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.

Full multi grid method for electric field computation in point-to-plane streamer discharge in air at atmospheric pressure

NASA Astrophysics Data System (ADS)

Kacem, S.; Eichwald, O.; Ducasse, O.; Renon, N.; Yousfi, M.; Charrada, K.

2012-01-01

Streamers dynamics are characterized by the fast propagation of ionized shock waves at the nanosecond scale under very sharp space charge variations. The streamer dynamics modelling needs the solution of charged particle transport equations coupled to the elliptic Poisson's equation. The latter has to be solved at each time step of the streamers evolution in order to follow the propagation of the resulting space charge electric field. In the present paper, a full multi grid (FMG) and a multi grid (MG) methods have been adapted to solve Poisson's equation for streamer discharge simulations between asymmetric electrodes. The validity of the FMG method for the computation of the potential field is first shown by performing direct comparisons with analytic solution of the Laplacian potential in the case of a point-to-plane geometry. The efficiency of the method is also compared with the classical successive over relaxation method (SOR) and MUltifrontal massively parallel solver (MUMPS). MG method is then applied in the case of the simulation of positive streamer propagation and its efficiency is evaluated from comparisons to SOR and MUMPS methods in the chosen point-to-plane configuration. Very good agreements are obtained between the three methods for all electro-hydrodynamics characteristics of the streamer during its propagation in the inter-electrode gap. However in the case of MG method, the computational time to solve the Poisson's equation is at least 2 times faster in our simulation conditions.

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

PubMed

Womack, James C; Anton, Lucian; Dziedzic, Jacek; Hasnip, Phil J; Probert, Matt I J; Skylaris, Chris-Kriton

2018-03-13

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10 9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.

An exterior Poisson solver using fast direct methods and boundary integral equations with applications to nonlinear potential flow

NASA Technical Reports Server (NTRS)

Young, D. P.; Woo, A. C.; Bussoletti, J. E.; Johnson, F. T.

1986-01-01

A general method is developed combining fast direct methods and boundary integral equation methods to solve Poisson's equation on irregular exterior regions. The method requires O(N log N) operations where N is the number of grid points. Error estimates are given that hold for regions with corners and other boundary irregularities. Computational results are given in the context of computational aerodynamics for a two-dimensional lifting airfoil. Solutions of boundary integral equations for lifting and nonlifting aerodynamic configurations using preconditioned conjugate gradient are examined for varying degrees of thinness.

An efficient three-dimensional Poisson solver for SIMD high-performance-computing architectures

NASA Technical Reports Server (NTRS)

Cohl, H.

1994-01-01

We present an algorithm that solves the three-dimensional Poisson equation on a cylindrical grid. The technique uses a finite-difference scheme with operator splitting. This splitting maps the banded structure of the operator matrix into a two-dimensional set of tridiagonal matrices, which are then solved in parallel. Our algorithm couples FFT techniques with the well-known ADI (Alternating Direction Implicit) method for solving Elliptic PDE's, and the implementation is extremely well suited for a massively parallel environment like the SIMD architecture of the MasPar MP-1. Due to the highly recursive nature of our problem, we believe that our method is highly efficient, as it avoids excessive interprocessor communication.

Research in computer science

NASA Technical Reports Server (NTRS)

Ortega, J. M.

1986-01-01

Various graduate research activities in the field of computer science are reported. Among the topics discussed are: (1) failure probabilities in multi-version software; (2) Gaussian Elimination on parallel computers; (3) three dimensional Poisson solvers on parallel/vector computers; (4) automated task decomposition for multiple robot arms; (5) multi-color incomplete cholesky conjugate gradient methods on the Cyber 205; and (6) parallel implementation of iterative methods for solving linear equations.

The Poisson-Boltzmann theory for the two-plates problem: some exact results.

PubMed

Xing, Xiang-Jun

2011-12-01

The general solution to the nonlinear Poisson-Boltzmann equation for two parallel charged plates, either inside a symmetric electrolyte, or inside a 2q:-q asymmetric electrolyte, is found in terms of Weierstrass elliptic functions. From this we derive some exact asymptotic results for the interaction between charged plates, as well as the exact form of the renormalized surface charge density.

Evaluation of the accuracy of the Rotating Parallel Ray Omnidirectional Integration for instantaneous pressure reconstruction from the measured pressure gradient

NASA Astrophysics Data System (ADS)

Moreto, Jose; Liu, Xiaofeng

2017-11-01

The accuracy of the Rotating Parallel Ray omnidirectional integration for pressure reconstruction from the measured pressure gradient (Liu et al., AIAA paper 2016-1049) is evaluated against both the Circular Virtual Boundary omnidirectional integration (Liu and Katz, 2006 and 2013) and the conventional Poisson equation approach. Dirichlet condition at one boundary point and Neumann condition at all other boundary points are applied to the Poisson solver. A direct numerical simulation database of isotropic turbulence flow (JHTDB), with a homogeneously distributed random noise added to the entire field of DNS pressure gradient, is used to assess the performance of the methods. The random noise, generated by the Matlab function Rand, has a magnitude varying randomly within the range of +/-40% of the maximum DNS pressure gradient. To account for the effect of the noise distribution pattern on the reconstructed pressure accuracy, a total of 1000 different noise distributions achieved by using different random number seeds are involved in the evaluation. Final results after averaging the 1000 realizations show that the error of the reconstructed pressure normalized by the DNS pressure variation range is 0.15 +/-0.07 for the Poisson equation approach, 0.028 +/-0.003 for the Circular Virtual Boundary method and 0.027 +/-0.003 for the Rotating Parallel Ray method, indicating the robustness of the Rotating Parallel Ray method in pressure reconstruction. Sponsor: The San Diego State University UGP program.

Poisson Coordinates.

PubMed

Li, Xian-Ying; Hu, Shi-Min

2013-02-01

Harmonic functions are the critical points of a Dirichlet energy functional, the linear projections of conformal maps. They play an important role in computer graphics, particularly for gradient-domain image processing and shape-preserving geometric computation. We propose Poisson coordinates, a novel transfinite interpolation scheme based on the Poisson integral formula, as a rapid way to estimate a harmonic function on a certain domain with desired boundary values. Poisson coordinates are an extension of the Mean Value coordinates (MVCs) which inherit their linear precision, smoothness, and kernel positivity. We give explicit formulas for Poisson coordinates in both continuous and 2D discrete forms. Superior to MVCs, Poisson coordinates are proved to be pseudoharmonic (i.e., they reproduce harmonic functions on n-dimensional balls). Our experimental results show that Poisson coordinates have lower Dirichlet energies than MVCs on a number of typical 2D domains (particularly convex domains). As well as presenting a formula, our approach provides useful insights for further studies on coordinates-based interpolation and fast estimation of harmonic functions.

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 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

Simulation of Devices with Molecular Potentials

DTIC Science & Technology

2013-12-22

10] W. R. Frensley, Wigner - function model of a resonant-tunneling semiconductor de- vice, Phys. Rev. B, 36 (1987), pp. 1570–1580. 6 [11] M. J...develop the principal investigator’s Wigner -Poisson code and extend that code to deal with longer devices and more complex barrier profiles. Over...Research Triangle Park, NC 27709-2211 Molecular Confirmation, Sparse Interpolation, Wigner -Poisson Equation, Parallel Algorithms REPORT DOCUMENTATION PAGE 11

DICE/ColDICE: 6D collisionless phase space hydrodynamics using a lagrangian tesselation

NASA Astrophysics Data System (ADS)

Sousbie, Thierry

2018-01-01

DICE is a C++ template library designed to solve collisionless fluid dynamics in 6D phase space using massively parallel supercomputers via an hybrid OpenMP/MPI parallelization. ColDICE, based on DICE, implements a cosmological and physical VLASOV-POISSON solver for cold systems such as dark matter (CDM) dynamics.

Algorithms for parallel and vector computations

NASA Technical Reports Server (NTRS)

Ortega, James M.

