computational framework that integrates the coupled fluid dynamics with the noise generation. Such a framework is developed where the fluid motion is modeled with a two-dimensional unsteady boundary element method that includes a vortex-particle wake. The unsteady surface forces from the potential flow solver are then passed to an acoustic boundary element solver to predict the radiated sound in low-Mach-number flows. The use of the boundary element method for both the hydrodynamic and acoustic solvers permits dramatic computational acceleration by application of the fast multiple method. The reduced order of calculations due to the fast multipole method allows for greater spatial resolution of the vortical wake per unit of computational time. The coupled flow-acoustic solver is validated against canonical vortex-sound problems. The capability of the coupled solver is demonstrated by analyzing the performance and noise production of an isolated bio-inspired swimmer and of tandem swimmers.

The role of elective-nodal irradiation for esthesioneuroblastoma patients with clinically negative neck

PubMed Central

Jiang, Wen; Mohamed, Abdallah Sherif; Fuller, Clifton David; Kim, Betty Y.S.; Tang, Chad; Gunn, G. Brandon; Hanna, Ehab Y.; Frank, Steven J.; Su, Shirley Y.; Diaz, Eduardo; Kupferman, Michael E.; Beadle, Beth M.; Morrison, William H.; Skinner, Heath; Lai, Stephen Y.; El-Naggar, Adel K.; DeMonte, Franco; Rosenthal, David I.; Garden, Adam S.; Phan, Jack

2017-01-01

Purpose Although adjuvant radiation to the tumor bed has been reported to improve the clinic outcomes of esthesioneuroblastoma (ENB) patients, the role of elective neck irradiation (ENI) in clinically node negative (N0) patients remains controversial. Here, we evaluated the effects of ENI on neck nodal relapse risk in ENB patients treated with radiotherapy as a component of multi-modality treatment. Methods and Materials Seventy-one N0 ENB patients irradiated at XXXXXXXXX between 1970 and 2013 were identified. ENI was performed on 22 of these patients (31%). Survival analysis was performed with focus on comparative outcomes of those patients who did and did not receive ENI. Results The median follow up time for our cohort is 80.8 months (range 6 – 350 month). Among N0 patients, 13 (18.3%) developed neck nodal relapses, with a median time to progression of 62.5 months. None of these 13 patients received prophylactic neck irradiation. ENI was associated with significantly improved regional nodal control at 5-year (regional control rate of 100% for ENI vs 82%, p < 0.001), but not overall survival or disease-free survival. Eleven patients without ENI developed isolated neck recurrences. All had further treatment for their neck disease, including neck dissection (n=10), radiation (n=10), or chemotherapy (n=5). Six of these 11 patients (54.5%) demonstrated no evidence of further recurrence with a median follow up of 55.5 month. Conclusion ENI significantly reduces the risk of cervical nodal recurrence in ENB patients with clinically N0 neck but this did not translate to a survival benefit. Multimodality treatment for isolated neck recurrence provides a reasonable salvage rate. The greatest benefit for ENI appeared to be among younger patients who presented with Kadish C disease. Further studies are needed to confirm these findings. PMID:26979544

Evaluating the performance of the two-phase flow solver interFoam

NASA Astrophysics Data System (ADS)

Deshpande, Suraj S.; Anumolu, Lakshman; Trujillo, Mario F.

2012-01-01

The performance of the open source multiphase flow solver, interFoam, is evaluated in this work. The solver is based on a modified volume of fluid (VoF) approach, which incorporates an interfacial compression flux term to mitigate the effects of numerical smearing of the interface. It forms a part of the C + + libraries and utilities of OpenFOAM and is gaining popularity in the multiphase flow research community. However, to the best of our knowledge, the evaluation of this solver is confined to the validation tests of specific interest to the users of the code and the extent of its applicability to a wide range of multiphase flow situations remains to be explored. In this work, we have performed a thorough investigation of the solver performance using a variety of verification and validation test cases, which include (i) verification tests for pure advection (kinematics), (ii) dynamics in the high Weber number limit and (iii) dynamics of surface tension-dominated flows. With respect to (i), the kinematics tests show that the performance of interFoam is generally comparable with the recent algebraic VoF algorithms; however, it is noticeably worse than the geometric reconstruction schemes. For (ii), the simulations of inertia-dominated flows with large density ratios {\\sim }\\mathscr {O}(10^3) yielded excellent agreement with analytical and experimental results. In regime (iii), where surface tension is important, consistency of pressure-surface tension formulation and accuracy of curvature are important, as established by Francois et al (2006 J. Comput. Phys. 213 141-73). Several verification tests were performed along these lines and the main findings are: (a) the algorithm of interFoam ensures a consistent formulation of pressure and surface tension; (b) the curvatures computed by the solver converge to a value slightly (10%) different from the analytical value and a scope for improvement exists in this respect. To reduce the disruptive effects of spurious

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).

SediFoam: A general-purpose, open-source CFD-DEM solver for particle-laden flow with emphasis on sediment transport

NASA Astrophysics Data System (ADS)

Sun, Rui; Xiao, Heng

2016-04-01

With the growth of available computational resource, CFD-DEM (computational fluid dynamics-discrete element method) becomes an increasingly promising and feasible approach for the study of sediment transport. Several existing CFD-DEM solvers are applied in chemical engineering and mining industry. However, a robust CFD-DEM solver for the simulation of sediment transport is still desirable. In this work, the development of a three-dimensional, massively parallel, and open-source CFD-DEM solver SediFoam is detailed. This solver is built based on open-source solvers OpenFOAM and LAMMPS. OpenFOAM is a CFD toolbox that can perform three-dimensional fluid flow simulations on unstructured meshes; LAMMPS is a massively parallel DEM solver for molecular dynamics. Several validation tests of SediFoam are performed using cases of a wide range of complexities. The results obtained in the present simulations are consistent with those in the literature, which demonstrates the capability of SediFoam for sediment transport applications. In addition to the validation test, the parallel efficiency of SediFoam is studied to test the performance of the code for large-scale and complex simulations. The parallel efficiency tests show that the scalability of SediFoam is satisfactory in the simulations using up to O(107) particles.

Using the Gurobi Solvers on the Peregrine System | High-Performance

Science.gov Websites

Peregrine System Gurobi Optimizer is a suite of solvers for mathematical programming. It is licensed for ('GRB_MATLAB_PATH') >> path(path,grb) Gurobi and GAMS GAMS is a high-level modeling system for mathematical

Atlas of the thoracic lymph nodal delineation and recommendations for lymph nodal CTV of esophageal squamous cell cancer in radiation therapy from China.

PubMed

Huang, Wei; Huang, Yong; Sun, Jujie; Liu, Xibin; Zhang, Jian; Zhou, Tao; Zhang, Baijiang; Li, Baosheng

2015-07-01

To construct an anatomical atlas of thoracic lymph node regions of esophageal cancer (EC) based on definitions from The Japan Esophageal Society (JES) and generate a consensus to delineate the nodal clinical target volume (CTVn) for elective nodal radiation (ENI) of esophageal squamous cell carcinoma (ESCC). An interdisciplinary group including two dedicated radiation oncologists, an experienced radiologist, a pathologist and two thoracic surgeons were gathered to generate a three-dimensional radiological description for the mediastinal lymph node regions of EC on axial CT scans. Then the radiological boundaries of lymph node regions were validated by a relatively large number of physicians in multiple institutions. An atlas of detailed anatomic boundaries of lymph node station No. 105-114 was defined on axial CT, along with illustrations. From the previous work, the study provided a guide of CTVn contouring for ENI of thoracic ESCC from a single center. It is feasible to use such an atlas of thoracic lymph node stations for radiotherapy planning. A phase III study based on the atlas is ongoing in China to measure quantitatively the ENI received by patients with ESCC. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Nearly Interactive Parabolized Navier-Stokes Solver for High Speed Forebody and Inlet Flows

NASA Technical Reports Server (NTRS)

Benson, Thomas J.; Liou, May-Fun; Jones, William H.; Trefny, Charles J.

2009-01-01

A system of computer programs is being developed for the preliminary design of high speed inlets and forebodies. The system comprises four functions: geometry definition, flow grid generation, flow solver, and graphics post-processor. The system runs on a dedicated personal computer using the Windows operating system and is controlled by graphical user interfaces written in MATLAB (The Mathworks, Inc.). The flow solver uses the Parabolized Navier-Stokes equations to compute millions of mesh points in several minutes. Sample two-dimensional and three-dimensional calculations are demonstrated in the paper.

Activin- and Nodal-related factors control antero-posterior patterning of the zebrafish embryo.

PubMed

Thisse, B; Wright, C V; Thisse, C

2000-01-27

Definition of cell fates along the dorso-ventral axis depends on an antagonistic relationship between ventralizing transforming growth factor-beta superfamily members, the bone morphogenetic proteins and factors secreted from the dorsal organizer, such as Noggin and Chordin. The extracellular binding of the last group to the bone morphogenetic proteins prevents them from activating their receptors, and the relative ventralizer:antagonist ratio is thought to specify different dorso-ventral cell fates. Here, by taking advantage of a non-genetic interference method using a specific competitive inhibitor, the Lefty-related gene product Antivin, we provide evidence that cell fate along the antero-posterior axis of the zebrafish embryo is controlled by the morphogenetic activity of another transforming growth factor-beta superfamily subgroup--the Activin and Nodal-related factors. Increasing antivin doses progressively deleted posterior fates within the ectoderm, eventually resulting in the removal of all fates except forebrain and eyes. In contrast, overexpression of activin or nodal-related factors converted ectoderm that was fated to be forebrain into more posterior ectodermal or mesendodermal fates. We propose that modulation of intercellular signalling by Antivin/Activin and Nodal-related factors provides a mechanism for the graded establishment of cell fates along the antero-posterior axis of the zebrafish embryo.

On improving linear solver performance: a block variant of GMRES

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.more » 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.« less

A study of hydrogen diffusion flames using PDF turbulence model

NASA Technical Reports Server (NTRS)

Hsu, Andrew T.

1991-01-01

The application of probability density function (pdf) turbulence models is addressed. For the purpose of accurate prediction of turbulent combustion, an algorithm that combines a conventional computational fluid dynamic (CFD) flow solver with the Monte Carlo simulation of the pdf evolution equation was developed. The algorithm was validated using experimental data for a heated turbulent plane jet. The study of H2-F2 diffusion flames was carried out using this algorithm. Numerical results compared favorably with experimental data. The computations show that the flame center shifts as the equivalence ratio changes, and that for the same equivalence ratio, similarity solutions for flames exist.

A study of hydrogen diffusion flames using PDF turbulence model

NASA Technical Reports Server (NTRS)

Hsu, Andrew T.

1991-01-01

The application of probability density function (pdf) turbulence models is addressed in this work. For the purpose of accurate prediction of turbulent combustion, an algorithm that combines a conventional CFD flow solver with the Monte Carlo simulation of the pdf evolution equation has been developed. The algorithm has been validated using experimental data for a heated turbulent plane jet. The study of H2-F2 diffusion flames has been carried out using this algorithm. Numerical results compared favorably with experimental data. The computuations show that the flame center shifts as the equivalence ratio changes, and that for the same equivalence ratio, similarity solutions for flames exist.

[Does nodal irradiation (clavicular and internal mammary chains) increase the toxicity of adjuvant breast radiotherapy?].

PubMed

Riou, O; Bourgier, C; Fenoglietto, P; Azria, D

2015-06-01

Treatment volume is a major risk factor of radiation-induced toxicity. As nodal irradiation increases treatment volume, radiation toxicity should be greater. Nevertheless, scientific randomised data do not support this fact. However, a radiation-induced toxicity is possible outside tangential fields in the nodal volumes not related to breast-only treatment. Treatment should not be adapted only to the disease but personalized to the individual risk of toxicity for each patient. Copyright © 2015 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

The development of an intelligent interface to a computational fluid dynamics flow-solver code

NASA Technical Reports Server (NTRS)

Williams, Anthony D.

1988-01-01

Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, 3-D, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

The development of an intelligent interface to a computational fluid dynamics flow-solver code

NASA Technical Reports Server (NTRS)

Williams, Anthony D.

1988-01-01

Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, three-dimensional, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

Notes on the ExactPack Implementation of the DSD Rate Stick Solver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaul, Ann

It has been shown above that the discretization scheme implemented in the ExactPack solver for the DSD Rate Stick equation is consistent with the Rate Stick PDE. In addition, a stability analysis has provided a CFL condition for a stable time step. Together, consistency and stability imply convergence of the scheme, which is expected to be close to first-order in time and second-order in space. It is understood that the nonlinearity of the underlying PDE will affect this rate somewhat. In the solver I implemented in ExactPack, I used the one-sided boundary condition described above at the outer boundary. Inmore » addition, I used 80% of the time step calculated in the stability analysis above. By making these two changes, I was able to implement a solver that calculates the solution without any arbitrary limits placed on the values of the curvature at the boundary. Thus, the calculation is driven directly by the conditions at the boundary as formulated in the DSD theory. The chosen scheme is completely coherent and defensible from a mathematical standpoint.« less

Flutter and Forced Response Analyses of Cascades using a Two-Dimensional Linearized Euler Solver

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Srivastava, R.; Mehmed, O.

1999-01-01

Flutter and forced response analyses for a cascade of blades in subsonic and transonic flow is presented. The structural model for each blade is a typical section with bending and torsion degrees of freedom. The unsteady aerodynamic forces due to bending and torsion motions. and due to a vortical gust disturbance are obtained by solving unsteady linearized Euler equations. The unsteady linearized equations are obtained by linearizing the unsteady nonlinear equations about the steady flow. The predicted unsteady aerodynamic forces include the effect of steady aerodynamic loading due to airfoil shape, thickness and angle of attack. The aeroelastic equations are solved in the frequency domain by coupling the un- steady aerodynamic forces to the aeroelastic solver MISER. The present unsteady aerodynamic solver showed good correlation with published results for both flutter and forced response predictions. Further improvements are required to use the unsteady aerodynamic solver in a design cycle.