1995-01-01

This is a final report on work performed under NASA grant NAG-1-1112-FOP during the period March, 1990 through February 1995. Four major topics are covered: (1) solution of nonlinear poisson-type equations; (2) parallel reduced system conjugate gradient method; (3) orderings for conjugate gradient preconditioners, and (4) SOR as a preconditioner.

Parallel SOR methods with a parabolic-diffusion acceleration technique for solving an unstructured-grid Poisson equation on 3D arbitrary geometries

NASA Astrophysics Data System (ADS)

Zapata, M. A. Uh; Van Bang, D. Pham; Nguyen, K. D.

2016-05-01

This paper presents a parallel algorithm for the finite-volume discretisation of the Poisson equation on three-dimensional arbitrary geometries. The proposed method is formulated by using a 2D horizontal block domain decomposition and interprocessor data communication techniques with message passing interface. The horizontal unstructured-grid cells are reordered according to the neighbouring relations and decomposed into blocks using a load-balanced distribution to give all processors an equal amount of elements. In this algorithm, two parallel successive over-relaxation methods are presented: a multi-colour ordering technique for unstructured grids based on distributed memory and a block method using reordering index following similar ideas of the partitioning for structured grids. In all cases, the parallel algorithms are implemented with a combination of an acceleration iterative solver. This solver is based on a parabolic-diffusion equation introduced to obtain faster solutions of the linear systems arising from the discretisation. Numerical results are given to evaluate the performances of the methods showing speedups better than linear.

On some Aitken-like acceleration of the Schwarz method

NASA Astrophysics Data System (ADS)

Garbey, M.; Tromeur-Dervout, D.

2002-12-01

In this paper we present a family of domain decomposition based on Aitken-like acceleration of the Schwarz method seen as an iterative procedure with a linear rate of convergence. We first present the so-called Aitken-Schwarz procedure for linear differential operators. The solver can be a direct solver when applied to the Helmholtz problem with five-point finite difference scheme on regular grids. We then introduce the Steffensen-Schwarz variant which is an iterative domain decomposition solver that can be applied to linear and nonlinear problems. We show that these solvers have reasonable numerical efficiency compared to classical fast solvers for the Poisson problem or multigrids for more general linear and nonlinear elliptic problems. However, the salient feature of our method is that our algorithm has high tolerance to slow network in the context of distributed parallel computing and is attractive, generally speaking, to use with computer architecture for which performance is limited by the memory bandwidth rather than the flop performance of the CPU. This is nowadays the case for most parallel. computer using the RISC processor architecture. We will illustrate this highly desirable property of our algorithm with large-scale computing experiments.

Accelerated iteration schemes for transonic flow calculations using fast poisson solvers. [aerodynamics

NASA Technical Reports Server (NTRS)

Jameson, A.

1975-01-01

The use of a fast elliptic solver in combination with relaxation is presented as an effective way to accelerate the convergence of transonic flow calculations, particularly when a marching scheme can be used to treat the supersonic zone in the relaxation process.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

Computational time analysis of the numerical solution of 3D electrostatic Poisson's equation

NASA Astrophysics Data System (ADS)

Kamboh, Shakeel Ahmed; Labadin, Jane; Rigit, Andrew Ragai Henri; Ling, Tech Chaw; Amur, Khuda Bux; Chaudhary, Muhammad Tayyab

2015-05-01

3D Poisson's equation is solved numerically to simulate the electric potential in a prototype design of electrohydrodynamic (EHD) ion-drag micropump. Finite difference method (FDM) is employed to discretize the governing equation. The system of linear equations resulting from FDM is solved iteratively by using the sequential Jacobi (SJ) and sequential Gauss-Seidel (SGS) methods, simulation results are also compared to examine the difference between the results. The main objective was to analyze the computational time required by both the methods with respect to different grid sizes and parallelize the Jacobi method to reduce the computational time. In common, the SGS method is faster than the SJ method but the data parallelism of Jacobi method may produce good speedup over SGS method. In this study, the feasibility of using parallel Jacobi (PJ) method is attempted in relation to SGS method. MATLAB Parallel/Distributed computing environment is used and a parallel code for SJ method is implemented. It was found that for small grid size the SGS method remains dominant over SJ method and PJ method while for large grid size both the sequential methods may take nearly too much processing time to converge. Yet, the PJ method reduces computational time to some extent for large grid sizes.

An efficient parallel sampling technique for Multivariate Poisson-Lognormal model: Analysis with two crash count datasets

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

Zhan, Xianyuan; Aziz, H. M. Abdul; Ukkusuri, Satish V.

Our study investigates the Multivariate Poisson-lognormal (MVPLN) model that jointly models crash frequency and severity accounting for correlations. The ordinary univariate count models analyze crashes of different severity level separately ignoring the correlations among severity levels. The MVPLN model is capable to incorporate the general correlation structure and takes account of the over dispersion in the data that leads to a superior data fitting. But, the traditional estimation approach for MVPLN model is computationally expensive, which often limits the use of MVPLN model in practice. In this work, a parallel sampling scheme is introduced to improve the original Markov Chainmore » Monte Carlo (MCMC) estimation approach of the MVPLN model, which significantly reduces the model estimation time. Two MVPLN models are developed using the pedestrian vehicle crash data collected in New York City from 2002 to 2006, and the highway-injury data from Washington State (5-year data from 1990 to 1994) The Deviance Information Criteria (DIC) is used to evaluate the model fitting. The estimation results show that the MVPLN models provide a superior fit over univariate Poisson-lognormal (PLN), univariate Poisson, and Negative Binomial models. Moreover, the correlations among the latent effects of different severity levels are found significant in both datasets that justifies the importance of jointly modeling crash frequency and severity accounting for correlations.« less

An efficient parallel sampling technique for Multivariate Poisson-Lognormal model: Analysis with two crash count datasets

DOE PAGES

Zhan, Xianyuan; Aziz, H. M. Abdul; Ukkusuri, Satish V.

2015-11-19

Our study investigates the Multivariate Poisson-lognormal (MVPLN) model that jointly models crash frequency and severity accounting for correlations. The ordinary univariate count models analyze crashes of different severity level separately ignoring the correlations among severity levels. The MVPLN model is capable to incorporate the general correlation structure and takes account of the over dispersion in the data that leads to a superior data fitting. But, the traditional estimation approach for MVPLN model is computationally expensive, which often limits the use of MVPLN model in practice. In this work, a parallel sampling scheme is introduced to improve the original Markov Chainmore » Monte Carlo (MCMC) estimation approach of the MVPLN model, which significantly reduces the model estimation time. Two MVPLN models are developed using the pedestrian vehicle crash data collected in New York City from 2002 to 2006, and the highway-injury data from Washington State (5-year data from 1990 to 1994) The Deviance Information Criteria (DIC) is used to evaluate the model fitting. The estimation results show that the MVPLN models provide a superior fit over univariate Poisson-lognormal (PLN), univariate Poisson, and Negative Binomial models. Moreover, the correlations among the latent effects of different severity levels are found significant in both datasets that justifies the importance of jointly modeling crash frequency and severity accounting for correlations.« less

Complex wet-environments in electronic-structure calculations

NASA Astrophysics Data System (ADS)

Fisicaro, Giuseppe; Genovese, Luigi; Andreussi, Oliviero; Marzari, Nicola; Goedecker, Stefan

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 an applied electrochemical potentials, including complex electrostatic screening coming from the solvent. In the present work we present a solver to handle both the Generalized Poisson and the Poisson-Boltzmann equation. A preconditioned conjugate gradient (PCG) method has been implemented for the Generalized Poisson and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations. On the other hand, a self-consistent procedure enables us to solve the Poisson-Boltzmann problem. The algorithms take advantage of a preconditioning procedure based on the BigDFT Poisson solver for the standard Poisson equation. They exhibit very high accuracy and parallel efficiency, and allow different boundary conditions, including surfaces. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and it will be released as a independent program, suitable for integration in other codes. We present test calculations for large proteins to demonstrate efficiency and performances. This work was done within the PASC and NCCR MARVEL projects. Computer resources were provided by the Swiss National Supercomputing Centre (CSCS) under Project ID s499. LG acknowledges also support from the EXTMOS EU project.