Large-scale 3-D EM modelling with a Block Low-Rank multifrontal direct solver

NASA Astrophysics Data System (ADS)

Shantsev, Daniil V.; Jaysaval, Piyoosh; de la Kethulle de Ryhove, Sébastien; Amestoy, Patrick R.; Buttari, Alfredo; L'Excellent, Jean-Yves; Mary, Theo

2017-06-01

We put forward the idea of using a Block Low-Rank (BLR) multifrontal direct solver to efficiently solve the linear systems of equations arising from a finite-difference discretization of the frequency-domain Maxwell equations for 3-D electromagnetic (EM) problems. The solver uses a low-rank representation for the off-diagonal blocks of the intermediate dense matrices arising in the multifrontal method to reduce the computational load. A numerical threshold, the so-called BLR threshold, controlling the accuracy of low-rank representations was optimized by balancing errors in the computed EM fields against savings in floating point operations (flops). Simulations were carried out over large-scale 3-D resistivity models representing typical scenarios for marine controlled-source EM surveys, and in particular the SEG SEAM model which contains an irregular salt body. The flop count, size of factor matrices and elapsed run time for matrix factorization are reduced dramatically by using BLR representations and can go down to, respectively, 10, 30 and 40 per cent of their full-rank values for our largest system with N = 20.6 million unknowns. The reductions are almost independent of the number of MPI tasks and threads at least up to 90 × 10 = 900 cores. The BLR savings increase for larger systems, which reduces the factorization flop complexity from O(N2) for the full-rank solver to O(Nm) with m = 1.4-1.6. The BLR savings are significantly larger for deep-water environments that exclude the highly resistive air layer from the computational domain. A study in a scenario where simulations are required at multiple source locations shows that the BLR solver can become competitive in comparison to iterative solvers as an engine for 3-D controlled-source electromagnetic Gauss-Newton inversion that requires forward modelling for a few thousand right-hand sides.

Extending Clause Learning of SAT Solvers with Boolean Gröbner Bases

NASA Astrophysics Data System (ADS)

Zengler, Christoph; Küchlin, Wolfgang

We extend clause learning as performed by most modern SAT Solvers by integrating the computation of Boolean Gröbner bases into the conflict learning process. Instead of learning only one clause per conflict, we compute and learn additional binary clauses from a Gröbner basis of the current conflict. We used the Gröbner basis engine of the logic package Redlog contained in the computer algebra system Reduce to extend the SAT solver MiniSAT with Gröbner basis learning. Our approach shows a significant reduction of conflicts and a reduction of restarts and computation time on many hard problems from the SAT 2009 competition.

Modeling hemodynamics in intracranial aneurysms: Comparing accuracy of CFD solvers based on finite element and finite volume schemes.

PubMed

Botti, Lorenzo; Paliwal, Nikhil; Conti, Pierangelo; Antiga, Luca; Meng, Hui

2018-06-01

Image-based computational fluid dynamics (CFD) has shown potential to aid in the clinical management of intracranial aneurysms (IAs) but its adoption in the clinical practice has been missing, partially due to lack of accuracy assessment and sensitivity analysis. To numerically solve the flow-governing equations CFD solvers generally rely on two spatial discretization schemes: Finite Volume (FV) and Finite Element (FE). Since increasingly accurate numerical solutions are obtained by different means, accuracies and computational costs of FV and FE formulations cannot be compared directly. To this end, in this study we benchmark two representative CFD solvers in simulating flow in a patient-specific IA model: (1) ANSYS Fluent, a commercial FV-based solver and (2) VMTKLab multidGetto, a discontinuous Galerkin (dG) FE-based solver. The FV solver's accuracy is improved by increasing the spatial mesh resolution (134k, 1.1m, 8.6m and 68.5m tetrahedral element meshes). The dGFE solver accuracy is increased by increasing the degree of polynomials (first, second, third and fourth degree) on the base 134k tetrahedral element mesh. Solutions from best FV and dGFE approximations are used as baseline for error quantification. On average, velocity errors for second-best approximations are approximately 1cm/s for a [0,125]cm/s velocity magnitude field. Results show that high-order dGFE provide better accuracy per degree of freedom but worse accuracy per Jacobian non-zero entry as compared to FV. Cross-comparison of velocity errors demonstrates asymptotic convergence of both solvers to the same numerical solution. Nevertheless, the discrepancy between under-resolved velocity fields suggests that mesh independence is reached following different paths. This article is protected by copyright. All rights reserved.

Exploring the Role of Intrinsic Nodal Activation on the Spread of Influence in Complex Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Visweswara Sathanur, Arun; Halappanavar, Mahantesh; Shi, Yi

In many complex networked systems such as online social networks, at any given time, activity originates at certain nodes and subsequently spreads on the network through influence. To model the spread of influence in such a scenario, we consider the problem of identification of influential entities in a complex network when nodal activation can happen through two different mechanisms. The first mode of activation is due mechanisms intrinsic to the node. The second mechanism is through the influence of connected neighbors. In this work, we present a simple probabilistic formulation that models such self-evolving systems where information diffusion occurs primarilymore » because of the intrinsic activity of users and the spread of activity occurs due to influence. We provide an algorithm to mine for the influential seeds in such a scenario by modifying the well-known influence maximization framework with the independent cascade diffusion model. We provide small motivating examples to provide an intuitive understanding of the effect of including the intrinsic activation mechanism. We sketch a proof of the submodularity of the influence function under the new formulation and demonstrate the same with larger graphs. We then show by means of additional experiments on a real-world twitter dataset how the formulation can be applied to real-world social media datasets. Finally we derive a computationally efficient centrality metric that takes into account, both the mechanisms of activation and provides for an accurate as well as computationally efficient alternative approach to the problem of identifying influencers under intrinsic activation.« less

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.

Nodal gap detection through polar angle-resolved density of states measurements in uniaxial superconductors

NASA Astrophysics Data System (ADS)

Tsutsumi, Yasumasa; Nomoto, Takuya; Ikeda, Hiroaki; Machida, Kazushige

2016-12-01

We propose a spectroscopic method to identify the nodal gap structure in unconventional superconductors. This method is best suited for locating the horizontal line node and for pinpointing the isolated point nodes by measuring polar angle (θ ) resolved zero-energy density of states N (θ ) . This is measured by specific heat or thermal conductivity at low temperatures under a magnetic field. We examine a variety of uniaxially symmetric nodal structures, including point and/or line nodes with linear and quadratic dispersions, by solving the Eilenberger equation in vortex states. It is found that (a) the maxima of N (θ ) continuously shift from the antinodal to the nodal direction (θn) as a field increases accompanying the oscillation pattern reversal at low and high fields. Furthermore, (b) local minima emerge next to θn on both sides, except for the case of the linear point node. These features are robust and detectable experimentally. Experimental results of N (θ ) performed on several superconductors, UPd2Al3,URu2Si2,CuxBi2Se3 , and UPt3, are examined and commented on in light of the present theory.

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.

Nodal endoplasmic reticulum, a specialized form of endoplasmic reticulum found in gravity-sensing root tip columella cells

NASA Technical Reports Server (NTRS)

Zheng, H. Q.; Staehelin, L. A.

2001-01-01

The endoplasmic reticulum (ER) of columella root cap cells has been postulated to play a role in gravity sensing. We have re-examined the ultrastructure of columella cells in tobacco (Nicotiana tabacum) root tips preserved by high-pressure freezing/freeze-substitution techniques to gain more precise information about the organization of the ER in such cells. The most notable findings are: the identification of a specialized form of ER, termed "nodal ER," which is found exclusively in columella cells; the demonstration that the bulk of the ER is organized in the form of a tubular network that is confined to a peripheral layer under the plasma membrane; and the discovery that this ER-rich peripheral region excludes Golgi stacks, vacuoles, and amyloplasts but not mitochondria. Nodal ER domains consist of an approximately 100-nm-diameter central rod composed of oblong subunits to which usually seven sheets of rough ER are attached along their margins. These domains form patches at the interface between the peripheral ER network and the ER-free central region of the cells, and they occupy defined positions within central and flanking columella cells. Over one-half of the nodal ER domains are located along the outer tangential walls of the flanking cells. Cytochalasin D and latrunculin A cause an increase in size and a decrease in numbers of nodal ER domains. We postulate that the nodal ER membranes locally modulate the gravisensing signals produced by the sedimenting amyloplasts, and that the confinement of all ER membranes to the cell periphery serves to enhance the sedimentability of the amyloplasts in the central region of columella cells.

Amesos2 and Belos: Direct and Iterative Solvers for Large Sparse Linear Systems

DOE PAGES

Bavier, Eric; Hoemmen, Mark; Rajamanickam, Sivasankaran; ...

2012-01-01

Solvers for large sparse linear systems come in two categories: direct and iterative. Amesos2, a package in the Trilinos software project, provides direct methods, and Belos, another Trilinos package, provides iterative methods. Amesos2 offers a common interface to many different sparse matrix factorization codes, and can handle any implementation of sparse matrices and vectors, via an easy-to-extend C++ traits interface. It can also factor matrices whose entries have arbitrary “Scalar” type, enabling extended-precision and mixed-precision algorithms. Belos includes many different iterative methods for solving large sparse linear systems and least-squares problems. Unlike competing iterative solver libraries, Belos completely decouples themore » algorithms from the implementations of the underlying linear algebra objects. This lets Belos exploit the latest hardware without changes to the code. Belos favors algorithms that solve higher-level problems, such as multiple simultaneous linear systems and sequences of related linear systems, faster than standard algorithms. The package also supports extended-precision and mixed-precision algorithms. Together, Amesos2 and Belos form a complete suite of sparse linear solvers.« less

Patterns of practice of regional nodal irradiation in breast cancer: results of the European Organization for Research and Treatment of Cancer (EORTC) NOdal Radiotherapy (NORA) survey.

PubMed

Belkacemi, Y; Kaidar-Person, O; Poortmans, P; Ozsahin, M; Valli, M-C; Russell, N; Kunkler, I; Hermans, J; Kuten, A; van Tienhoven, G; Westenberg, H

2015-03-01

Predicting outcome of breast cancer (BC) patients based on sentinel lymph node (SLN) status without axillary lymph node dissection (ALND) is an area of uncertainty. It influences the decision-making for regional nodal irradiation (RNI). The aim of the NORA (NOdal RAdiotherapy) survey was to examine the patterns of RNI. A web-questionnaire, including several clinical scenarios, was distributed to 88 EORTC-affiliated centers. Responses were received between July 2013 and January 2014. A total of 84 responses were analyzed. While three-dimensional (3D) radiotherapy (RT) planning is carried out in 81 (96%) centers, nodal areas are delineated in only 51 (61%) centers. Only 14 (17%) centers routinely link internal mammary chain (IMC) and supraclavicular node (SCN) RT indications. In patients undergoing total mastectomy (TM) with ALND, SCN-RT is recommend by 5 (6%), 53 (63%) and 51 (61%) centers for patients with pN0(i+), pN(mi) and pN1, respectively. Extra-capsular extension (ECE) is the main factor influencing decision-making RNI after breast conserving surgery (BCS) and TM. After primary systemic therapy (PST), 49 (58%) centers take into account nodal fibrotic changes in ypN0 patients for RNI indications. In ypN0 patients with inner/central tumors, 23 (27%) centers indicate SCN-RT and IMC-RT. In ypN1 patients, SCN-RT is delivered by less than half of the centers in patients with ypN(i+) and ypN(mi). Twenty-one (25%) of the centers recommend ALN-RT in patients with ypN(mi) or 1-2N+ after ALND. Seventy-five (90%) centers state that age is not considered a limiting factor for RNI. The NORA survey is unique in evaluating the impact of SLNB/ALND status on adjuvant RNI decision-making and volumes after BCS/TM with or without PST. ALN-RT is often indicated in pN1 patients, particularly in the case of ECE. Besides the ongoing NSABP-B51/RTOG and ALLIANCE trials, NORA could help to design future specific RNI trials in the SLNB era without ALND in patients receiving or not PST. �

A two-dimensional Riemann solver with self-similar sub-structure - Alternative formulation based on least squares projection

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Vides, Jeaniffer; Gurski, Katharine; Nkonga, Boniface; Dumbser, Michael; Garain, Sudip; Audit, Edouard

2016-01-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The self-similar formulation of Balsara [16] proves especially useful for this purpose. While that work is based on a Galerkin projection, in this paper we present an analogous self-similar formulation that is based on a different interpretation. In the present formulation, we interpret the shock jumps at the boundary of the strongly-interacting state quite literally. The enforcement of the shock jump conditions is done with a least squares projection (Vides, Nkonga and Audit [67]). With that interpretation, we again show that the multidimensional Riemann solver can be endowed with sub-structure. However, we find that the most efficient implementation arises when we use a flux vector splitting and a least squares projection. An alternative formulation that is based on the full characteristic matrices is also presented. The multidimensional Riemann solvers that are demonstrated here use one-dimensional HLLC Riemann solvers as building blocks. Several stringent test problems drawn from hydrodynamics and MHD are presented to show that the method works. Results from structured and unstructured meshes demonstrate the versatility of our method. The reader is also invited to watch a video introduction to multidimensional Riemann solvers on http://www.nd.edu/ dbalsara/Numerical-PDE-Course.

Observation of topological nodal fermion semimetal phase in ZrSiS

DOE PAGES

Neupane, Madhab; Belopolski, Ilya; Hosen, M. Mofazzel; ...

2016-05-11

We present that unveiling new topological phases of matter is one of the current objectives in condensed matter physics. Recent experimental discoveries of Dirac and Weyl semimetals prompt the search for other exotic phases of matter. Here we present a systematic angle-resolved photoemission spectroscopy study of ZrSiS, a prime topological nodal semimetal candidate. Our wider Brillouin zone (BZ) mapping shows multiple Fermi surface pockets such as the diamond-shaped Fermi surface, elliptical-shaped Fermi surface, and a small electron pocket encircling at the zone center (Γ) point, the M point, and the X point of the BZ, respectively. We experimentally establish themore » spinless nodal fermion semimetal phase in ZrSiS, which is supported by our first-principles calculations. Our findings evidence that the ZrSiS-type of material family is a new platform on which to explore exotic states of quantum matter; these materials are expected to provide an avenue for engineering two-dimensional topological insulator systems.« less

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.

Jacobian-free approximate solvers for hyperbolic systems: Application to relativistic magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Castro, Manuel J.; Gallardo, José M.; Marquina, Antonio

2017-10-01

We present recent advances in PVM (Polynomial Viscosity Matrix) methods based on internal approximations to the absolute value function, and compare them with Chebyshev-based PVM solvers. These solvers only require a bound on the maximum wave speed, so no spectral decomposition is needed. Another important feature of the proposed methods is that they are suitable to be written in Jacobian-free form, in which only evaluations of the physical flux are used. This is particularly interesting when considering systems for which the Jacobians involve complex expressions, e.g., the relativistic magnetohydrodynamics (RMHD) equations. On the other hand, the proposed Jacobian-free solvers have also been extended to the case of approximate DOT (Dumbser-Osher-Toro) methods, which can be regarded as simple and efficient approximations to the classical Osher-Solomon method, sharing most of it interesting features and being applicable to general hyperbolic systems. To test the properties of our schemes a number of numerical experiments involving the RMHD equations are presented, both in one and two dimensions. The obtained results are in good agreement with those found in the literature and show that our schemes are robust and accurate, running stable under a satisfactory time step restriction. It is worth emphasizing that, although this work focuses on RMHD, the proposed schemes are suitable to be applied to general hyperbolic systems.

A Comparison of Monte Carlo and Deterministic Solvers for keff and Sensitivity Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haeck, Wim; Parsons, Donald Kent; White, Morgan Curtis

Verification and validation of our solutions for calculating the neutron reactivity for nuclear materials is a key issue to address for many applications, including criticality safety, research reactors, power reactors, and nuclear security. Neutronics codes solve variations of the Boltzmann transport equation. The two main variants are Monte Carlo versus deterministic solutions, e.g. the MCNP [1] versus PARTISN [2] codes, respectively. There have been many studies over the decades that examined the accuracy of such solvers and the general conclusion is that when the problems are well-posed, either solver can produce accurate results. However, the devil is always in themore » details. The current study examines the issue of self-shielding and the stress it puts on deterministic solvers. Most Monte Carlo neutronics codes use continuous-energy descriptions of the neutron interaction data that are not subject to this effect. The issue of self-shielding occurs because of the discretisation of data used by the deterministic solutions. Multigroup data used in these solvers are the average cross section and scattering parameters over an energy range. Resonances in cross sections can occur that change the likelihood of interaction by one to three orders of magnitude over a small energy range. Self-shielding is the numerical effect that the average cross section in groups with strong resonances can be strongly affected as neutrons within that material are preferentially absorbed or scattered out of the resonance energies. This affects both the average cross section and the scattering matrix.« less

Application of a fast Newton-Krylov solver for equilibrium simulations of phosphorus and oxygen

NASA Astrophysics Data System (ADS)

Fu, Weiwei; Primeau, François

2017-11-01

Model drift due to inadequate spinup is a serious problem that complicates the interpretation of climate change simulations. Even after a 300 year spinup we show that solutions are not only still drifting but often drifting away from their eventual equilibrium over large parts of the ocean. Here we present a Newton-Krylov solver for computing cyclostationary equilibrium solutions of a biogeochemical model for the cycling of phosphorus and oxygen. In addition to using previously developed preconditioning strategies - time-averaging and coarse-graining the Jacobian matrix - we also introduce a new strategy: the adiabatic elimination of a fast variable (particulate organic phosphorus) by slaving it to a slow variable (dissolved inorganic phosphorus). We use transport matrices derived from the Community Earth System Model (CESM) with a nominal horizontal resolution of 1° × 1° and 60 vertical levels to implement and test the solver. We find that the new solver obtains seasonally-varying equilibrium solutions with no visible drift using no more than 80 simulation years.

Numerical Investigation of Vertical Plunging Jet Using a Hybrid Multifluid–VOF Multiphase CFD Solver

DOE PAGES

Shonibare, Olabanji Y.; Wardle, Kent E.

2015-06-28

A novel hybrid multiphase flow solver has been used to conduct simulations of a vertical plunging liquid jet. This solver combines a multifluid methodology with selective interface sharpening to enable simulation of both the initial jet impingement and the long-time entrained bubble plume phenomena. Models are implemented for variable bubble size capturing and dynamic switching of interface sharpened regions to capture transitions between the initially fully segregated flow types into the dispersed bubbly flow regime. It was found that the solver was able to capture the salient features of the flow phenomena under study and areas for quantitative improvement havemore » been explored and identified. In particular, a population balance approach is employed and detailed calibration of the underlying models with experimental data is required to enable quantitative prediction of bubble size and distribution to capture the transition between segregated and dispersed flow types with greater fidelity.« less

Pushing Memory Bandwidth Limitations Through Efficient Implementations of Block-Krylov Space Solvers on GPUs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, M. A.; Strelchenko, Alexei; Vaquero, Alejandro

Lattice quantum chromodynamics simulations in nuclear physics have benefited from a tremendous number of algorithmic advances such as multigrid and eigenvector deflation. These improve the time to solution but do not alleviate the intrinsic memory-bandwidth constraints of the matrix-vector operation dominating iterative solvers. Batching this operation for multiple vectors and exploiting cache and register blocking can yield a super-linear speed up. Block-Krylov solvers can naturally take advantage of such batched matrix-vector operations, further reducing the iterations to solution by sharing the Krylov space between solves. However, practical implementations typically suffer from the quadratic scaling in the number of vector-vector operations.more » Using the QUDA library, we present an implementation of a block-CG solver on NVIDIA GPUs which reduces the memory-bandwidth complexity of vector-vector operations from quadratic to linear. We present results for the HISQ discretization, showing a 5x speedup compared to highly-optimized independent Krylov solves on NVIDIA's SaturnV cluster.« less

NODAL in the Uterus Is Necessary for Proper Placental Development and Maintenance of Pregnancy1

PubMed Central

Park, Craig B.; DeMayo, Francesco J.; Lydon, John P.; Dufort, Daniel

2012-01-01

Preterm birth is the single leading cause of perinatal mortality in developed countries, affecting approximately 12% of pregnancies and accounting for 75% of neonatal loss in the United States. Despite the prevalence and severity of premature delivery, the causes and mechanisms that underlie spontaneous and idiopathic preterm birth remain unknown. Our inability to elucidate these fundamental causes has been attributed to a poor understanding of the signaling pathways associated with the premature induction of parturition and a lack of suitable animal models available for preterm birth research. In this study, we describe the generation and analysis of a novel conditional knockout of the transforming growth factor beta (TGFB) superfamily member, Nodal, from the maternal reproductive tract of mice. Strikingly, uterine Nodal knockout females exhibited a severe malformation of the maternal decidua basalis during placentation, leading to significant intrauterine growth restriction, and ultimately preterm birth and fetal loss on Day 17.5 of gestation. Using several approaches, we characterized aberrant placental development and demonstrated that reduced proliferation combined with increased apoptosis resulted in a diminished decidua basalis and compromised maternal-fetal interface. Last, we evaluated various components of the established parturition cascade and determined that preterm birth derived from the maternal Nodal knockout occurs prior to PTGS2 (COX-2) upregulation at the placental interface. Taken together, the results presented in this study highlight an in vivo role for maternal NODAL during placentation, present an interesting link between disrupted decidua basalis formation and premature parturition, and describe a potentially valuable model toward elucidating the complex processes that underlie preterm birth. PMID:22378764

Input-output-controlled nonlinear equation solvers

NASA Technical Reports Server (NTRS)

Padovan, Joseph

1988-01-01

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

The Use of Sparse Direct Solver in Vector Finite Element Modeling for Calculating Two Dimensional (2-D) Magnetotelluric Responses in Transverse Electric (TE) Mode

NASA Astrophysics Data System (ADS)

Yihaa Roodhiyah, Lisa’; Tjong, Tiffany; Nurhasan; Sutarno, D.

2018-04-01

The late research, linear matrices of vector finite element in two dimensional(2-D) magnetotelluric (MT) responses modeling was solved by non-sparse direct solver in TE mode. Nevertheless, there is some weakness which have to be improved especially accuracy in the low frequency (10-3 Hz-10-5 Hz) which is not achieved yet and high cost computation in dense mesh. In this work, the solver which is used is sparse direct solver instead of non-sparse direct solverto overcome the weaknesses of solving linear matrices of vector finite element metod using non-sparse direct solver. Sparse direct solver will be advantageous in solving linear matrices of vector finite element method because of the matrix properties which is symmetrical and sparse. The validation of sparse direct solver in solving linear matrices of vector finite element has been done for a homogen half-space model and vertical contact model by analytical solution. Thevalidation result of sparse direct solver in solving linear matrices of vector finite element shows that sparse direct solver is more stable than non-sparse direct solver in computing linear problem of vector finite element method especially in low frequency. In the end, the accuracy of 2D MT responses modelling in low frequency (10-3 Hz-10-5 Hz) has been reached out under the efficient allocation memory of array and less computational time consuming.

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

Differential role of Sloan–Kettering Institute (Ski) protein in Nodal and transforming growth factor-beta (TGF-β)-induced Smad signaling in prostate cancer cells

PubMed Central

Khan, Shafiq A.

2012-01-01

Transforming growth factor-beta (TGF-β) signaling pathways contain both tumor suppressor and tumor promoting activities. We have demonstrated that Nodal, another member of the TGF-β superfamily, and its receptors are expressed in prostate cancer cells. Nodal and TGF-β exerted similar biological effects on prostate cells; both inhibited proliferation in WPE, RWPE1 and DU145 cells, whereas neither had any effect on the proliferation of LNCaP or PC3 cells. Interestingly, Nodal and TGF-β induced migration in PC3 cells, but not in DU145 cells. TGF-β induced predominantly phosphorylation of Smad3, whereas Nodal induced phosphorylation of only Smad2. We also determined the expression and differential role of Ski, a corepressor of Smad2/3, in Nodal and TGF-β signaling in prostate cancer cells. Similar levels of Ski mRNA were found in several established prostate cell lines; however, high levels of Ski protein were only detected in prostate cancer cells and prostate cancer tissue samples. Exogenous Nodal and TGF-β had no effects on Ski mRNA levels. On the other hand, TGF-β induced a rapid degradation of Ski protein mediated by the proteasomal pathway, whereas Nodal had no effect on Ski protein. Reduced Ski levels correlated with increased basal and TGF-β-induced Smad2/3 phosphorylation. Knockdown of endogenous Ski reduced proliferation in DU145 cells and enhanced migration of PC3 cells. We conclude that high levels of Ski expression in prostate cancer cells may be responsible for repression of TGF-β and Smad3 signaling, but Ski protein levels do not influence Nodal and Smad2 signaling. PMID:22843506

A Numerical Study of Scalable Cardiac Electro-Mechanical Solvers on HPC Architectures

PubMed Central

Colli Franzone, Piero; Pavarino, Luca F.; Scacchi, Simone

2018-01-01

We introduce and study some scalable domain decomposition preconditioners for cardiac electro-mechanical 3D simulations on parallel HPC (High Performance Computing) architectures. The electro-mechanical model of the cardiac tissue is composed of four coupled sub-models: (1) the static finite elasticity equations for the transversely isotropic deformation of the cardiac tissue; (2) the active tension model describing the dynamics of the intracellular calcium, cross-bridge binding and myofilament tension; (3) the anisotropic Bidomain model describing the evolution of the intra- and extra-cellular potentials in the deforming cardiac tissue; and (4) the ionic membrane model describing the dynamics of ionic currents, gating variables, ionic concentrations and stretch-activated channels. This strongly coupled electro-mechanical model is discretized in time with a splitting semi-implicit technique and in space with isoparametric finite elements. The resulting scalable parallel solver is based on Multilevel Additive Schwarz preconditioners for the solution of the Bidomain system and on BDDC preconditioned Newton-Krylov solvers for the non-linear finite elasticity system. The results of several 3D parallel simulations show the scalability of both linear and non-linear solvers and their application to the study of both physiological excitation-contraction cardiac dynamics and re-entrant waves in the presence of different mechano-electrical feedbacks. PMID:29674971

Determination of the diffusivity, dispersion, skewness and kurtosis in heterogeneous porous flow. Part I: Analytical solutions with the extended method of moments.

NASA Astrophysics Data System (ADS)

Ginzburg, Irina; Vikhansky, Alexander

2018-05-01

The extended method of moments (EMM) is elaborated in recursive algorithmic form for the prediction of the effective diffusivity, the Taylor dispersion dyadic and the associated longitudinal high-order coefficients in mean-concentration profiles and residence-time distributions. The method applies in any streamwise-periodic stationary d-dimensional velocity field resolved in the piecewise continuous heterogeneous porosity field. It is demonstrated that EMM reduces to the method of moments and the volume-averaging formulation in microscopic velocity field and homogeneous soil, respectively. The EMM simultaneously constructs two systems of moments, the spatial and the temporal, without resorting to solving of the high-order upscaled PDE. At the same time, the EMM is supported with the reconstruction of distribution from its moments, allowing to visualize the deviation from the classical ADE solution. The EMM can be handled by any linear advection-diffusion solver with explicit mass-source and diffusive-flux jump condition on the solid boundary and permeable interface. The prediction of the first four moments is decisive in the optimization of the dispersion, asymmetry, peakedness and heavy-tails of the solute distributions, through an adequate design of the composite materials, wetlands, chemical devices or oil recovery. The symbolic solutions for dispersion, skewness and kurtosis are constructed in basic configurations: diffusion process and Darcy flow through two porous blocks in "series", straight and radial Poiseuille flow, porous flow governed by the Stokes-Brinkman-Darcy channel equation and a fracture surrounded by penetrable diffusive matrix or embedded in porous flow. We examine the moments dependency upon porosity contrast, aspect ratio, Péclet and Darcy numbers, but also for their response on the effective Brinkman viscosity applied in flow modeling. Two numerical Lattice Boltzmann algorithms, a direct solver of the microscopic ADE in heterogeneous

Brady's Geothermal Field Nodal Seismometer Active Source Data Sample

DOE Data Explorer

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.

Complex index of refraction estimation from degree of polarization with diffuse scattering consideration.

PubMed

Zhan, Hanyu; Voelz, David G; Cho, Sang-Yeon; Xiao, Xifeng

2015-11-20

The estimation of the refractive index from optical scattering off a target's surface is an important task for remote sensing applications. Optical polarimetry is an approach that shows promise for refractive index estimation. However, this estimation often relies on polarimetric models that are limited to specular targets involving single surface scattering. Here, an analytic model is developed for the degree of polarization (DOP) associated with reflection from a rough surface that includes the effect of diffuse scattering. A multiplicative factor is derived to account for the diffuse component and evaluation of the model indicates that diffuse scattering can significantly affect the DOP values. The scattering model is used in a new approach for refractive index estimation from a series of DOP values that involves jointly estimating n, k, and ρ(d)with a nonlinear equation solver. The approach is shown to work well with simulation data and additive noise. When applied to laboratory-measured DOP values, the approach produces significantly improved index estimation results relative to reference values.

Parallel Nonnegative Least Squares Solvers for Model Order Reduction

DTIC Science & Technology

2016-03-01

NNLS problems that arise when the Energy Conserving Sampling and Weighting hyper -reduction procedure is used when constructing a reduced-order model...ScaLAPACK and performance results are presented. nonnegative least squares, model order reduction, hyper -reduction, Energy Conserving Sampling and...optimal solution. ........................................ 20 Table 6 Reduced mesh sizes produced for each solver in the ECSW hyper -reduction step

PITX2 and NODAL expression during axis formation in the early rabbit embryo.