Measurement of Poisson's ratio of nonmetallic materials by laser holographic interferometry

NASA Astrophysics Data System (ADS)

Zhu, Jian T.

1991-12-01

By means of the off-axis collimated plane wave coherent light arrangement and a loading device by pure bending, Poisson's ratio values of CFRP (carbon fiber-reinforced plactics plates, lay-up 0 degree(s), 90 degree(s)), GFRP (glass fiber-reinforced plactics plates, radial direction) and PMMA (polymethyl methacrylate, x, y direction) have been measured. In virtue of this study, the ministry standard for the Ministry of Aeronautical Industry (Testing method for the measurement of Poisson's ratio of non-metallic by laser holographic interferometry) has been published. The measurement process is fast and simple. The measuring results are reliable and accurate.

Fuzzy classifier based support vector regression framework for Poisson ratio determination

NASA Astrophysics Data System (ADS)

Asoodeh, Mojtaba; Bagheripour, Parisa

2013-09-01

Poisson ratio is considered as one of the most important rock mechanical properties of hydrocarbon reservoirs. Determination of this parameter through laboratory measurement is time, cost, and labor intensive. Furthermore, laboratory measurements do not provide continuous data along the reservoir intervals. Hence, a fast, accurate, and inexpensive way of determining Poisson ratio which produces continuous data over the whole reservoir interval is desirable. For this purpose, support vector regression (SVR) method based on statistical learning theory (SLT) was employed as a supervised learning algorithm to estimate Poisson ratio from conventional well log data. SVR is capable of accurately extracting the implicit knowledge contained in conventional well logs and converting the gained knowledge into Poisson ratio data. Structural risk minimization (SRM) principle which is embedded in the SVR structure in addition to empirical risk minimization (EMR) principle provides a robust model for finding quantitative formulation between conventional well log data and Poisson ratio. Although satisfying results were obtained from an individual SVR model, it had flaws of overestimation in low Poisson ratios and underestimation in high Poisson ratios. These errors were eliminated through implementation of fuzzy classifier based SVR (FCBSVR). The FCBSVR significantly improved accuracy of the final prediction. This strategy was successfully applied to data from carbonate reservoir rocks of an Iranian Oil Field. Results indicated that SVR predicted Poisson ratio values are in good agreement with measured values.

Statistical characteristics of climbing fiber spikes necessary for efficient cerebellar learning.

PubMed

Kuroda, S; Yamamoto, K; Miyamoto, H; Doya, K; Kawat, M

2001-03-01

Mean firing rates (MFRs), with analogue values, have thus far been used as information carriers of neurons in most brain theories of learning. However, the neurons transmit the signal by spikes, which are discrete events. The climbing fibers (CFs), which are known to be essential for cerebellar motor learning, fire at the ultra-low firing rates (around 1 Hz), and it is not yet understood theoretically how high-frequency information can be conveyed and how learning of smooth and fast movements can be achieved. Here we address whether cerebellar learning can be achieved by CF spikes instead of conventional MFR in an eye movement task, such as the ocular following response (OFR), and an arm movement task. There are two major afferents into cerebellar Purkinje cells: parallel fiber (PF) and CF, and the synaptic weights between PFs and Purkinje cells have been shown to be modulated by the stimulation of both types of fiber. The modulation of the synaptic weights is regulated by the cerebellar synaptic plasticity. In this study we simulated cerebellar learning using CF signals as spikes instead of conventional MFR. To generate the spikes we used the following four spike generation models: (1) a Poisson model in which the spike interval probability follows a Poisson distribution, (2) a gamma model in which the spike interval probability follows the gamma distribution, (3) a max model in which a spike is generated when a synaptic input reaches maximum, and (4) a threshold model in which a spike is generated when the input crosses a certain small threshold. We found that, in an OFR task with a constant visual velocity, learning was successful with stochastic models, such as Poisson and gamma models, but not in the deterministic models, such as max and threshold models. In an OFR with a stepwise velocity change and an arm movement task, learning could be achieved only in the Poisson model. In addition, for efficient cerebellar learning, the distribution of CF spike-occurrence time after stimulus onset must capture at least the first, second and third moments of the temporal distribution of error signals.

A fast immersed boundary method for external incompressible viscous flows using lattice Green's functions

NASA Astrophysics Data System (ADS)

Liska, Sebastian; Colonius, Tim

2017-02-01

A new parallel, computationally efficient immersed boundary method for solving three-dimensional, viscous, incompressible flows on unbounded domains is presented. Immersed surfaces with prescribed motions are generated using the interpolation and regularization operators obtained from the discrete delta function approach of the original (Peskin's) immersed boundary method. Unlike Peskin's method, boundary forces are regarded as Lagrange multipliers that are used to satisfy the no-slip condition. The incompressible Navier-Stokes equations are discretized on an unbounded staggered Cartesian grid and are solved in a finite number of operations using lattice Green's function techniques. These techniques are used to automatically enforce the natural free-space boundary conditions and to implement a novel block-wise adaptive grid that significantly reduces the run-time cost of solutions by limiting operations to grid cells in the immediate vicinity and near-wake region of the immersed surface. These techniques also enable the construction of practical discrete viscous integrating factors that are used in combination with specialized half-explicit Runge-Kutta schemes to accurately and efficiently solve the differential algebraic equations describing the discrete momentum equation, incompressibility constraint, and no-slip constraint. Linear systems of equations resulting from the time integration scheme are efficiently solved using an approximation-free nested projection technique. The algebraic properties of the discrete operators are used to reduce projection steps to simple discrete elliptic problems, e.g. discrete Poisson problems, that are compatible with recent parallel fast multipole methods for difference equations. Numerical experiments on low-aspect-ratio flat plates and spheres at Reynolds numbers up to 3700 are used to verify the accuracy and physical fidelity of the formulation.

Hybrid massively parallel fast sweeping method for static Hamilton-Jacobi equations

NASA Astrophysics Data System (ADS)

Detrixhe, Miles; Gibou, Frédéric

2016-10-01

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton-Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling, and show state-of-the-art speedup values for the fast sweeping method.

Scalable direct Vlasov solver with discontinuous Galerkin method on unstructured mesh.

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

Xu, J.; Ostroumov, P. N.; Mustapha, B.

2010-12-01

This paper presents the development of parallel direct Vlasov solvers with discontinuous Galerkin (DG) method for beam and plasma simulations in four dimensions. Both physical and velocity spaces are in two dimesions (2P2V) with unstructured mesh. Contrary to the standard particle-in-cell (PIC) approach for kinetic space plasma simulations, i.e., solving Vlasov-Maxwell equations, direct method has been used in this paper. There are several benefits to solving a Vlasov equation directly, such as avoiding noise associated with a finite number of particles and the capability to capture fine structure in the plasma. The most challanging part of a direct Vlasov solvermore » comes from higher dimensions, as the computational cost increases as N{sup 2d}, where d is the dimension of the physical space. Recently, due to the fast development of supercomputers, the possibility has become more realistic. Many efforts have been made to solve Vlasov equations in low dimensions before; now more interest has focused on higher dimensions. Different numerical methods have been tried so far, such as the finite difference method, Fourier Spectral method, finite volume method, and spectral element method. This paper is based on our previous efforts to use the DG method. The DG method has been proven to be very successful in solving Maxwell equations, and this paper is our first effort in applying the DG method to Vlasov equations. DG has shown several advantages, such as local mass matrix, strong stability, and easy parallelization. These are particularly suitable for Vlasov equations. Domain decomposition in high dimensions has been used for parallelization; these include a highly scalable parallel two-dimensional Poisson solver. Benchmark results have been shown and simulation results will be reported.« less

A 2D electrostatic PIC code for the Mark III Hypercube

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

Ferraro, R.D.; Liewer, P.C.; Decyk, V.K.