PubMed

Plöger, Ruben; Viebahn, Christoph

2018-04-26

Attaining molecular and morphological axial polarity during gastrulation is a fundamental early requirement for normal development of the embryo. In mammals, the first morphological sign of the anterior-posterior axis appears anteriorly in the form of the anterior marginal crescent (or anterior visceral endoderm) while in the avian the first such sign is the Koller's sickle at the posterior pole of the embryonic disc. Despite this inverse mode of axis formation many genes and molecular pathways involved in various steps of this process seem to be evolutionary conserved amongst amniotes, the nodal gene being a well-known example with its functional involvement prior and during gastrulation. The pitx2 gene, however, is a new candidate described in the chick as an early marker for anterior-posterior polarity and as regulator of axis formation including twinning. To find out whether pitx2 has retained its inductive and early marker function during the evolution of mammals, this study analyzes pitx2 and nodal expression at parallel stages during formation of the anterior-posterior polarity in the early rabbit embryo using whole-mount in situ hybridization and serial light-microscopical sections. At a late pre-gastrulation stage a localized reduction of nodal expression presages the position of the anterior pole of the embryonic disc and thus serves as the earliest molecular marker of anterior-posterior polarity known so far. pitx2 is expressed in a polarized manner in the anterior marginal crescent and in the posterior half of the embryonic disc during further development only while nodal expression in the anterior segment of the posterior pitx2 expression domain helps to define the so-called anterior streak domain (ASD), a novel progenitor region of the anterior half of the primitive streak. The expression patterns of both genes thus serve as signs of a conserved involvement in early axis formation in amniotes and, possibly, in twinning in mammals as well. Copyright �

The role of elective nodal irradiation for esthesioneuroblastoma patients with clinically negative neck.

PubMed

Jiang, Wen; Mohamed, Abdallah S R; Fuller, Clifton David; Kim, Betty Y S; Tang, Chad; Gunn, G Brandon; Hanna, Ehab Y; Frank, Steven J; Su, Shirley Y; Diaz, Eduardo; Kupferman, Michael E; Beadle, Beth M; Morrison, William H; Skinner, Heath; Lai, Stephen Y; El-Naggar, Adel K; DeMonte, Franco; Rosenthal, David I; Garden, Adam S; Phan, Jack

2016-01-01

Although adjuvant radiation to the tumor bed has been reported to improve the clinic outcomes of esthesioneuroblastoma (ENB) patients, the role of elective neck irradiation (ENI) in clinically node-negative (N0) patients remains controversial. Here, we evaluated the effects of ENI on neck nodal relapse risk in ENB patients treated with radiation therapy as a component of multimodality treatment. Seventy-one N0 ENB patients irradiated at the University of Texas MD Anderson Cancer Center between 1970 and 2013 were identified. ENI was performed on 22 of these patients (31%). Survival analysis was performed with focus on comparative outcomes of those patients who did and did not receive ENI. The median follow-up time for our cohort is 80.8 months (range, 6-350 months). Among N0 patients, 13 (18.3%) developed neck nodal relapses, with a median time to progression of 62.5 months. None of these 13 patients received prophylactic neck irradiation. ENI was associated with significantly improved regional nodal control at 5 years (regional control rate of 100% for ENI vs 82%, P < .001), but not overall survival or disease-free survival. Eleven patients without ENI developed isolated neck recurrences. All had further treatment for their neck disease, including neck dissection (n = 10), radiation (n = 10), or chemotherapy (n = 5). Six of these 11 patients (54.5%) demonstrated no evidence of further recurrence with a median follow-up of 55.5 months. ENI significantly reduces the risk of cervical nodal recurrence in ENB patients with clinically N0 neck, but this did not translate to a survival benefit. Multimodality treatment for isolated neck recurrence provides a reasonable salvage rate. The greatest benefit for ENI appeared to be among younger patients who presented with Kadish C disease. Further studies are needed to confirm these findings. Copyright © 2016 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

A fast Poisson solver for unsteady incompressible Navier-Stokes equations on the half-staggered grid

NASA Technical Reports Server (NTRS)

Golub, G. H.; Huang, L. C.; Simon, H.; Tang, W. -P.

1995-01-01

In this paper, a fast Poisson solver for unsteady, incompressible Navier-Stokes equations with finite difference methods on the non-uniform, half-staggered grid is presented. To achieve this, new algorithms for diagonalizing a semi-definite pair are developed. Our fast solver can also be extended to the three dimensional case. The motivation and related issues in using this second kind of staggered grid are also discussed. Numerical testing has indicated the effectiveness of this algorithm.

Calm water resistance prediction of a bulk carrier using Reynolds averaged Navier-Stokes based solver

NASA Astrophysics Data System (ADS)

Rahaman, Md. Mashiur; Islam, Hafizul; Islam, Md. Tariqul; Khondoker, Md. Reaz Hasan

2017-12-01

Maneuverability and resistance prediction with suitable accuracy is essential for optimum ship design and propulsion power prediction. This paper aims at providing some of the maneuverability characteristics of a Japanese bulk carrier model, JBC in calm water using a computational fluid dynamics solver named SHIP Motion and OpenFOAM. The solvers are based on the Reynolds average Navier-Stokes method (RaNS) and solves structured grid using the Finite Volume Method (FVM). This paper comprises the numerical results of calm water test for the JBC model with available experimental results. The calm water test results include the total drag co-efficient, average sinkage, and trim data. Visualization data for pressure distribution on the hull surface and free water surface have also been included. The paper concludes that the presented solvers predict the resistance and maneuverability characteristics of the bulk carrier with reasonable accuracy utilizing minimum computational resources.

Scanning Tunneling Microscopy Study on Dirac Nodal-line Semimetal ZrSiS

NASA Astrophysics Data System (ADS)

Su, Chih-Chuan; Guan, Syu-You; Wang, Tzu-Cheng; Sankar, Raman; Guo, Guang-Yu; Chou, Fangcheng; Chang, Chia-Seng; Chuang, Tien-Ming

The discovery of 3D Dirac nodal-line protected by non-symmophic symmetry in ZrSiS family has been reported by angle resolved photoemission spectroscopy (ARPES) and quantum oscillation measurements. ZrSiS also exhibits a butterfly shaped titanic angular magnetoresistance and strong Zeeman splitting in quantum oscillation. These observations with its layered crystal structure make the ZrSiS family an interesting candidate to understand the novel properties of the nodal-line semimetals. Here, we study the electronic structures of the single crystal ZrSiS by using spectroscopic-imaging scanning tunneling microscope at T= 4.2K. Our quasiparticle scattering interference imaging reveals the characteristic wave vectors with linear dispersion from Dirac line nodes in the bulk and its surface states. Our results are in excellent agreement with the first principle calculation, and also in consistent with ARPES and quantum oscillation measurements.

The effect of viscosity on steady transonic flow with a nodal solution topology

NASA Technical Reports Server (NTRS)

Owocki, Stanley P.; Zank, Gary P.

1991-01-01

The effect of viscosity on a steady, transonic flow for which the inviscid limit has a nodal solution topology near the critical point is investigated. For the accelerating case, viscous solutions tend to repel each other, so that a very delicate choice of initial conditions is required to prevent them from diverging. Only the two critical solutions extend to arbitrarily large distances into both the subsonic and supersonic flows. For the decelerating case, the solutions tend to attract, and so an entire two-parameter family of solutions now extends over large distances. The general effect of viscosity on the solution degeneracy of a nodal topology is thus to reduce or limit it for the accelerating case and to enhance it for the decelerating case. The astrophysical implications of these findings are addressed.

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.

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

ASIS v1.0: an adaptive solver for the simulation of atmospheric chemistry

NASA Astrophysics Data System (ADS)

Cariolle, Daniel; Moinat, Philippe; Teyssèdre, Hubert; Giraud, Luc; Josse, Béatrice; Lefèvre, Franck

2017-04-01

This article reports on the development and tests of the adaptive semi-implicit scheme (ASIS) solver for the simulation of atmospheric chemistry. To solve the ordinary differential equation systems associated with the time evolution of the species concentrations, ASIS adopts a one-step linearized implicit scheme with specific treatments of the Jacobian of the chemical fluxes. It conserves mass and has a time-stepping module to control the accuracy of the numerical solution. In idealized box-model simulations, ASIS gives results similar to the higher-order implicit schemes derived from the Rosenbrock's and Gear's methods and requires less computation and run time at the moderate precision required for atmospheric applications. When implemented in the MOCAGE chemical transport model and the Laboratoire de Météorologie Dynamique Mars general circulation model, the ASIS solver performs well and reveals weaknesses and limitations of the original semi-implicit solvers used by these two models. ASIS can be easily adapted to various chemical schemes and further developments are foreseen to increase its computational efficiency, and to include the computation of the concentrations of the species in aqueous-phase in addition to gas-phase chemistry.

Motion deficit in nodal interphalangeal joint osteoarthritis by digital goniometer in housewives.

PubMed

Ventura-Ríos, L; Hayes-Salinas, M; Ferrusquia-Toriz, D; Cariño-Escobar, R I; Cruz-Arenas, E; Gutiérrez-Martínez, J; González-Ramírez, L; Hernández-Díaz, C

2018-06-01

Range of motion (ROM) measured objectively in nodal hand osteoarthritis (NHOA) is missing. Evaluation of collateral ligaments by ultrasound (US) is unknown in NHOA also. To compare ROM in interphalangeal joints in housewives with nodal OA, with a control group by a digital system using angle to voltage (Multielgon). The second objective was to assess correlation between collateral radial and ulnar ligaments thickness and ROM. For this cross-sectional observational study, we assessed 60 hands with symptomatic NHOA and 30 hands of healthy housewives matched for age. We obtained clinical and demographic characteristics (a complete standardized physical examination of hand joints, DASH questionnaire, pain surveys, gross grasp hand goniometer, and ROM measurements by Multielgon. Presence of synovitis, power Doppler signal, osteophytes, and collateral ligaments thickness was evaluated by US. We used descriptive statistics, Spearman correlation, X 2 test, t test and odds ratio. Significant less gross grasp and ROM in the right hand were observed in NHOA (p = 0.01 for both). Presence of OA, painful joints, disease duration, and score DASH were significant correlated with reduced ROM (OR 4.12, 4.12, 1.04 and 1.09, respectively). Reduced ROM was statistical significant in thumb MCP and IP joints, second and third DIP in dominant hand. There was no association between collateral radial and ulnar ligaments and reduced ROM. Synovitis and osteophytes were more prevalent in OA group. Multielgon demonstrated the pattern of reduced ROM in nodal OA of housewives particularly in MCP and IP thumb joints, second and third distal interphalangeal joints.

A User's Manual for ROTTILT Solver: Tiltrotor Fountain Flow Field Prediction

NASA Technical Reports Server (NTRS)

Tadghighi, Hormoz; Rajagopalan, R. Ganesh

1999-01-01

A CFD solver has been developed to provide the time averaged details of the fountain flow typical for tiltrotor aircraft in hover. This Navier-Stokes solver, designated as ROTTILT, assumes the 3-D fountain flowfield to be steady and incompressible. The theoretical background is described in this manual. In order to enable the rotor trim solution in the presence of tiltrotor aircraft components such as wing, nacelle, and fuselage, the solver is coupled with a set of trim routines which are highly efficient in CPU and suitable for CFD analysis. The Cartesian grid technique utilized provides the user with a unique capability for insertion or elimination of any components of the bodies considered for a given tiltrotor aircraft configuration. The flowfield associated with either a semi or full-span configuration can be computed through user options in the ROTTILT input file. Full details associated with the numerical solution implemented in ROTTILT and assumptions are presented. A description of input surface mesh topology is provided in the appendices along with a listing of all preprocessor programs. Input variable definitions and default values are provided for the V22 aircraft. Limited predicted results using the coupled ROTTILT/WOPWOP program for the V22 in hover are made and compared with measurement. To visualize the V22 aircraft and predictions, a preprocessor graphics program GNU-PLOT3D was used. This program is described and example graphic results presented.

Three-dimensional conformal radiation therapy for esophageal squamous cell carcinoma: is elective nodal irradiation necessary?

PubMed

Zhao, Kuai-le; Ma, Jin-bo; Liu, Guang; Wu, Kai-liang; Shi, Xue-hui; Jiang, Guo-liang

2010-02-01

To evaluate the local control, survival, and toxicity associated with three-dimensional conformal radiotherapy (3D-CRT) for squamous cell carcinoma (SCC) of the esophagus, to determine the appropriate target volumes, and to determine whether elective nodal irradiation is necessary in these patients. A prospective study of 3D-CRT was undertaken in patients with esophageal SCC without distant metastases. Patients received 68.4 Gy in 41 fractions over 44 days using late-course accelerated hyperfractionated 3D-CRT. Only the primary tumor and positive lymph nodes were irradiated. Isolated out-of-field regional nodal recurrence was defined as a recurrence in an initially uninvolved regional lymph node. All 53 patients who made up the study population tolerated the irradiation well. No acute or late Grade 4 or 5 toxicity was observed. The median survival time was 30 months (95% confidence interval, 17.7-41.8). The overall survival rate at 1, 2, and 3 years was 77%, 56%, and 41%, respectively. The local control rate at 1, 2, and 3 years was 83%, 74%, and 62%, respectively. Thirty-nine of the 53 patients (74%) showed treatment failure. Seventeen of the 39 (44%) developed an in-field recurrence, 18 (46%) distant metastasis with or without regional failure, and 3 (8%) an isolated out-of-field nodal recurrence only. One patient died of disease in an unknown location. In patients treated with 3D-CRT for esophageal SCC, the omission of elective nodal irradiation was not associated with a significant amount of failure in lymph node regions not included in the planning target volume. Local failure and distant metastases remained the predominant problems. Copyright 2010 Elsevier Inc. All rights reserved.

F18 FDG positron emission tomography revelation of primary testicular lymphoma with concurrent multiple extra nodal involvement

PubMed Central

Vamsy, Mohana; Dattatreya, PS; Parakh, Megha; Dayal, Monal; Rao, VVS Prabhakar

2013-01-01

Primary testicular lymphoma (PTL) a relatively rare disease of non-Hodgkin's lymphomas occurring with a lesser incidence of 1-2% has a propensity to occur at later ages above 50 years. PTL spreads to extra nodal sites due to deficiency of extra cellular adhesion molecules. We present detection of multiple sites of extra nodal involvement of PTL by F-18 positron emission tomography/computed tomography study aiding early detection of the dissemination thus aiding in staging and management. PMID:24019676

Detailed analysis of the effects of stencil spatial variations with arbitrary high-order finite-difference Maxwell solver

DOE PAGES

Vincenti, H.; Vay, J. -L.