We have implemented a 2D electrostastic plasma particle in cell (PIC) simulation code on the Caltech/JPL Mark IIIfp Hypercube. The code simulates plasma effects by evolving in time the trajectories of thousands to millions of charged particles subject to their self-consistent fields. Each particle`s position and velocity is advanced in time using a leap frog method for integrating Newton`s equations of motion in electric and magnetic fields. The electric field due to these moving charged particles is calculated on a spatial grid at each time by solving Poisson`s equation in Fourier space. These two tasks represent the largest part ofmore » the computation. To obtain efficient operation on a distributed memory parallel computer, we are using the General Concurrent PIC (GCPIC) algorithm previously developed for a 1D parallel PIC code.« less

A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

PubMed Central

Kurnikova, M G; Coalson, R D; Graf, P; Nitzan, A

1999-01-01

A lattice relaxation algorithm is developed to solve the Poisson-Nernst-Planck (PNP) equations for ion transport through arbitrary three-dimensional volumes. Calculations of systems characterized by simple parallel plate and cylindrical pore geometries are presented in order to calibrate the accuracy of the method. A study of ion transport through gramicidin A dimer is carried out within this PNP framework. Good agreement with experimental measurements is obtained. Strengths and weaknesses of the PNP approach are discussed. PMID:9929470

Parallel Fast Multipole Method For Molecular Dynamics

DTIC Science & Technology

2007-06-01

Parallel Fast Multipole Method For Molecular Dynamics THESIS Reid G. Ormseth, Captain, USAF AFIT/GAP/ENP/07-J02 DEPARTMENT OF THE AIR FORCE AIR...the United States Government. AFIT/GAP/ENP/07-J02 Parallel Fast Multipole Method For Molecular Dynamics THESIS Presented to the Faculty Department of...has also been provided by ‘The Art of Molecular Dynamics Simulation ’ by Dennis Rapaport. This work is the clearest treatment of the Fast Multipole

Hybrid massively parallel fast sweeping method for static Hamilton–Jacobi equations

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

Detrixhe, Miles, E-mail: mdetrixhe@engineering.ucsb.edu; University of California Santa Barbara, Santa Barbara, CA, 93106; Gibou, Frédéric, E-mail: fgibou@engineering.ucsb.edu

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton–Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling,more » and show state-of-the-art speedup values for the fast sweeping method.« less

Crustal origin of trench-parallel shear-wave fast polarizations in the Central Andes

NASA Astrophysics Data System (ADS)

Wölbern, I.; Löbl, U.; Rümpker, G.

2014-04-01

In this study, SKS and local S phases are analyzed to investigate variations of shear-wave splitting parameters along two dense seismic profiles across the central Andean Altiplano and Puna plateaus. In contrast to previous observations, the vast majority of the measurements reveal fast polarizations sub-parallel to the subduction direction of the Nazca plate with delay times between 0.3 and 1.2 s. Local phases show larger variations of fast polarizations and exhibit delay times ranging between 0.1 and 1.1 s. Two 70 km and 100 km wide sections along the Altiplano profile exhibit larger delay times and are characterized by fast polarizations oriented sub-parallel to major fault zones. Based on finite-difference wavefield calculations for anisotropic subduction zone models we demonstrate that the observations are best explained by fossil slab anisotropy with fast symmetry axes oriented sub-parallel to the slab movement in combination with a significant component of crustal anisotropy of nearly trench-parallel fast-axis orientation. From the modeling we exclude a sub-lithospheric origin of the observed strong anomalies due to the short-scale variations of the fast polarizations. Instead, our results indicate that anisotropy in the Central Andes generally reflects the direction of plate motion while the observed trench-parallel fast polarizations likely originate in the continental crust above the subducting slab.

QCAD simulation and optimization of semiconductor double quantum dots

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

Nielsen, Erik; Gao, Xujiao; Kalashnikova, Irina

2013-12-01

We present the Quantum Computer Aided Design (QCAD) simulator that targets modeling quantum devices, particularly silicon double quantum dots (DQDs) developed for quantum qubits. The simulator has three di erentiating features: (i) its core contains nonlinear Poisson, e ective mass Schrodinger, and Con guration Interaction solvers that have massively parallel capability for high simulation throughput, and can be run individually or combined self-consistently for 1D/2D/3D quantum devices; (ii) the core solvers show superior convergence even at near-zero-Kelvin temperatures, which is critical for modeling quantum computing devices; (iii) it couples with an optimization engine Dakota that enables optimization of gate voltagesmore » in DQDs for multiple desired targets. The Poisson solver includes Maxwell- Boltzmann and Fermi-Dirac statistics, supports Dirichlet, Neumann, interface charge, and Robin boundary conditions, and includes the e ect of dopant incomplete ionization. The solver has shown robust nonlinear convergence even in the milli-Kelvin temperature range, and has been extensively used to quickly obtain the semiclassical electrostatic potential in DQD devices. The self-consistent Schrodinger-Poisson solver has achieved robust and monotonic convergence behavior for 1D/2D/3D quantum devices at very low temperatures by using a predictor-correct iteration scheme. The QCAD simulator enables the calculation of dot-to-gate capacitances, and comparison with experiment and between solvers. It is observed that computed capacitances are in the right ballpark when compared to experiment, and quantum con nement increases capacitance when the number of electrons is xed in a quantum dot. In addition, the coupling of QCAD with Dakota allows to rapidly identify which device layouts are more likely leading to few-electron quantum dots. Very efficient QCAD simulations on a large number of fabricated and proposed Si DQDs have made it possible to provide fast feedback for design comparison and optimization.« less

Parallel and pipeline computation of fast unitary transforms

NASA Technical Reports Server (NTRS)

Fino, B. J.; Algazi, V. R.

1975-01-01

The letter discusses the parallel and pipeline organization of fast-unitary-transform algorithms such as the fast Fourier transform, and points out the efficiency of a combined parallel-pipeline processor of a transform such as the Haar transform, in which (2 to the n-th power) -1 hardware 'butterflies' generate a transform of order 2 to the n-th power every computation cycle.

A note on parallel and pipeline computation of fast unitary transforms

NASA Technical Reports Server (NTRS)

Fino, B. J.; Algazi, V. R.

1974-01-01

The parallel and pipeline organization of fast unitary transform algorithms such as the Fast Fourier Transform are discussed. The efficiency is pointed out of a combined parallel-pipeline processor of a transform such as the Haar transform in which 2 to the n minus 1 power hardware butterflies generate a transform of order 2 to the n power every computation cycle.

Tensorial Basis Spline Collocation Method for Poisson's Equation

NASA Astrophysics Data System (ADS)

Plagne, Laurent; Berthou, Jean-Yves

2000-01-01

This paper aims to describe the tensorial basis spline collocation method applied to Poisson's equation. In the case of a localized 3D charge distribution in vacuum, this direct method based on a tensorial decomposition of the differential operator is shown to be competitive with both iterative BSCM and FFT-based methods. We emphasize the O(h4) and O(h6) convergence of TBSCM for cubic and quintic splines, respectively. We describe the implementation of this method on a distributed memory parallel machine. Performance measurements on a Cray T3E are reported. Our code exhibits high performance and good scalability: As an example, a 27 Gflops performance is obtained when solving Poisson's equation on a 2563 non-uniform 3D Cartesian mesh by using 128 T3E-750 processors. This represents 215 Mflops per processors.

A stochastic-dynamic model for global atmospheric mass field statistics

NASA Technical Reports Server (NTRS)

Ghil, M.; Balgovind, R.; Kalnay-Rivas, E.

1981-01-01

A model that yields the spatial correlation structure of atmospheric mass field forecast errors was developed. The model is governed by the potential vorticity equation forced by random noise. Expansion in spherical harmonics and correlation function was computed analytically using the expansion coefficients. The finite difference equivalent was solved using a fast Poisson solver and the correlation function was computed using stratified sampling of the individual realization of F(omega) and hence of phi(omega). A higher order equation for gamma was derived and solved directly in finite differences by two successive applications of the fast Poisson solver. The methods were compared for accuracy and efficiency and the third method was chosen as clearly superior. The results agree well with the latitude dependence of observed atmospheric correlation data. The value of the parameter c sub o which gives the best fit to the data is close to the value expected from dynamical considerations.