2015-11-22

Due to discretization effects and truncation to finite domains, many electromagnetic simulations present non-physical modifications of Maxwell's equations in space that may generate spurious signals affecting the overall accuracy of the result. Such modifications for instance occur when Perfectly Matched Layers (PMLs) are used at simulation domain boundaries to simulate open media. Another example is the use of arbitrary order Maxwell solver with domain decomposition technique that may under some condition involve stencil truncations at subdomain boundaries, resulting in small spurious errors that do eventually build up. In each case, a careful evaluation of the characteristics and magnitude of themore » errors resulting from these approximations, and their impact at any frequency and angle, requires detailed analytical and numerical studies. To this end, we present a general analytical approach that enables the evaluation of numerical discretization errors of fully three-dimensional arbitrary order finite-difference Maxwell solver, with arbitrary modification of the local stencil in the simulation domain. The analytical model is validated against simulations of domain decomposition technique and PMLs, when these are used with very high-order Maxwell solver, as well as in the infinite order limit of pseudo-spectral solvers. Results confirm that the new analytical approach enables exact predictions in each case. It also confirms that the domain decomposition technique can be used with very high-order Maxwell solver and a reasonably low number of guard cells with negligible effects on the whole accuracy of the simulation.« less

Fast immersed interface Poisson solver for 3D unbounded problems around arbitrary geometries

NASA Astrophysics Data System (ADS)

Gillis, T.; Winckelmans, G.; Chatelain, P.

2018-02-01

We present a fast and efficient Fourier-based solver for the Poisson problem around an arbitrary geometry in an unbounded 3D domain. This solver merges two rewarding approaches, the lattice Green's function method and the immersed interface method, using the Sherman-Morrison-Woodbury decomposition formula. The method is intended to be second order up to the boundary. This is verified on two potential flow benchmarks. We also further analyse the iterative process and the convergence behavior of the proposed algorithm. The method is applicable to a wide range of problems involving a Poisson equation around inner bodies, which goes well beyond the present validation on potential flows.

An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formation

NASA Technical Reports Server (NTRS)

Yu, Jr-Kai; Holland, Linda Z.; Holland, Nicholas D.

2002-01-01

The full-length sequence and zygotic expression of an amphioxus nodal gene are described. Expression is first detected in the early gastrula just within the dorsal lip of the blastopore in a region of hypoblast that is probably comparable with the vertebrate Spemann's organizer. In the late gastrula and early neurula, expression remains bilaterally symmetrical, limited to paraxial mesoderm and immediately overlying regions of the neural plate. Later in the neurula stage, all neural expression disappears, and mesodermal expression disappears from the right side. All along the left side of the neurula, mesodermal expression spreads into the left side of the gut endoderm. Soon thereafter, all expression is down-regulated except near the anterior and posterior ends of the animal, where transcripts are still found in the mesoderm and endoderm on the left side. At this time, expression also begins in the ectoderm on the left side of the head, in the region where the mouth later forms. These results suggest that amphioxus and vertebrate nodal genes play evolutionarily conserved roles in establishing Spemann's organizer, patterning the mesoderm rostrocaudally and setting up the asymmetrical left-right axis of the body.

Nodal enhances the activity of FoxO3a and its synergistic interaction with Smads to regulate cyclin G2 transcription in ovarian cancer cells.

PubMed

Fu, G; Peng, C

2011-09-15

Nodal, a member of the transforming growth factor-β superfamily, has been recently shown to suppress cell proliferation and to stimulate the expression of cyclin G2 (CCNG2) in human epithelial ovarian cancer cells. However, the precise mechanisms underlying these events are not fully understood. In this study, we investigated the transcriptional regulation of CCNG2 by the Nodal signaling pathway. In ovarian cancer cells, overexpression of Nodal or its receptors, activin receptor-like kinase 7 (ALK7) or ALK4, resulted in an increase in the CCNG2 promoter activity. Several putative Forkhead box class O (FoxO)3a-binding sites are present in the human CCNG2 promoter and overexpression of FoxO3a enhanced the CCNG2 promoter activity. The functional FoxO3a-binding element (FBE) was mapped to a proximal region located between -398 and -380 bp (FBE1) through deletion and mutation analyses, as well as chromatin immunoprecipitation (IP) assay. Interestingly, mutation of the FBE1 not only abolished the effect of FoxO3a, but also blocked Nodal-induced CCNG2 transcription. Nodal stimulated FoxO3a mRNA and protein expression through the canonical Smad pathway and suppressed FoxO3a inactivation by inhibiting AKT activity. Silencing of FoxO3a using small interfering RNA significantly reduced the effect of Nodal on the CCNG2 promoter activity. On the other hand, overexpression of Smad2 and Smad3 enhanced the FoxO3a-induced CCNG2 promoter activity whereas knockdown of Smad4 blocked the activity of FoxO3a. Furthermore, IP assays revealed that FoxO3a formed complexes with Smad proteins and that Nodal enhanced the binding of FoxO3a to the CCNG2 promoter. Finally, silencing of FoxO3a reversed the inhibitory effect of Nodal on cell proliferation. Taken together, these findings demonstrated that Nodal signaling promotes CCNG2 transcription by upregulating FoxO3a expression, inhibiting FoxO3a phosphorylation and enhancing its synergistic interaction with Smads. These results also suggest

Application of Nearly Linear Solvers to Electric Power System Computation

NASA Astrophysics Data System (ADS)

Grant, Lisa L.

To meet the future needs of the electric power system, improvements need to be made in the areas of power system algorithms, simulation, and modeling, specifically to achieve a time frame that is useful to industry. If power system time-domain simulations could run in real-time, then system operators would have situational awareness to implement online control and avoid cascading failures, significantly improving power system reliability. Several power system applications rely on the solution of a very large linear system. As the demands on power systems continue to grow, there is a greater computational complexity involved in solving these large linear systems within reasonable time. This project expands on the current work in fast linear solvers, developed for solving symmetric and diagonally dominant linear systems, in order to produce power system specific methods that can be solved in nearly-linear run times. The work explores a new theoretical method that is based on ideas in graph theory and combinatorics. The technique builds a chain of progressively smaller approximate systems with preconditioners based on the system's low stretch spanning tree. The method is compared to traditional linear solvers and shown to reduce the time and iterations required for an accurate solution, especially as the system size increases. A simulation validation is performed, comparing the solution capabilities of the chain method to LU factorization, which is the standard linear solver for power flow. The chain method was successfully demonstrated to produce accurate solutions for power flow simulation on a number of IEEE test cases, and a discussion on how to further improve the method's speed and accuracy is included.

Uncertainty Quantification For Physical and Numerical Diffusion Models In Inertial Confinement Fusion Simulations

NASA Astrophysics Data System (ADS)

Rana, Verinder S.

thermal transport. The numerical approximation uncertainties are introduced by the choice of a hydrodynamic solver for a particular flow. Solvers tend to be diffusive at material interfaces and the Front Tracking (FT) algorithm, which is an already available software code in the form of an API, helps to ameliorate such effects. The FT algorithm has also been implemented in FLASH and we use this to study the effect that divots can have on the hot spot properties.

An installed nacelle design code using a multiblock Euler solver. Volume 1: Theory document

NASA Technical Reports Server (NTRS)

Chen, H. C.

1992-01-01

An efficient multiblock Euler design code was developed for designing a nacelle installed on geometrically complex airplane configurations. This approach employed a design driver based on a direct iterative surface curvature method developed at LaRC. A general multiblock Euler flow solver was used for computing flow around complex geometries. The flow solver used a finite-volume formulation with explicit time-stepping to solve the Euler Equations. It used a multiblock version of the multigrid method to accelerate the convergence of the calculations. The design driver successively updated the surface geometry to reduce the difference between the computed and target pressure distributions. In the flow solver, the change in surface geometry was simulated by applying surface transpiration boundary conditions to avoid repeated grid generation during design iterations. Smoothness of the designed surface was ensured by alternate application of streamwise and circumferential smoothings. The capability and efficiency of the code was demonstrated through the design of both an isolated nacelle and an installed nacelle at various flow conditions. Information on the execution of the computer program is provided in volume 2.

Extension of the Time-Spectral Approach to Overset Solvers for Arbitrary Motion

NASA Technical Reports Server (NTRS)

Leffell, Joshua Isaac; Murman, Scott M.; Pulliam, Thomas H.

2012-01-01

Forced periodic flows arise in a broad range of aerodynamic applications such as rotorcraft, turbomachinery, and flapping wing configurations. Standard practice involves solving the unsteady flow equations forward in time until the initial transient exits the domain and a statistically stationary flow is achieved. It is often required to simulate through several periods to remove the initial transient making unsteady design optimization prohibitively expensive for most realistic problems. An effort to reduce the computational cost of these calculations led to the development of the Harmonic Balance method [1, 2] which capitalizes on the periodic nature of the solution. The approach exploits the fact that forced temporally periodic flow, while varying in the time domain, is invariant in the frequency domain. Expanding the temporal variation at each spatial node into a Fourier series transforms the unsteady governing equations into a steady set of equations in integer harmonics that can be tackled with the acceleration techniques afforded to steady-state flow solvers. Other similar approaches, such as the Nonlinear Frequency Domain [3,4,5], Reduced Frequency [6] and Time-Spectral [7, 8, 9] methods, were developed shortly thereafter. Additionally, adjoint-based optimization techniques can be applied [10, 11] as well as frequency-adaptive methods [12, 13, 14] to provide even more flexibility to the method. The Fourier temporal basis functions imply spectral convergence as the number of harmonic modes, and correspondingly number of time samples, N, is increased. Some elect to solve the equations in the frequency domain directly, while others choose to transform the equations back into the time domain to simplify the process of adding this capability to existing solvers, but each harnesses the underlying steady solution in the frequency domain. These temporal projection methods will herein be collectively referred to as Time-Spectral methods. Time-Spectral methods have

Association of Nodal Metastasis and Mortality With Vermilion vs Cutaneous Lip Location in Cutaneous Squamous Cell Carcinoma of the Lip.

PubMed

Wang, David M; Kraft, Stefan; Rohani, Pooyan; Murphy, George F; Besaw, Robert J; Karia, Pritesh S; Morgan, Frederick C; Schmults, Chrysalyne D

2018-06-01

Although the lip is considered a high-risk location in cutaneous squamous cell carcinoma (cSCC), it has not been established whether this risk stems from vermilion or cutaneous locations or both. To compare differences in risks of recurrence, metastasis, and death from cSCCs on the vermilion vs cutaneous lip. Retrospective cohort study of 303 patients with 310 primary cSCCs of the lip (138 cutaneous, 172 vermilion) diagnosed between 2000 and 2015 at 2 academic tertiary care centers in Boston, Massachusetts. Development of local recurrence, nodal metastasis, distant metastasis, disease-specific death, and all-cause death. Of the 303 study participants with 310 SCCs of the lip, 153 (50.5%) were men, and 150 (49.5%) were women; median age at diagnosis, 68 years (range, 27-93 years). Outcomes were as follows for vermilion vs cutaneous locations: local recurrence, 6.4% (11 of 172) vs 2.9% (4 of 138); nodal metastasis, 7.6% (13 of 172) vs 1.5% (2 of 138); distant metastasis, 0.6% (1 of 172) vs 0.7% (1 of 138); disease-specific death, 3.5% (6 of 172) vs 2.9% (4 of 138); and all-cause death, 26.7% (46 of 172) vs 29.0% (40 of 138). The difference was statistically significant for nodal metastasis (P = .01). In multivariable analysis, nodal metastasis was associated with vermilion lip location (subhazard ratio, 5.0; 95% CI, 1.1-23.8) and invasion beyond fat (fascia or beyond for vermilion lip) (subhazard ratio, 4.4; 95% CI, 1.3-14.9). The risk of nodal metastasis is 5-fold greater for cSCCs on the vermilion lip compared with those on the cutaneous lip. Squamous cell carcinomas of the cutaneous lip have a nodal metastasis risk similar to cSCCs in general (1.5%). Thus, vermilion involvement appears responsible for the increased risk associated with cSCC of lip. Vermilion involvement may merit radiologic nodal staging and inclusion in future tumor staging, since it was independently associated with higher-risk cSCC of the lip region.

Optical solver for a system of ordinary differential equations based on an external feedback assisted microring resonator.

PubMed

Hou, Jie; Dong, Jianji; Zhang, Xinliang

2017-06-15

Systems of ordinary differential equations (SODEs) are crucial for describing the dynamic behaviors in various systems such as modern control systems which require observability and controllability. In this Letter, we propose and experimentally demonstrate an all-optical SODE solver based on the silicon-on-insulator platform. We use an add/drop microring resonator to construct two different ordinary differential equations (ODEs) and then introduce two external feedback waveguides to realize the coupling between these ODEs, thus forming the SODE solver. A temporal coupled mode theory is used to deduce the expression of the SODE. A system experiment is carried out for further demonstration. For the input 10 GHz NRZ-like pulses, the measured output waveforms of the SODE solver agree well with the calculated results.

Object-Oriented Design for Sparse Direct Solvers

NASA Technical Reports Server (NTRS)

Dobrian, Florin; Kumfert, Gary; Pothen, Alex

1999-01-01

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

Left-right asymmetry in the level of active Nodal protein produced in the node is translated into left-right asymmetry in the lateral plate of mouse embryos.

PubMed

Kawasumi, Aiko; Nakamura, Tetsuya; Iwai, Naomi; Yashiro, Kenta; Saijoh, Yukio; Belo, Jose Antonio; Shiratori, Hidetaka; Hamada, Hiroshi

2011-05-15

Left-right (L-R) asymmetry in the mouse embryo is generated in the node and is dependent on cilia-driven fluid flow, but how the initial asymmetry is transmitted from the node to the lateral plate has remained unknown. We have now identified a transcriptional enhancer (ANE) in the human LEFTY1 gene that exhibits marked L>R asymmetric activity in perinodal cells of the mouse embryo. Dissection of ANE revealed that it is activated in the perinodal cells on the left side by Nodal signaling, suggesting that Nodal activity in the node is asymmetric at a time when Nodal expression is symmetric. Phosphorylated Smad2/3 (pSmad2) indeed manifested an L-R asymmetric distribution at the node, being detected in perinodal cells preferentially on the left side. This asymmetry in pSmad2 distribution was found to be generated not by unidirectional transport of Nodal but rather as a result of LNodal antagonist Cerl2. For various mutant embryos examined, the asymmetry in pSmad2 distribution among the perinodal cells closely matched that in lateral plate mesoderm (LPM). However, autocrine-paracrine Nodal signaling in perinodal cells is dispensable for L-R patterning of LPM, given that its inhibition by expression of dominant negative forms of Smad3 or ALK4 was still associated with normal (left-sided) Nodal expression in LPM. Our results suggest that LPM is the direct target of Nodal secreted by the perinodal cells, and that an L>R distribution of active Nodal in the node is translated into the asymmetry in LPM. Copyright © 2011 Elsevier Inc. All rights reserved.

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.

Predicting the nodal status in gastric cancers: The role of apparent diffusion coefficient histogram characteristic analysis.