A GPU accelerated and error-controlled solver for the unbounded Poisson equation in three dimensions

NASA Astrophysics Data System (ADS)

Exl, Lukas

2017-12-01

An efficient solver for the three dimensional free-space Poisson equation is presented. The underlying numerical method is based on finite Fourier series approximation. While the error of all involved approximations can be fully controlled, the overall computation error is driven by the convergence of the finite Fourier series of the density. For smooth and fast-decaying densities the proposed method will be spectrally accurate. The method scales with O(N log N) operations, where N is the total number of discretization points in the Cartesian grid. The majority of the computational costs come from fast Fourier transforms (FFT), which makes it ideal for GPU computation. Several numerical computations on CPU and GPU validate the method and show efficiency and convergence behavior. Tests are performed using the Vienna Scientific Cluster 3 (VSC3). A free MATLAB implementation for CPU and GPU is provided to the interested community.

Variability of visual responses of superior colliculus neurons depends on stimulus velocity.

PubMed

Mochol, Gabriela; Wójcik, Daniel K; Wypych, Marek; Wróbel, Andrzej; Waleszczyk, Wioletta J

2010-03-03

Visually responding neurons in the superficial, retinorecipient layers of the cat superior colliculus receive input from two primarily parallel information processing channels, Y and W, which is reflected in their velocity response profiles. We quantified the time-dependent variability of responses of these neurons to stimuli moving with different velocities by Fano factor (FF) calculated in discrete time windows. The FF for cells responding to low-velocity stimuli, thus receiving W inputs, increased with the increase in the firing rate. In contrast, the dynamics of activity of the cells responding to fast moving stimuli, processed by Y pathway, correlated negatively with FF whether the response was excitatory or suppressive. These observations were tested against several types of surrogate data. Whereas Poisson description failed to reproduce the variability of all collicular responses, the inclusion of secondary structure to the generating point process recovered most of the observed features of responses to fast moving stimuli. Neither model could reproduce the variability of low-velocity responses, which suggests that, in this case, more complex time dependencies need to be taken into account. Our results indicate that Y and W channels may differ in reliability of responses to visual stimulation. Apart from previously reported morphological and physiological differences of the cells belonging to Y and W channels, this is a new feature distinguishing these two pathways.

Fast polyenergetic forward projection for image formation using OpenCL on a heterogeneous parallel computing platform.

PubMed

Zhou, Lili; Clifford Chao, K S; Chang, Jenghwa

2012-11-01

Simulated projection images of digital phantoms constructed from CT scans have been widely used for clinical and research applications but their quality and computation speed are not optimal for real-time comparison with the radiography acquired with an x-ray source of different energies. In this paper, the authors performed polyenergetic forward projections using open computing language (OpenCL) in a parallel computing ecosystem consisting of CPU and general purpose graphics processing unit (GPGPU) for fast and realistic image formation. The proposed polyenergetic forward projection uses a lookup table containing the NIST published mass attenuation coefficients (μ∕ρ) for different tissue types and photon energies ranging from 1 keV to 20 MeV. The CT images of interested sites are first segmented into different tissue types based on the CT numbers and converted to a three-dimensional attenuation phantom by linking each voxel to the corresponding tissue type in the lookup table. The x-ray source can be a radioisotope or an x-ray generator with a known spectrum described as weight w(n) for energy bin E(n). The Siddon method is used to compute the x-ray transmission line integral for E(n) and the x-ray fluence is the weighted sum of the exponential of line integral for all energy bins with added Poisson noise. To validate this method, a digital head and neck phantom constructed from the CT scan of a Rando head phantom was segmented into three (air, gray∕white matter, and bone) regions for calculating the polyenergetic projection images for the Mohan 4 MV energy spectrum. To accelerate the calculation, the authors partitioned the workloads using the task parallelism and data parallelism and scheduled them in a parallel computing ecosystem consisting of CPU and GPGPU (NVIDIA Tesla C2050) using OpenCL only. The authors explored the task overlapping strategy and the sequential method for generating the first and subsequent DRRs. A dispatcher was designed to drive the high-degree parallelism of the task overlapping strategy. Numerical experiments were conducted to compare the performance of the OpenCL∕GPGPU-based implementation with the CPU-based implementation. The projection images were similar to typical portal images obtained with a 4 or 6 MV x-ray source. For a phantom size of 512 × 512 × 223, the time for calculating the line integrals for a 512 × 512 image panel was 16.2 ms on GPGPU for one energy bin in comparison to 8.83 s on CPU. The total computation time for generating one polyenergetic projection image of 512 × 512 was 0.3 s (141 s for CPU). The relative difference between the projection images obtained with the CPU-based and OpenCL∕GPGPU-based implementations was on the order of 10(-6) and was virtually indistinguishable. The task overlapping strategy was 5.84 and 1.16 times faster than the sequential method for the first and the subsequent digitally reconstruction radiographies, respectively. The authors have successfully built digital phantoms using anatomic CT images and NIST μ∕ρ tables for simulating realistic polyenergetic projection images and optimized the processing speed with parallel computing using GPGPU∕OpenCL-based implementation. The computation time was fast (0.3 s per projection image) enough for real-time IGRT (image-guided radiotherapy) applications.

Parallel multigrid smoothing: polynomial versus Gauss-Seidel

NASA Astrophysics Data System (ADS)

Adams, Mark; Brezina, Marian; Hu, Jonathan; Tuminaro, Ray

2003-07-01

Gauss-Seidel is often the smoother of choice within multigrid applications. In the context of unstructured meshes, however, maintaining good parallel efficiency is difficult with multiplicative iterative methods such as Gauss-Seidel. This leads us to consider alternative smoothers. We discuss the computational advantages of polynomial smoothers within parallel multigrid algorithms for positive definite symmetric systems. Two particular polynomials are considered: Chebyshev and a multilevel specific polynomial. The advantages of polynomial smoothing over traditional smoothers such as Gauss-Seidel are illustrated on several applications: Poisson's equation, thin-body elasticity, and eddy current approximations to Maxwell's equations. While parallelizing the Gauss-Seidel method typically involves a compromise between a scalable convergence rate and maintaining high flop rates, polynomial smoothers achieve parallel scalable multigrid convergence rates without sacrificing flop rates. We show that, although parallel computers are the main motivation, polynomial smoothers are often surprisingly competitive with Gauss-Seidel smoothers on serial machines.

STDP allows fast rate-modulated coding with Poisson-like spike trains.

PubMed

Gilson, Matthieu; Masquelier, Timothée; Hugues, Etienne

2011-10-01

Spike timing-dependent plasticity (STDP) has been shown to enable single neurons to detect repeatedly presented spatiotemporal spike patterns. This holds even when such patterns are embedded in equally dense random spiking activity, that is, in the absence of external reference times such as a stimulus onset. Here we demonstrate, both analytically and numerically, that STDP can also learn repeating rate-modulated patterns, which have received more experimental evidence, for example, through post-stimulus time histograms (PSTHs). Each input spike train is generated from a rate function using a stochastic sampling mechanism, chosen to be an inhomogeneous Poisson process here. Learning is feasible provided significant covarying rate modulations occur within the typical timescale of STDP (~10-20 ms) for sufficiently many inputs (~100 among 1000 in our simulations), a condition that is met by many experimental PSTHs. Repeated pattern presentations induce spike-time correlations that are captured by STDP. Despite imprecise input spike times and even variable spike counts, a single trained neuron robustly detects the pattern just a few milliseconds after its presentation. Therefore, temporal imprecision and Poisson-like firing variability are not an obstacle to fast temporal coding. STDP provides an appealing mechanism to learn such rate patterns, which, beyond sensory processing, may also be involved in many cognitive tasks.

STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains

PubMed Central

Hugues, Etienne

2011-01-01

Spike timing-dependent plasticity (STDP) has been shown to enable single neurons to detect repeatedly presented spatiotemporal spike patterns. This holds even when such patterns are embedded in equally dense random spiking activity, that is, in the absence of external reference times such as a stimulus onset. Here we demonstrate, both analytically and numerically, that STDP can also learn repeating rate-modulated patterns, which have received more experimental evidence, for example, through post-stimulus time histograms (PSTHs). Each input spike train is generated from a rate function using a stochastic sampling mechanism, chosen to be an inhomogeneous Poisson process here. Learning is feasible provided significant covarying rate modulations occur within the typical timescale of STDP (∼10–20 ms) for sufficiently many inputs (∼100 among 1000 in our simulations), a condition that is met by many experimental PSTHs. Repeated pattern presentations induce spike-time correlations that are captured by STDP. Despite imprecise input spike times and even variable spike counts, a single trained neuron robustly detects the pattern just a few milliseconds after its presentation. Therefore, temporal imprecision and Poisson-like firing variability are not an obstacle to fast temporal coding. STDP provides an appealing mechanism to learn such rate patterns, which, beyond sensory processing, may also be involved in many cognitive tasks. PMID:22046113

Comment on: Accurate and fast numerical solution of Poisson s equation for arbitrary, space-filling Voronoi polyhedra: Near-field corrections revisited

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

Gonis, Antonios; Zhang, Xiaoguang

2012-01-01

This is a comment on the paper by Aftab Alam, Brian G. Wilson, and D. D. Johnson [1], proposing the solution of the near-field corrections (NFC s) problem for the Poisson equation for extended, e.g., space filling, charge densities. We point out that the problem considered by the authors can be simply avoided by means of performing certain integrals in a particular order, while their method does not address the genuine problem of NFC s that arises when the solution of the Poisson equation is attempted within multiple scattering theory. We also point out a flaw in their line ofmore » reasoning leading to the expression for the potential inside the bounding sphere of a cell that makes it inapplicable to certain geometries.« less

Comment on ``Accurate and fast numerical solution of Poisson's equation for arbitrary, space-filling Voronoi polyhedra: Near-field corrections revisited''

NASA Astrophysics Data System (ADS)

Gonis, A.; Zhang, X.-G.

2012-09-01

This is a Comment on the paper by Alam, Wilson, and Johnson [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.84.205106 84, 205106 (2011)], proposing the solution of the near-field corrections (NFCs) problem for the Poisson equation for extended, e.g., space-filling charge densities. We point out that the problem considered by the authors can be simply avoided by means of performing certain integrals in a particular order, whereas, their method does not address the genuine problem of NFCs that arises when the solution of the Poisson equation is attempted within multiple-scattering theory. We also point out a flaw in their line of reasoning, leading to the expression for the potential inside the bounding sphere of a cell that makes it inapplicable for certain geometries.

Fast parallel approach for 2-D DHT-based real-valued discrete Gabor transform.

PubMed

Tao, Liang; Kwan, Hon Keung

2009-12-01

Two-dimensional fast Gabor transform algorithms are useful for real-time applications due to the high computational complexity of the traditional 2-D complex-valued discrete Gabor transform (CDGT). This paper presents two block time-recursive algorithms for 2-D DHT-based real-valued discrete Gabor transform (RDGT) and its inverse transform and develops a fast parallel approach for the implementation of the two algorithms. The computational complexity of the proposed parallel approach is analyzed and compared with that of the existing 2-D CDGT algorithms. The results indicate that the proposed parallel approach is attractive for real time image processing.

LIMEPY: Lowered Isothermal Model Explorer in PYthon

NASA Astrophysics Data System (ADS)

Gieles, Mark; Zocchi, Alice

2017-10-01

LIMEPY solves distribution function (DF) based lowered isothermal models. It solves Poisson's equation used on input parameters and offers fast solutions for isotropic/anisotropic, single/multi-mass models, normalized DF values, density and velocity moments, projected properties, and generates discrete samples.

The impact of short term synaptic depression and stochastic vesicle dynamics on neuronal variability

PubMed Central

Reich, Steven

2014-01-01

Neuronal variability plays a central role in neural coding and impacts the dynamics of neuronal networks. Unreliability of synaptic transmission is a major source of neural variability: synaptic neurotransmitter vesicles are released probabilistically in response to presynaptic action potentials and are recovered stochastically in time. The dynamics of this process of vesicle release and recovery interacts with variability in the arrival times of presynaptic spikes to shape the variability of the postsynaptic response. We use continuous time Markov chain methods to analyze a model of short term synaptic depression with stochastic vesicle dynamics coupled with three different models of presynaptic spiking: one model in which the timing of presynaptic action potentials are modeled as a Poisson process, one in which action potentials occur more regularly than a Poisson process (sub-Poisson) and one in which action potentials occur more irregularly (super-Poisson). We use this analysis to investigate how variability in a presynaptic spike train is transformed by short term depression and stochastic vesicle dynamics to determine the variability of the postsynaptic response. We find that sub-Poisson presynaptic spiking increases the average rate at which vesicles are released, that the number of vesicles released over a time window is more variable for smaller time windows than larger time windows and that fast presynaptic spiking gives rise to Poisson-like variability of the postsynaptic response even when presynaptic spike times are non-Poisson. Our results complement and extend previously reported theoretical results and provide possible explanations for some trends observed in recorded data. PMID:23354693

Analysis techniques for diagnosing runaway ion distributions in the reversed field pinch

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

Kim, J., E-mail: jkim536@wisc.edu; Anderson, J. K.; Capecchi, W.

2016-11-15

An advanced neutral particle analyzer (ANPA) on the Madison Symmetric Torus measures deuterium ions of energy ranges 8-45 keV with an energy resolution of 2-4 keV and time resolution of 10 μs. Three different experimental configurations measure distinct portions of the naturally occurring fast ion distributions: fast ions moving parallel, anti-parallel, or perpendicular to the plasma current. On a radial-facing port, fast ions moving perpendicular to the current have the necessary pitch to be measured by the ANPA. With the diagnostic positioned on a tangent line through the plasma core, a chord integration over fast ion density, background neutral density,more » and local appropriate pitch defines the measured sample. The plasma current can be reversed to measure anti-parallel fast ions in the same configuration. Comparisons of energy distributions for the three configurations show an anisotropic fast ion distribution favoring high pitch ions.« less

Performance and capacity analysis of Poisson photon-counting based Iter-PIC OCDMA systems.

PubMed

Li, Lingbin; Zhou, Xiaolin; Zhang, Rong; Zhang, Dingchen; Hanzo, Lajos

2013-11-04

In this paper, an iterative parallel interference cancellation (Iter-PIC) technique is developed for optical code-division multiple-access (OCDMA) systems relying on shot-noise limited Poisson photon-counting reception. The novel semi-analytical tool of extrinsic information transfer (EXIT) charts is used for analysing both the bit error rate (BER) performance as well as the channel capacity of these systems and the results are verified by Monte Carlo simulations. The proposed Iter-PIC OCDMA system is capable of achieving two orders of magnitude BER improvements and a 0.1 nats of capacity improvement over the conventional chip-level OCDMA systems at a coding rate of 1/10.

The Nonhomogeneous Poisson Process for Fast Radio Burst Rates

DOE PAGES

Lawrence, Earl; Wiel, Scott Vander; Law, Casey; ...

2017-08-30

This paper presents the non-homogeneous Poisson process (NHPP) for modeling the rate of fast radio bursts (FRBs) and other infrequently observed astronomical events. The NHPP, well-known in statistics, can model dependence of the rate on both astronomical features and the details of an observing campaign. This is particularly helpful for rare events like FRBs because the NHPP can combine information across surveys, making the most of all available information. The goal of the paper is two-fold. First, it is intended to be a tutorial on the use of the NHPP. Second, we build an NHPP model that incorporates beam patternsmore » and a power law flux distribution for the rate of FRBs. Using information from 12 surveys including 15 detections, we find an all-sky FRB rate of 587 events per sky per day above a flux of 1 Jy (95% CI: 272, 924) and a flux power-law index of 0:91 (95% CI: 0.57, 1.25).« less

Multirate-based fast parallel algorithms for 2-D DHT-based real-valued discrete Gabor transform.