PubMed

Liu, Song; Zhang, Yujuan; Xia, Jie; Chen, Ling; Guan, Wenxian; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang

2017-10-01

To explore the application of histogram analysis in preoperative T and N staging of gastric cancers, with a focus on characteristic parameters of apparent diffusion coefficient (ADC) maps. Eighty-seven patients with gastric cancers underwent diffusion weighted magnetic resonance imaging (b=0, 1000s/mm 2 ), which generated ADC maps. Whole-volume histogram analysis was performed on ADC maps and 7 characteristic parameters were obtained. All those patients underwent surgery and postoperative pathologic T and N stages were determined. Four parameters, including skew, kurtosis, s-sD av and sample number, showed significant differences among gastric cancers at different T and N stages. Most parameters correlated with T and N stages significantly and worked in differentiating gastric cancers at different T or N stages. Especially skew yielded a sensitivity of 0.758, a specificity of 0.810, and an area under the curve (AUC) of 0.802 for differentiating gastric cancers with and without lymph node metastasis (P<0.001). All the parameters, except AUC low , showed good or excellent inter-observer agreement with intra-class correlation coefficients ranging from 0.710 to 0.991. Characteristic parameters derived from whole-volume ADC histogram analysis could help assessing preoperative T and N stages of gastric cancers. Copyright © 2017. Published by Elsevier Inc.

A LAGRANGIAN GAUSS-NEWTON-KRYLOV SOLVER FOR MASS- AND INTENSITY-PRESERVING DIFFEOMORPHIC IMAGE REGISTRATION.

PubMed

Mang, Andreas; Ruthotto, Lars

2017-01-01

We present an efficient solver for diffeomorphic image registration problems in the framework of Large Deformations Diffeomorphic Metric Mappings (LDDMM). We use an optimal control formulation, in which the velocity field of a hyperbolic PDE needs to be found such that the distance between the final state of the system (the transformed/transported template image) and the observation (the reference image) is minimized. Our solver supports both stationary and non-stationary (i.e., transient or time-dependent) velocity fields. As transformation models, we consider both the transport equation (assuming intensities are preserved during the deformation) and the continuity equation (assuming mass-preservation). We consider the reduced form of the optimal control problem and solve the resulting unconstrained optimization problem using a discretize-then-optimize approach. A key contribution is the elimination of the PDE constraint using a Lagrangian hyperbolic PDE solver. Lagrangian methods rely on the concept of characteristic curves. We approximate these curves using a fourth-order Runge-Kutta method. We also present an efficient algorithm for computing the derivatives of the final state of the system with respect to the velocity field. This allows us to use fast Gauss-Newton based methods. We present quickly converging iterative linear solvers using spectral preconditioners that render the overall optimization efficient and scalable. Our method is embedded into the image registration framework FAIR and, thus, supports the most commonly used similarity measures and regularization functionals. We demonstrate the potential of our new approach using several synthetic and real world test problems with up to 14.7 million degrees of freedom.

Coexistence of tunable Weyl points and topological nodal lines in ternary transition-metal telluride TaIrT e4

NASA Astrophysics Data System (ADS)

Zhou, Xiaoqing; Liu, Qihang; Wu, QuanSheng; Nummy, Tom; Li, Haoxiang; Griffith, Justin; Parham, Stephen; Waugh, Justin; Emmanouilidou, Eve; Shen, Bing; Yazyev, Oleg V.; Ni, Ni; Dessau, Daniel

2018-06-01

We report a combined theoretical and experimental study on TaIrT e4 , a potential candidate for a minimal model of type-II Weyl semimetals. Unexpectedly, an intriguing node structure with 12 Weyl points and a pair of nodal lines protected by mirror symmetry was found by first-principles calculations. Some signatures of the complex electronic structure, such as topologically nontrivial band crossings and topologically trivial Fermi arcs, are cross-validated by angle-resolved photoemission spectroscopy. Through external strain, the number of Weyl points can be reduced to a theoretical minimum of four, and the appearance of the nodal lines can be switched between different mirror planes in momentum space. The coexistence of switchable Weyl points and nodal lines establishes transition-metal chalcogenides as a unique test ground for topological state characterization and engineering.

Potential clinical value of PET/CT in predicting occult nodal metastasis in T1-T2N0M0 lung cancer patients staged by PET/CT

PubMed Central

Zhou, Xiang; Chen, Ruohua; Huang, Gang; Liu, Jianjun

2017-01-01

We assessed the clinical value of 2-fluoro-2-deoxyglucose (18F-FDG) PET/CT imaging for predicting occult nodal metastasis in non-small cell lung cancer (NSCLC) patients. This retrospective study included 54 patients with T1-2N0M0 NSCLC who had undergone 18F-FDG PET/CT before surgery. Occult nodal metastasis was detected in 25.9% (14/54) of the patients. Immunohistochemical analysis revealed that increased glucose transporter 1 expression was associated with occult nodal metastasis, but hexokinase 2 expression was not. Compared to the negative nodal metastasis group, the positive nodal metastasis group was associated with increased maximum standardized uptake value (SUVmax) and tumor size. Multivariate analysis indicated that SUVmax and tumor size were associated with nodal metastasis. Nodal metastasis could be predicted with a sensitivity of 92.9% and a specificity of 55.0% when the SUVmax cutoff was 4.35. When patients were divided into low-risk (tumor size ≤ 2.5 cm and SUVmax ≤ 4.35), moderate-risk (tumor size ≤ 2.5 cm and SUVmax > 4.35 or tumor size > 2.5 cm and SUVmax ≤ 4.35) and high-risk (tumor size > 2.5 cm and SUVmax > 4.35) groups, the lymph node metastasis rates were 4.3%, 22.7%, and 88.9%, respectively. These results indicate that the combination of SUVmax and tumor size has potential clinical value for predicting occult nodal metastasis in NSCLC patients. PMID:29137276

From nodal-ring topological superfluids to spiral Majorana modes in cold atomic systems

NASA Astrophysics Data System (ADS)

He, Wen-Yu; Xu, Dong-Hui; Zhou, Benjamin T.; Zhou, Qi; Law, K. T.

2018-04-01

In this work, we consider a three-dimensional (3D) cubic optical lattice composed of coupled 1D wires with 1D spin-orbit coupling. When the s -wave pairing is induced through Feshbach resonance, the system becomes a topological superfluid with ring nodes, which are the ring nodal degeneracies in the bulk, and supports a large number of surface Majorana zero-energy modes. The large number of surface Majorana modes remain at zero energy even in the presence of disorder due to the protection from a chiral symmetry. When the chiral symmetry is broken, the system becomes a Weyl topological superfluid with Majorana arcs. With 3D spin-orbit coupling, the Weyl superfluid becomes a gapless phase with spiral Majorana modes on the surface. A spatial-resolved radio-frequency spectroscopy is suggested to detect this nodal-ring topological superfluid phase.

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.

Extranodal involvement of diffuse large B-cell lymphoma in the head and neck: An indicator of good prognosis.

PubMed

Lee, Doh Young; Kang, Karam; Jung, Hwaejoon; Park, Young Min; Cho, Jae-Gu; Baek, Seung-Kuk; Kwon, Soon-Young; Jung, Kwang-Yoon; Woo, Jeong-Soo

2018-05-31

In this study, we analyzed clinicopathological characteristics and survival outcomes according to extranodal involvement of diffuse large B-cell lymphoma (DLBCL) in the head and neck. A retrospective analysis was conducted on 110 patients from 2004 to 2014 with CD20-positive DLBCL involving the head and neck area. Patients were categorized into two groups, extranodal and nodal, according to involvement of extranodal sites in the head and neck. Outcome measurements for the groups included clinical response to treatment and recurrence rates. Palatine tonsils were the most frequently involved extranodal site in the head and neck (29.1%). Among clinicopathological parameters, proportion of patients with lactate dehydrogenase over 350 IU/L (p=0.033), cell of origin (p<0.001), and treatment outcomes (p=0.007) were significantly different between the two groups. Among cell origin markers CD10, Bcl6, and MUM1, MUM1 was significantly correlated with extranodal involvement (p=0.029). Recurrence rates were similar between groups, while disease-specific survival was significantly higher in the extranodal group (p=0.011). Disease-specific survival of the extranodal group was also higher than the nodal group with extranodal involvement of other body sites (p=0.010). Among patients with negative expression of CD10 (p=0.015), Bcl6 (p=0.018), and MUM1 (p=0.005), survival was longer in the extranodal than the nodal group. DLBCL patients with extranodal involvement of the head and neck may have longer survival outcomes than patients with solely nodal involvement. Increased survival may be more prominent in patients with negative expression of CD10, Bcl6, and MUM1. Copyright © 2018 Elsevier B.V. All rights reserved.

From cluster structures to nuclear molecules: The role of nodal structure of the single-particle wave functions

NASA Astrophysics Data System (ADS)

Afanasjev, A. V.; Abusara, H.

2018-02-01

The nodal structure of the density distributions of the single-particle states occupied in rod-shaped, hyper- and megadeformed structures of nonrotating and rotating N ˜Z nuclei has been investigated in detail. The single-particle states with the Nilsson quantum numbers of the [N N 0 ]1 /2 (with N from 0 to 5) and [N ,N -1 ,1 ]Ω (with N from 1 to 3 and Ω =1 /2 , 3/2) types are considered. These states are building blocks of extremely deformed shapes in the nuclei with mass numbers A ≤50 . Because of (near) axial symmetry and large elongation of such structures, the wave functions of the single-particle states occupied are dominated by a single basis state in cylindrical basis. This basis state defines the nodal structure of the single-particle density distribution. The nodal structure of the single-particle density distributions allows us to understand in a relatively simple way the necessary conditions for α clusterization and the suppression of the α clusterization with the increase of mass number. It also explains in a natural way the coexistence of ellipsoidal mean-field-type structures and nuclear molecules at similar excitation energies and the features of particle-hole excitations connecting these two types of the structures. Our analysis of the nodal structure of the single-particle density distributions does not support the existence of quantum liquid phase for the deformations and nuclei under study.

Identification of nodal tissue in the living heart using rapid scanning fiber-optics confocal microscopy and extracellular fluorophores.

PubMed

Huang, Chao; Kaza, Aditya K; Hitchcock, Robert W; Sachse, Frank B

2013-09-01

Risks associated with pediatric reconstructive heart surgery include injury of the sinoatrial node (SAN) and atrioventricular node (AVN), requiring cardiac rhythm management using implantable pacemakers. These injuries are the result of difficulties in identifying nodal tissues intraoperatively. Here we describe an approach based on confocal microscopy and extracellular fluorophores to quantify tissue microstructure and identify nodal tissue. Using conventional 3-dimensional confocal microscopy we investigated the microstructural arrangement of SAN, AVN, and atrial working myocardium (AWM) in fixed rat heart. AWM exhibited a regular striated arrangement of the extracellular space. In contrast, SAN and AVN had an irregular, reticulated arrangement. AWM, SAN, and AVN tissues were beneath a thin surface layer of tissue that did not obstruct confocal microscopic imaging. Subsequently, we imaged tissues in living rat hearts with real-time fiber-optics confocal microscopy. Fiber-optics confocal microscopy images resembled images acquired with conventional confocal microscopy. We investigated spatial regularity of tissue microstructure from Fourier analysis and second-order image moments. Fourier analysis of fiber-optics confocal microscopy images showed that the spatial regularity of AWM was greater than that of nodal tissues (37.5 ± 5.0% versus 24.3 ± 3.9% for SAN and 23.8 ± 3.7% for AVN; P<0.05). Similar differences of spatial regularities were revealed from second-order image moments (50.0 ± 7.3% for AWM versus 29.3 ± 6.7% for SAN and 27.3 ± 5.5% for AVN; P<0.05). The study demonstrates feasibility of identifying nodal tissue in living heart using extracellular fluorophores and fiber-optics confocal microscopy. Application of the approach in pediatric reconstructive heart surgery may reduce risks of injuring nodal tissues.

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…

Radiofrequency ablation versus cryoablation for atrioventricular nodal re-entrant tachycardia in children: a value comparison.

PubMed

Oster, Matthew E; Yang, Zhou; Stewart-Huey, Kay; Glanville, Michelle; Porter, Arlene; Campbell, Robert; Webb, Brad; Strieper, Margaret

2017-03-01

It is unclear whether cryoablation or radiofrequency ablation offers better value for treating atrioventricular nodal re-entrant tachycardia in children. We aimed to compare the value of these procedures for treating atrioventricular nodal re-entrant tachycardia in children, with value being outcomes relative to costs. We performed a retrospective cohort study of all atrioventricular nodal re-entrant tachycardia ablations for children (age⩽18 years) from July, 2009 to June, 2011 at our institution. Costs included fixed costs, miscellaneous hospital costs, and labour costs, and key outcomes were acute and long-term success (6 months) of the ablations. We conducted T-tests and regression analyses to investigate the associations between the ablation procedure type and the cost and success of the ablations. Of 96 unique cases performed by three paediatric electrophysiologists, 48 were cryoablation only, 42 radiofrequency ablation only, and six were a combination. Acute success was 100% for the cryoablation only and radiofrequency ablation only cases and 83% for the combination cases. There were no notable adverse events. The average total cost was $9636 for cryoablation cases, $9708 for radiofrequency ablation cases, and $10,967 for combination cases (p=0.51 for cryoablation only versus radiofrequency ablation only). The long-term success rate was 79.1% for cryoablation only, 92.8% for radiofrequency ablation only, and 66.7% for the combination (p=0.01 for cryoablation only versus radiofrequency ablation only), but long-term success varied notably by provider. Cryoablation and radiofrequency ablation offer similar value in the short term for the treatment of atrioventricular nodal re-entrant tachycardia in children. Differences in long-term success may vary substantially by physician, and thus may lead to differences in long-term value.

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

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

Nodal aberration theory applied to freeform surfaces

NASA Astrophysics Data System (ADS)

Fuerschbach, Kyle; Rolland, Jannick P.; Thompson, Kevin P.

2014-12-01

When new three-dimensional packages are developed for imaging optical systems, the rotational symmetry of the optical system is often broken, changing its imaging behavior and making the optical performance worse. A method to restore the performance is to use freeform optical surfaces that compensate directly the aberrations introduced from tilting and decentering the optical surfaces. In order to effectively optimize the shape of a freeform surface to restore optical functionality, it is helpful to understand the aberration effect the surface may induce. Using nodal aberration theory the aberration fields induced by a freeform surface in an optical system are explored. These theoretical predications are experimentally validated with the design and implementation of an aberration generating telescope.

Study of the adaptive refinement on an open source 2D shallow-water flow solver using quadtree grid for flash flood simulations.