PubMed

Tao, Liang; Kwan, Hon Keung

2012-07-01

Novel algorithms for the multirate and fast parallel implementation of the 2-D discrete Hartley transform (DHT)-based real-valued discrete Gabor transform (RDGT) and its inverse transform are presented in this paper. A 2-D multirate-based analysis convolver bank is designed for the 2-D RDGT, and a 2-D multirate-based synthesis convolver bank is designed for the 2-D inverse RDGT. The parallel channels in each of the two convolver banks have a unified structure and can apply the 2-D fast DHT algorithm to speed up their computations. The computational complexity of each parallel channel is low and is independent of the Gabor oversampling rate. All the 2-D RDGT coefficients of an image are computed in parallel during the analysis process and can be reconstructed in parallel during the synthesis process. The computational complexity and time of the proposed parallel algorithms are analyzed and compared with those of the existing fastest algorithms for 2-D discrete Gabor transforms. The results indicate that the proposed algorithms are the fastest, which make them attractive for real-time image processing.

NHPP for FRBs, Version 1.0

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

Lawrence, Earl; Wiel, Scott Vander

This code implements the non-homogeneous poisson process model for estimating the rate of fast radio bursts. It includes modeling terms for the distribution of events in the Universe and the detection sensitivity of the radio telescopes and arrays used in observation. The model is described in LA-UR-16-26261.

AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

NASA Astrophysics Data System (ADS)

Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

2010-06-01

A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Program summaryProgram title: AFMPB: Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier: AEGB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 453 649 No. of bytes in distributed program, including test data, etc.: 8 764 754 Distribution format: tar.gz Programming language: Fortran Computer: Any Operating system: Any RAM: Depends on the size of the discretized biomolecular system Classification: 3 External routines: Pre- and post-processing tools are required for generating the boundary elements and for visualization. Users can use MSMS ( http://www.scripps.edu/~sanner/html/msms_home.html) for pre-processing, and VMD ( http://www.ks.uiuc.edu/Research/vmd/) for visualization. Sub-programs included: An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad ( http://www-users.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html), and the fast multipole methods subroutines from FMMSuite ( http://www.fastmultipole.org/). Nature of problem: Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Solution method: A novel node-patch scheme is used to discretize the well-conditioned boundary integral equation formulation of the linearized Poisson-Boltzmann equation. Various Krylov subspace solvers can be subsequently applied to solve the resulting linear system, with a bounded number of iterations independent of the number of discretized unknowns. The matrix-vector multiplication at each iteration is accelerated by the adaptive new versions of fast multipole methods. The AFMPB solver requires other stand-alone pre-processing tools for boundary mesh generation, post-processing tools for data analysis and visualization, and can be conveniently coupled with different time stepping methods for dynamics simulation. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/~lubz/afmpb.html and http://mccammon.ucsd.edu/ for updates and changes. Running time: The running time varies with the number of discretized elements ( N) in the system and their distributions. In most cases, it scales linearly as a function of N.

Fast Time and Space Parallel Algorithms for Solution of Parabolic Partial Differential Equations

NASA Technical Reports Server (NTRS)

Fijany, Amir

1993-01-01

In this paper, fast time- and Space -Parallel agorithms for solution of linear parabolic PDEs are developed. It is shown that the seemingly strictly serial iterations of the time-stepping procedure for solution of the problem can be completed decoupled.

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Some fast elliptic solvers on parallel architectures and their complexities

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Y.

1989-01-01

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

Some fast elliptic solvers on parallel architectures and their complexities

NASA Technical Reports Server (NTRS)

Gallopoulos, E.; Saad, Youcef

1989-01-01

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

Fast adaptive composite grid methods on distributed parallel architectures

NASA Technical Reports Server (NTRS)

Lemke, Max; Quinlan, Daniel

1992-01-01

The fast adaptive composite (FAC) grid method is compared with the adaptive composite method (AFAC) under variety of conditions including vectorization and parallelization. Results are given for distributed memory multiprocessor architectures (SUPRENUM, Intel iPSC/2 and iPSC/860). It is shown that the good performance of AFAC and its superiority over FAC in a parallel environment is a property of the algorithm and not dependent on peculiarities of any machine.

Relation Between Firing Statistics of Spiking Neuron with Delayed Fast Inhibitory Feedback and Without Feedback

NASA Astrophysics Data System (ADS)

Vidybida, Alexander; Shchur, Olha

We consider a class of spiking neuronal models, defined by a set of conditions typical for basic threshold-type models, such as the leaky integrate-and-fire or the binding neuron model and also for some artificial neurons. A neuron is fed with a Poisson process. Each output impulse is applied to the neuron itself after a finite delay Δ. This impulse acts as being delivered through a fast Cl-type inhibitory synapse. We derive a general relation which allows calculating exactly the probability density function (pdf) p(t) of output interspike intervals of a neuron with feedback based on known pdf p0(t) for the same neuron without feedback and on the properties of the feedback line (the Δ value). Similar relations between corresponding moments are derived. Furthermore, we prove that the initial segment of pdf p0(t) for a neuron with a fixed threshold level is the same for any neuron satisfying the imposed conditions and is completely determined by the input stream. For the Poisson input stream, we calculate that initial segment exactly and, based on it, obtain exactly the initial segment of pdf p(t) for a neuron with feedback. That is the initial segment of p(t) is model-independent as well. The obtained expressions are checked by means of Monte Carlo simulation. The course of p(t) has a pronounced peculiarity, which makes it impossible to approximate p(t) by Poisson or another simple stochastic process.

IMFIT: A FAST, FLEXIBLE NEW PROGRAM FOR ASTRONOMICAL IMAGE FITTING

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

Erwin, Peter; Universitäts-Sternwarte München, Scheinerstrasse 1, D-81679 München

2015-02-01

I describe a new, open-source astronomical image-fitting program called IMFIT, specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. A key characteristic of the program is an object-oriented design that allows new types of image components (two-dimensional surface-brightness functions) to be easily written and added to the program. Image functions provided with IMFIT include the usual suspects for galaxy decompositions (Sérsic, exponential, Gaussian), along with Core-Sérsic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through three-dimensional luminosity-density models of disks and rings seen at arbitrary inclinations. Available minimization algorithmsmore » include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard χ{sup 2} statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or Poisson-based maximum-likelihood statistics; the latter approach is particularly appropriate for cases of Poisson data in the low-count regime. I show that fitting low-signal-to-noise ratio galaxy images using χ{sup 2} minimization and individual-pixel Gaussian uncertainties can lead to significant biases in fitted parameter values, which are avoided if a Poisson-based statistic is used; this is true even when Gaussian read noise is present.« less

Wavelets, ridgelets, and curvelets for Poisson noise removal.

PubMed

Zhang, Bo; Fadili, Jalal M; Starck, Jean-Luc

2008-07-01

In order to denoise Poisson count data, we introduce a variance stabilizing transform (VST) applied on a filtered discrete Poisson process, yielding a near Gaussian process with asymptotic constant variance. This new transform, which can be deemed as an extension of the Anscombe transform to filtered data, is simple, fast, and efficient in (very) low-count situations. We combine this VST with the filter banks of wavelets, ridgelets and curvelets, leading to multiscale VSTs (MS-VSTs) and nonlinear decomposition schemes. By doing so, the noise-contaminated coefficients of these MS-VST-modified transforms are asymptotically normally distributed with known variances. A classical hypothesis-testing framework is adopted to detect the significant coefficients, and a sparsity-driven iterative scheme reconstructs properly the final estimate. A range of examples show the power of this MS-VST approach for recovering important structures of various morphologies in (very) low-count images. These results also demonstrate that the MS-VST approach is competitive relative to many existing denoising methods.