NASA Astrophysics Data System (ADS)

Kirstetter, G.; Popinet, S.; Fullana, J. M.; Lagrée, P. Y.; Josserand, C.

2015-12-01

The full resolution of shallow-water equations for modeling flash floods may have a high computational cost, so that majority of flood simulation softwares used for flood forecasting uses a simplification of this model : 1D approximations, diffusive or kinematic wave approximations or exotic models using non-physical free parameters. These kind of approximations permit to save a lot of computational time by sacrificing in an unquantified way the precision of simulations. To reduce drastically the cost of such 2D simulations by quantifying the lost of precision, we propose a 2D shallow-water flow solver built with the open source code Basilisk1, which is using adaptive refinement on a quadtree grid. This solver uses a well-balanced central-upwind scheme, which is at second order in time and space, and treats the friction and rain terms implicitly in finite volume approach. We demonstrate the validity of our simulation on the case of the flood of Tewkesbury (UK) occurred in July 2007, as shown on Fig. 1. On this case, a systematic study of the impact of the chosen criterium for adaptive refinement is performed. The criterium which has the best computational time / precision ratio is proposed. Finally, we present the power law giving the computational time in respect to the maximum resolution and we show that this law for our 2D simulation is close to the one of 1D simulation, thanks to the fractal dimension of the topography. [1] http://basilisk.fr/

Conducting Automated Test Assembly Using the Premium Solver Platform Version 7.0 with Microsoft Excel and the Large-Scale LP/QP Solver Engine Add-In

ERIC Educational Resources Information Center

Cor, Ken; Alves, Cecilia; Gierl, Mark J.

2008-01-01

This review describes and evaluates a software add-in created by Frontline Systems, Inc., that can be used with Microsoft Excel 2007 to solve large, complex test assembly problems. The combination of Microsoft Excel 2007 with the Frontline Systems Premium Solver Platform is significant because Microsoft Excel is the most commonly used spreadsheet…

Aircraft High-Lift Aerodynamic Analysis Using a Surface-Vorticity Solver

NASA Technical Reports Server (NTRS)

Olson, Erik D.; Albertson, Cindy W.

2016-01-01

This study extends an existing semi-empirical approach to high-lift analysis by examining its effectiveness for use with a three-dimensional aerodynamic analysis method. The aircraft high-lift geometry is modeled in Vehicle Sketch Pad (OpenVSP) using a newly-developed set of techniques for building a three-dimensional model of the high-lift geometry, and for controlling flap deflections using scripted parameter linking. Analysis of the low-speed aerodynamics is performed in FlightStream, a novel surface-vorticity solver that is expected to be substantially more robust and stable compared to pressure-based potential-flow solvers and less sensitive to surface perturbations. The calculated lift curve and drag polar are modified by an empirical lift-effectiveness factor that takes into account the effects of viscosity that are not captured in the potential-flow solution. Analysis results are validated against wind-tunnel data for The Energy-Efficient Transport AR12 low-speed wind-tunnel model, a 12-foot, full-span aircraft configuration with a supercritical wing, full-span slats, and part-span double-slotted flaps.

Canine nodal marginal zone lymphoma: Descriptive insight into the biological behaviour.

PubMed

Cozzi, M; Marconato, L; Martini, V; Aresu, L; Riondato, F; Rossi, F; Stefanello, D; Comazzi, S

2018-06-01

Canine nodal marginal zone lymphoma (nMZL) is classified as an indolent lymphoma. Such lymphomas are typified by low mitotic rate and slow clinical progression. While the clinical behaviour of canine splenic MZL has been described, characterized by an indolent course and a good prognosis following splenectomy, there are no studies specifically describing nMZL. The aim of this study was to describe the clinical features of and outcome for canine nMZL. Dogs with histologically confirmed nMZL undergoing a complete staging work-up (including blood analysis, flow cytometry [FC] on lymph node [LN], peripheral blood and bone marrow, imaging, histology and immunohistochemistry on a surgically removed peripheral LN) were retrospectively enrolled. Treatment consisted of chemotherapy or chemo-immunotherapy. Endpoints were response rate (RR), time to progression (TTP) and lymphoma-specific survival (LSS). A total of 35 cases were enrolled. At diagnosis, all dogs showed generalized lymphadenopathy. One-third was systemically unwell. All dogs had stage V disease; one-third also had extranodal involvement. The LN population was mainly composed of medium-sized CD21+ cells with scant resident normal lymphocytes. Histology revealed diffuse LN involvement, referring to "late-stage" MZL. Median TTP and LSS were 149 and 259 days, respectively. Increased LDH activity and substage b were significantly associated with a shorter LSS. Dogs with nMZL may show generalized lymphadenopathy and an advanced disease stage. Overall, the outcome is poor, despite the "indolent" designation. The best treatment option still needs to be defined. © 2017 John Wiley & Sons Ltd.

Identification of lesion and nodal resistance in pea (Pisum sativum L.) to Sclerotinia sclerotiorum using genome-wide association studies and RNA-Seq

USDA-ARS?s Scientific Manuscript database

Nodal resistance in plants is a phenomenon where a fungal infection is prevented from passing through a node and the infection is limited to an internode region. Nodal resistance has been observed in some pathosystems such as the pea (Pisum sativum L.)-white mold (WM) (Sclerotinia sclerotiorum (Lib....

An Optimized Multicolor Point-Implicit Solver for Unstructured Grid Applications on Graphics Processing Units

NASA Technical Reports Server (NTRS)

Zubair, Mohammad; Nielsen, Eric; Luitjens, Justin; Hammond, Dana

2016-01-01

In the field of computational fluid dynamics, the Navier-Stokes equations are often solved using an unstructuredgrid approach to accommodate geometric complexity. Implicit solution methodologies for such spatial discretizations generally require frequent solution of large tightly-coupled systems of block-sparse linear equations. The multicolor point-implicit solver used in the current work typically requires a significant fraction of the overall application run time. In this work, an efficient implementation of the solver for graphics processing units is proposed. Several factors present unique challenges to achieving an efficient implementation in this environment. These include the variable amount of parallelism available in different kernel calls, indirect memory access patterns, low arithmetic intensity, and the requirement to support variable block sizes. In this work, the solver is reformulated to use standard sparse and dense Basic Linear Algebra Subprograms (BLAS) functions. However, numerical experiments show that the performance of the BLAS functions available in existing CUDA libraries is suboptimal for matrices representative of those encountered in actual simulations. Instead, optimized versions of these functions are developed. Depending on block size, the new implementations show performance gains of up to 7x over the existing CUDA library functions.

An Efficient Multicore Implementation of a Novel HSS-Structured Multifrontal Solver Using Randomized Sampling

DOE PAGES

Ghysels, Pieter; Li, Xiaoye S.; Rouet, Francois -Henry; ...

2016-10-27

Here, we present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which have low-rank off-diagonal blocks, to approximate the frontal matrices. For HSS matrix construction, a randomized sampling algorithm is used together with interpolative decompositions. The combination of the randomized compression with a fast ULV HSS factoriz ation leads to a solver with lower computational complexity than the standard multifrontal method for many applications, resulting in speedups up to 7 fold for problems in our test suite.more » The implementation targets many-core systems by using task parallelism with dynamic runtime scheduling. Numerical experiments show performance improvements over state-of-the-art sparse direct solvers. The implementation achieves high performance and good scalability on a range of modern shared memory parallel systems, including the Intel Xeon Phi (MIC). The code is part of a software package called STRUMPACK - STRUctured Matrices PACKage, which also has a distributed memory component for dense rank-structured matrices.« less

Shallow-water sloshing in a moving vessel with variable cross-section and wetting-drying using an extension of George's well-balanced finite volume solver

NASA Astrophysics Data System (ADS)

Alemi Ardakani, Hamid; Bridges, Thomas J.; Turner, Matthew R.

2016-06-01

A class of augmented approximate Riemann solvers due to George (2008) [12] is extended to solve the shallow-water equations in a moving vessel with variable bottom topography and variable cross-section with wetting and drying. A class of Roe-type upwind solvers for the system of balance laws is derived which respects the steady-state solutions. The numerical solutions of the new adapted augmented f-wave solvers are validated against the Roe-type solvers. The theory is extended to solve the shallow-water flows in moving vessels with arbitrary cross-section with influx-efflux boundary conditions motivated by the shallow-water sloshing in the ocean wave energy converter (WEC) proposed by Offshore Wave Energy Ltd. (OWEL) [1]. A fractional step approach is used to handle the time-dependent forcing functions. The numerical solutions are compared to an extended new Roe-type solver for the system of balance laws with a time-dependent source function. The shallow-water sloshing finite volume solver can be coupled to a Runge-Kutta integrator for the vessel motion.

Pelvic Nodal Dosing With Registration to the Prostate: Implications for High-Risk Prostate Cancer Patients Receiving Stereotactic Body Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kishan, Amar U., E-mail: aukishan@mednet.ucla.edu; Lamb, James M.; Jani, Shyam S.

2015-03-15

Purpose: To determine whether image guidance with rigid registration (RR) to intraprostatic markers (IPMs) yields acceptable coverage of the pelvic lymph nodes in the context of a stereotactic body radiation therapy (SBRT) regimen. Methods and Materials: Four to seven kilovoltage cone-beam CTs (CBCTs) from 12 patients with high-risk prostate cancer were analyzed, allowing approximation of an SBRT regimen. The nodal clinical target volume (CTV{sub N}) and bladder were contoured on all kilovoltage CBCTs. The V{sub 100} CTV{sub N}, expressed as a ratio to the same parameter on the initial plan, and the magnitude of translational shift between RR to themore » IPMs versus RR to the pelvic bones, were computed. The ability of a multimodality bladder filling protocol to minimize bladder height variation was assessed in a separate cohort of 4 patients. Results: Sixty-five CBCTs were assessed. The average V{sub 100} CTV{sub N} was 92.6%, but for a subset of 3 patients the average was 80.0%, compared with 97.8% for the others (P<.0001). The average overall and superior–inferior axis magnitudes of the bony-to-fiducial translations were significantly larger in the subgroup with suboptimal nodal coverage (8.1 vs 3.9 mm and 5.8 vs 2.4 mm, respectively; P<.0001). Relative bladder height changes were also significantly larger in the subgroup with suboptimal nodal coverage (42.9% vs 18.5%; P<.05). Use of a multimodality bladder-filling protocol minimized bladder height variation (P<.001). Conclusion: A majority of patients had acceptable nodal coverage after RR to IPMs, even when approximating SBRT. However, a subset of patients had suboptimal nodal coverage. These patients had large bony-to-fiducial translations and large variations in bladder height. Nodal coverage should be excellent if the superior–inferior axis bony-to-fiducial translation and the relative bladder height change (both easily measured on CBCT) are kept to a minimum. Implementation of a strict bladder

Differential membranous E-cadherin expression, cell proliferation and O-GlcNAcylation between primary and metastatic nodal lesion in colorectal cancer.

PubMed

Jang, Tae Jung

2016-02-01

O-GlcNAcylation is an O-linked β-N-acetylglucosamine (O-GlcNAc) moiety linked to the side chain hydroxyl of a serine or threonine residue. The E-cadherin/β-catenin system, an integral component of epithelial to mesenchymal transition (EMT)/mesenchymal to epithelial transition (MET), is affected through O-GlcNAcylation. The current study examined the status of EMT/MET in both the tumor center and invasive front of the primary colorectal carcinoma (CRC) and metastatic nodal lesions, which were compared to O-GlcNAcylation expression levels in those areas. In addition, the cliniopathological significance of O-GlcNAcylation was studied Immunohistochemical staining for E-cadherin, β-catenin, Snail, O-GlcNAc and Ki67 was performed in 40 primary CRC tissues, 40 nonneoplastic colons, and 17 nodal metastatic lesions. Western blot was also conducted in primary CRC tissue Membranous E-cadherin expression was lowest in the invasive front, but showed greater increases in metastatic nodal lesions. Moreover, its expression level was negatively correlated with that of nuclear β-catenin and Snail. The Ki67 labeling index (LI) was lowest in the invasive front, and increased in metastatic nodal lesions. Primary CRC showed higher expression of O-GlcNAcylation and O-GlcNAc-transferase (OGT) than nonneoplastic colons. O-GlcNAcylation expression decreased in metastatic nodal lesions compared to the invasive front and tumor center, and was inversely correlated with Ki67 LI. However, O-GlcNAcylation expression was only slightly changed between tumor center and invasive front. In addition, there was no correlation between its expression and the level of nuclear β-catenin, membranous E-cadherin and Snail. No significant relationship was observed between O-GlcNAcylation level and cliniopathological parameters. Differential membranous E-cadherin expression, cell proliferation and O-GlcNAcylation in metastatic nodal lesion compared to primary CRC may play role in establishing its lesions

Applying EXCEL Solver to a watershed management goal-programming problem

Treesearch

J. E. de Steiguer

2000-01-01

This article demonstrates the application of EXCEL® spreadsheet linear programming (LP) solver to a watershed management multiple use goal programming (GP) problem. The data used to demonstrate the application are from a published study for a watershed in northern Colorado. GP has been used by natural resource managers for many years. However, the GP solution by means...

Modeling of frequency-domain scalar wave equation with the average-derivative optimal scheme based on a multigrid-preconditioned iterative solver

NASA Astrophysics Data System (ADS)

Cao, Jian; Chen, Jing-Bo; Dai, Meng-Xue

2018-01-01

An efficient finite-difference frequency-domain modeling of seismic wave propagation relies on the discrete schemes and appropriate solving methods. The average-derivative optimal scheme for the scalar wave modeling is advantageous in terms of the storage saving for the system of linear equations and the flexibility for arbitrary directional sampling intervals. However, using a LU-decomposition-based direct solver to solve its resulting system of linear equations is very costly for both memory and computational requirements. To address this issue, we consider establishing a multigrid-preconditioned BI-CGSTAB iterative solver fit for the average-derivative optimal scheme. The choice of preconditioning matrix and its corresponding multigrid components is made with the help of Fourier spectral analysis and local mode analysis, respectively, which is important for the convergence. Furthermore, we find that for the computation with unequal directional sampling interval, the anisotropic smoothing in the multigrid precondition may affect the convergence rate of this iterative solver. Successful numerical applications of this iterative solver for the homogenous and heterogeneous models in 2D and 3D are presented where the significant reduction of computer memory and the improvement of computational efficiency are demonstrated by comparison with the direct solver. In the numerical experiments, we also show that the unequal directional sampling interval will weaken the advantage of this multigrid-preconditioned iterative solver in the computing speed or, even worse, could reduce its accuracy in some cases, which implies the need for a reasonable control of directional sampling interval in the discretization.

Progress Toward Overset-Grid Moving Body Capability for USM3D Unstructured Flow Solver

NASA Technical Reports Server (NTRS)

Pandyna, Mohagna J.; Frink, Neal T.; Noack, Ralph W.

2005-01-01

A static and dynamic Chimera overset-grid capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. Modifications to the solver primarily consist of a few strategic calls to the Donor interpolation Receptor Transaction library (DiRTlib) to facilitate communication of solution information between various grids. The assembly of multiple overlapping grids into a single-zone composite grid is performed by the Structured, Unstructured and Generalized Grid AssembleR (SUGGAR) code. Several test cases are presented to verify the implementation, assess overset-grid solution accuracy and convergence relative to single-grid solutions, and demonstrate the prescribed relative grid motion capability.

TemperSAT: A new efficient fair-sampling random k-SAT solver

NASA Astrophysics Data System (ADS)

Fang, Chao; Zhu, Zheng; Katzgraber, Helmut G.

The set membership problem is of great importance to many applications and, in particular, database searches for target groups. Recently, an approach to speed up set membership searches based on the NP-hard constraint-satisfaction problem (random k-SAT) has been developed. However, the bottleneck of the approach lies in finding the solution to a large SAT formula efficiently and, in particular, a large number of independent solutions is needed to reduce the probability of false positives. Unfortunately, traditional random k-SAT solvers such as WalkSAT are biased when seeking solutions to the Boolean formulas. By porting parallel tempering Monte Carlo to the sampling of binary optimization problems, we introduce a new algorithm (TemperSAT) whose performance is comparable to current state-of-the-art SAT solvers for large k with the added benefit that theoretically it can find many independent solutions quickly. We illustrate our results by comparing to the currently fastest implementation of WalkSAT, WalkSATlm.

Parallel satellite orbital situational problems solver for space missions design and control

NASA Astrophysics Data System (ADS)

Atanassov, Atanas Marinov

2016-11-01

Solving different scientific problems for space applications demands implementation of observations, measurements or realization of active experiments during time intervals in which specific geometric and physical conditions are fulfilled. The solving of situational problems for determination of these time intervals when the satellite instruments work optimally is a very important part of all activities on every stage of preparation and realization of space missions. The elaboration of universal, flexible and robust approach for situation analysis, which is easily portable toward new satellite missions, is significant for reduction of missions' preparation times and costs. Every situation problem could be based on one or more situation conditions. Simultaneously solving different kinds of situation problems based on different number and types of situational conditions, each one of them satisfied on different segments of satellite orbit requires irregular calculations. Three formal approaches are presented. First one is related to situation problems description that allows achieving flexibility in situation problem assembling and presentation in computer memory. The second formal approach is connected with developing of situation problem solver organized as processor that executes specific code for every particular situational condition. The third formal approach is related to solver parallelization utilizing threads and dynamic scheduling based on "pool of threads" abstraction and ensures a good load balance. The developed situation problems solver is intended for incorporation in the frames of multi-physics multi-satellite space mission's design and simulation tools.

Intensity-Modulated Radiation Therapy for the Treatment of Squamous Cell Anal Cancer With Para-aortic Nodal Involvement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hodges, Joseph C.; Das, Prajnan, E-mail: PrajDas@mdanderson.or; Eng, Cathy

2009-11-01

Purpose: To determine the rates of toxicity, locoregional control, distant control, and survival in anal cancer patients with para-aortic nodal involvement, treated with intensity-modulated radiotherapy (IMRT) and concurrent chemotherapy at a single institution. Methods and Materials: Between 2001 and 2007, 6 patients with squamous cell anal cancer and para-aortic nodal involvement were treated with IMRT and concurrent infusional 5-fluorouracil and cisplatin. The primary tumor was treated with a median dose of 57.5 Gy (range, 54-60 Gy), involved para-aortic, pelvic, and inguinal lymph nodes were treated with a median dose of 55 Gy (range, 50.5-55 Gy), and noninvolved nodal regions weremore » treated with a median dose of 45 Gy (range, 43.5-45 Gy). Results: After a median follow-up of 25 months, none of the patients had a recurrence at the primary tumor, pelvic/inguinal nodes, or para-aortic nodes, whereas 2 patients developed distant metastases to the liver. Four of the 6 patients are alive. The 3-year actuarial locoregional control, distant control, and overall survival rates were 100%, 56%, and 63%, respectively. Four of the 6 patients developed Grade 3 acute gastrointestinal toxicity during chemoradiation. Conclusions: Intensity-modulated radiotherapy and concurrent chemotherapy could potentially serve as definitive therapy in anal cancer patients with para-aortic nodal involvement. Adjuvant chemotherapy may be indicated in these patients, as demonstrated by the distant failure rates. These patients need to be followed carefully because of the potential for treatment-related toxicities.« less

A Computational-Experimental Development of Vortex Generator Use for a Transitioning S-Diffuser

NASA Technical Reports Server (NTRS)

Wendt, Bruce J.; Dudek, Julianne C.

1996-01-01

The development of an effective design strategy for surface-mounted vortex generator arrays in a subsonic diffuser is described in this report. This strategy uses the strengths of both computational and experimental analyses to determine beneficial vortex generator locations and sizes. A parabolized Navier-Stokes solver, RNS3D, was used to establish proper placement of the vortex generators for reduction in circumferential total pressure distortion. Experimental measurements were used to determine proper vortex generator sizing to minimize total pressure recovery losses associated with vortex generator device drag. The best result achieved a 59% reduction in the distortion index DC60, with a 0.3% reduction in total pressure recovery.

An assessment of the adaptive unstructured tetrahedral grid, Euler Flow Solver Code FELISA

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Erickson, Larry L.

1994-01-01

A three-dimensional solution-adaptive Euler flow solver for unstructured tetrahedral meshes is assessed, and the accuracy and efficiency of the method for predicting sonic boom pressure signatures about simple generic models are demonstrated. Comparison of computational and wind tunnel data and enhancement of numerical solutions by means of grid adaptivity are discussed. The mesh generation is based on the advancing front technique. The FELISA code consists of two solvers, the Taylor-Galerkin and the Runge-Kutta-Galerkin schemes, both of which are spacially discretized by the usual Galerkin weighted residual finite-element methods but with different explicit time-marching schemes to steady state. The solution-adaptive grid procedure is based on either remeshing or mesh refinement techniques. An alternative geometry adaptive procedure is also incorporated.

Nodal-line dynamics via exact polynomial solutions for coherent waves traversing aberrated imaging systems.

PubMed

Paganin, David M; Beltran, Mario A; Petersen, Timothy C

2018-03-01

We obtain exact polynomial solutions for two-dimensional coherent complex scalar fields propagating through arbitrary aberrated shift-invariant linear imaging systems. These solutions are used to model nodal-line dynamics of coherent fields output by such systems.

LSRN: A PARALLEL ITERATIVE SOLVER FOR STRONGLY OVER- OR UNDERDETERMINED SYSTEMS*

PubMed Central

Meng, Xiangrui; Saunders, Michael A.; Mahoney, Michael W.

2014-01-01

We describe a parallel iterative least squares solver named LSRN that is based on random normal projection. LSRN computes the min-length solution to minx∈ℝn ‖Ax − b‖2, where A ∈ ℝm × n with m ≫ n or m ≪ n, and where A may be rank-deficient. Tikhonov regularization may also be included. Since A is involved only in matrix-matrix and matrix-vector multiplications, it can be a dense or sparse matrix or a linear operator, and LSRN automatically speeds up when A is sparse or a fast linear operator. The preconditioning phase consists of a random normal projection, which is embarrassingly parallel, and a singular value decomposition of size ⌈γ min(m, n)⌉ × min(m, n), where γ is moderately larger than 1, e.g., γ = 2. We prove that the preconditioned system is well-conditioned, with a strong concentration result on the extreme singular values, and hence that the number of iterations is fully predictable when we apply LSQR or the Chebyshev semi-iterative method. As we demonstrate, the Chebyshev method is particularly efficient for solving large problems on clusters with high communication cost. Numerical results show that on a shared-memory machine, LSRN is very competitive with LAPACK’s DGELSD and a fast randomized least squares solver called Blendenpik on large dense problems, and it outperforms the least squares solver from SuiteSparseQR on sparse problems without sparsity patterns that can be exploited to reduce fill-in. Further experiments show that LSRN scales well on an Amazon Elastic Compute Cloud cluster. PMID:25419094

The a(4) Scheme-A High Order Neutrally Stable CESE Solver

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung

2009-01-01

The CESE development is driven by a belief that a solver should (i) enforce conservation laws in both space and time, and (ii) be built from a nondissipative (i.e., neutrally stable) core scheme so that the numerical dissipation can be controlled effectively. To provide a solid foundation for a systematic CESE development of high order schemes, in this paper we describe a new high order (4-5th order) and neutrally stable CESE solver of a 1D advection equation with a constant advection speed a. The space-time stencil of this two-level explicit scheme is formed by one point at the upper time level and two points at the lower time level. Because it is associated with four independent mesh variables (the numerical analogues of the dependent variable and its first, second, and third-order spatial derivatives) and four equations per mesh point, the new scheme is referred to as the a(4) scheme. As in the case of other similar CESE neutrally stable solvers, the a(4) scheme enforces conservation laws in space-time locally and globally, and it has the basic, forward marching, and backward marching forms. Except for a singular case, these forms are equivalent and satisfy a space-time inversion (STI) invariant property which is shared by the advection equation. Based on the concept of STI invariance, a set of algebraic relations is developed and used to prove the a(4) scheme must be neutrally stable when it is stable. Numerically, it has been established that the scheme is stable if the value of the Courant number is less than 1/3

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.

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.

The Impact of the Size of Nodal Metastases on Recurrence Risk in Breast Cancer Patients With 1-3 Positive Axillary Nodes After Mastectomy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Eleanor E.R., E-mail: Eleanor.harris@moffitt.org; Freilich, Jessica; Lin, Hui-Yi

Purpose: Use of postmastectomy radiation therapy (PMRT) in breast cancer patients with 1-3 positive nodes is controversial. The objective of this study was to determine whether the size of nodal metastases in this subset could predict who would benefit from PMRT. Methods and Materials: We analyzed 250 breast cancer patients with 1-3 positive nodes after mastectomy treated with contemporary surgery and systemic therapy at our institution. Of these patients, 204 did not receive PMRT and 46 did receive PMRT. Local and regional recurrence risks were stratified by the size of the largest nodal metastasis measured as less than or equalmore » to 5 mm or greater than 5 mm. Results: The median follow-up was 65.6 months. In the whole group, regional recurrences occurred in 2% of patients in whom the largest nodal metastasis measured 5 mm or less vs 6% for those with metastases measuring greater than 5 mm. For non-irradiated patients only, regional recurrence rates were 2% and 9%, respectively. Those with a maximal nodal size greater than 5 mm had a significantly higher cumulative incidence of regional recurrence (P=.013). The 5-year cumulative incidence of a regional recurrence in the non-irradiated group was 2.7% (95% confidence interval [CI], 0.7%-7.2%) for maximal metastasis size of 5 mm or less, 6.9% (95% CI, 1.7%-17.3%) for metastasis size greater than 5 mm, and 16% (95% CI, 3.4%-36.8%) for metastasis size greater than 10 mm. The impact of the maximal nodal size on regional recurrences became insignificant in the multivariable model. Conclusions: In patients with 1-3 positive lymph nodes undergoing mastectomy without radiation, nodal metastasis greater than 5 mm was associated with regional recurrence after mastectomy, but its effect was modified by other factors (such as tumor stage). The size of the largest nodal metastasis may be useful to identify high-risk patients who may benefit from radiation therapy after mastectomy.« less

Constitutional rho-kinase regulates atrioventricular nodal conduction and ventricular repolarization of the canine heart.

PubMed

Sugiyama, Atsushi; Takahara, Akira; Yatomi, Yutaka; Satoh, Yoshioki; Nakamura, Yuji; Hashimoto, Keitaro

2003-06-01

Given the limited information, physiological roles of Rho-kinase in the cardiac conduction system and ventricular repolarization process were assessed in comparison with those in the coronary vascular tone. A specific Rho-kinase inhibitor Y-27632 was administered to the nutrient coronary artery of the canine isolated, blood-perfused atrioventricular node preparation under the monitoring of the ventricular monophasic action potentials. Administration of Y-27632 moderately suppressed the atrioventricular nodal conduction, slightly but significantly accelerated the repolarization process, and potently increased the coronary blood flow, whereas it hardly affected the intraventricular conduction. The estimated concentrations of Y-27632 causing the currently observed effects were enough to inhibit Rho-kinase. These results suggest that constitutional Rho-kinase functions to moderately facilitate the atrioventricular nodal conduction, slightly delay ventricular repolarization process, and significantly increase the coronary vascular tone.

The Maternal Maverick/GDF15-like TGF-β Ligand Panda Directs Dorsal-Ventral Axis Formation by Restricting Nodal Expression in the Sea Urchin Embryo.

PubMed

Haillot, Emmanuel; Molina, Maria Dolores; Lapraz, François; Lepage, Thierry

2015-01-01

Specification of the dorsal-ventral axis in the highly regulative sea urchin embryo critically relies on the zygotic expression of nodal, but whether maternal factors provide the initial spatial cue to orient this axis is not known. Although redox gradients have been proposed to entrain the dorsal-ventral axis by acting upstream of nodal, manipulating the activity of redox gradients only has modest consequences, suggesting that other factors are responsible for orienting nodal expression and defining the dorsal-ventral axis. Here we uncover the function of Panda, a maternally provided transforming growth factor beta (TGF-β) ligand that requires the activin receptor-like kinases (Alk) Alk3/6 and Alk1/2 receptors to break the radial symmetry of the embryo and orient the dorsal-ventral axis by restricting nodal expression. We found that the double inhibition of the bone morphogenetic protein (BMP) type I receptors Alk3/6 and Alk1/2 causes a phenotype dramatically more severe than the BMP2/4 loss-of-function phenotype, leading to extreme ventralization of the embryo through massive ectopic expression of nodal, suggesting that an unidentified signal acting through BMP type I receptors cooperates with BMP2/4 to restrict nodal expression. We identified this ligand as the product of maternal Panda mRNA. Double inactivation of panda and bmp2/4 led to extreme ventralization, mimicking the phenotype caused by inactivation of the two BMP receptors. Inhibition of maternal panda mRNA translation disrupted the early spatial restriction of nodal, leading to persistent massive ectopic expression of nodal on the dorsal side despite the presence of Lefty. Phylogenetic analysis indicates that Panda is not a prototypical BMP ligand but a member of a subfamily of TGF-β distantly related to Inhibins, Lefty, and TGF-β that includes Maverick from Drosophila and GDF15 from vertebrates. Indeed, overexpression of Panda does not appear to directly or strongly activate phosphoSmad1