Dynamic grid refinement for partial differential equations on parallel computers

NASA Technical Reports Server (NTRS)

Mccormick, S.; Quinlan, D.

1989-01-01

The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids to provide adaptive resolution and fast solution of PDEs. An asynchronous version of FAC, called AFAC, that completely eliminates the bottleneck to parallelism is presented. This paper describes the advantage that this algorithm has in adaptive refinement for moving singularities on multiprocessor computers. This work is applicable to the parallel solution of two- and three-dimensional shock tracking problems.

HPCC Methodologies for Structural Design and Analysis on Parallel and Distributed Computing Platforms

NASA Technical Reports Server (NTRS)

Farhat, Charbel

1998-01-01

In this grant, we have proposed a three-year research effort focused on developing High Performance Computation and Communication (HPCC) methodologies for structural analysis on parallel processors and clusters of workstations, with emphasis on reducing the structural design cycle time. Besides consolidating and further improving the FETI solver technology to address plate and shell structures, we have proposed to tackle the following design related issues: (a) parallel coupling and assembly of independently designed and analyzed three-dimensional substructures with non-matching interfaces, (b) fast and smart parallel re-analysis of a given structure after it has undergone design modifications, (c) parallel evaluation of sensitivity operators (derivatives) for design optimization, and (d) fast parallel analysis of mildly nonlinear structures. While our proposal was accepted, support was provided only for one year.

Fast, Massively Parallel Data Processors

NASA Technical Reports Server (NTRS)

Heaton, Robert A.; Blevins, Donald W.; Davis, ED

1994-01-01

Proposed fast, massively parallel data processor contains 8x16 array of processing elements with efficient interconnection scheme and options for flexible local control. Processing elements communicate with each other on "X" interconnection grid with external memory via high-capacity input/output bus. This approach to conditional operation nearly doubles speed of various arithmetic operations.

SIERRA - A 3-D device simulator for reliability modeling

NASA Astrophysics Data System (ADS)

Chern, Jue-Hsien; Arledge, Lawrence A., Jr.; Yang, Ping; Maeda, John T.

1989-05-01

SIERRA is a three-dimensional general-purpose semiconductor-device simulation program which serves as a foundation for investigating integrated-circuit (IC) device and reliability issues. This program solves the Poisson and continuity equations in silicon under dc, transient, and small-signal conditions. Executing on a vector/parallel minisupercomputer, SIERRA utilizes a matrix solver which uses an incomplete LU (ILU) preconditioned conjugate gradient square (CGS, BCG) method. The ILU-CGS method provides a good compromise between memory size and convergence rate. The authors have observed a 5x to 7x speedup over standard direct methods in simulations of transient problems containing highly coupled Poisson and continuity equations such as those found in reliability-oriented simulations. The application of SIERRA to parasitic CMOS latchup and dynamic random-access memory single-event-upset studies is described.

A Domain Decomposition Parallelization of the Fast Marching Method

NASA Technical Reports Server (NTRS)

Herrmann, M.

2003-01-01

In this paper, the first domain decomposition parallelization of the Fast Marching Method for level sets has been presented. Parallel speedup has been demonstrated in both the optimal and non-optimal domain decomposition case. The parallel performance of the proposed method is strongly dependent on load balancing separately the number of nodes on each side of the interface. A load imbalance of nodes on either side of the domain leads to an increase in communication and rollback operations. Furthermore, the amount of inter-domain communication can be reduced by aligning the inter-domain boundaries with the interface normal vectors. In the case of optimal load balancing and aligned inter-domain boundaries, the proposed parallel FMM algorithm is highly efficient, reaching efficiency factors of up to 0.98. Future work will focus on the extension of the proposed parallel algorithm to higher order accuracy. Also, to further enhance parallel performance, the coupling of the domain decomposition parallelization to the G(sub 0)-based parallelization will be investigated.

S-HARP: A parallel dynamic spectral partitioner

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

Sohn, A.; Simon, H.

1998-01-01

Computational science problems with adaptive meshes involve dynamic load balancing when implemented on parallel machines. This dynamic load balancing requires fast partitioning of computational meshes at run time. The authors present in this report a fast parallel dynamic partitioner, called S-HARP. The underlying principles of S-HARP are the fast feature of inertial partitioning and the quality feature of spectral partitioning. S-HARP partitions a graph from scratch, requiring no partition information from previous iterations. Two types of parallelism have been exploited in S-HARP, fine grain loop level parallelism and coarse grain recursive parallelism. The parallel partitioner has been implemented in Messagemore » Passing Interface on Cray T3E and IBM SP2 for portability. Experimental results indicate that S-HARP can partition a mesh of over 100,000 vertices into 256 partitions in 0.2 seconds on a 64 processor Cray T3E. S-HARP is much more scalable than other dynamic partitioners, giving over 15 fold speedup on 64 processors while ParaMeTiS1.0 gives a few fold speedup. Experimental results demonstrate that S-HARP is three to 10 times faster than the dynamic partitioners ParaMeTiS and Jostle on six computational meshes of size over 100,000 vertices.« less

A general purpose subroutine for fast fourier transform on a distributed memory parallel machine

NASA Technical Reports Server (NTRS)

Dubey, A.; Zubair, M.; Grosch, C. E.

1992-01-01

One issue which is central in developing a general purpose Fast Fourier Transform (FFT) subroutine on a distributed memory parallel machine is the data distribution. It is possible that different users would like to use the FFT routine with different data distributions. Thus, there is a need to design FFT schemes on distributed memory parallel machines which can support a variety of data distributions. An FFT implementation on a distributed memory parallel machine which works for a number of data distributions commonly encountered in scientific applications is presented. The problem of rearranging the data after computing the FFT is also addressed. The performance of the implementation on a distributed memory parallel machine Intel iPSC/860 is evaluated.

Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method

PubMed Central

Zhang, Tingting; Kou, S. C.

2010-01-01

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure. PMID:21258615

Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method.

PubMed

Zhang, Tingting; Kou, S C

2010-01-01

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure.

Fast, adaptive summation of point forces in the two-dimensional Poisson equation

NASA Technical Reports Server (NTRS)

Van Dommelen, Leon; Rundensteiner, Elke A.

1989-01-01

A comparatively simple procedure is presented for the direct summation of the velocity field introduced by point vortices which significantly reduces the required number of operations by replacing selected partial sums by asymptotic series. Tables are presented which demonstrate the speed of this algorithm in terms of the mere doubling of computational time in dealing with a doubling of the number of vortices; current methods involve a computational time extension by a factor of 4. This procedure need not be restricted to the solution of the Poisson equation, and may be applied to other problems involving groups of points in which the interaction between elements of different groups can be simplified when the distance between groups is sufficiently great.

Two-Dimensional Grids About Airfoils and Other Shapes

NASA Technical Reports Server (NTRS)

Sorenson, R.

1982-01-01

GRAPE computer program generates two-dimensional finite-difference grids about airfoils and other shapes by use of Poisson differential equation. GRAPE can be used with any boundary shape, even one specified by tabulated points and including limited number of sharp corners. Numerically stable and computationally fast, GRAPE provides aerodynamic analyst with efficient and consistant means of grid generation.

Development of Fast Algorithms Using Recursion, Nesting and Iterations for Computational Electromagnetics

NASA Technical Reports Server (NTRS)

Chew, W. C.; Song, J. M.; Lu, C. C.; Weedon, W. H.

1995-01-01

In the first phase of our work, we have concentrated on laying the foundation to develop fast algorithms, including the use of recursive structure like the recursive aggregate interaction matrix algorithm (RAIMA), the nested equivalence principle algorithm (NEPAL), the ray-propagation fast multipole algorithm (RPFMA), and the multi-level fast multipole algorithm (MLFMA). We have also investigated the use of curvilinear patches to build a basic method of moments code where these acceleration techniques can be used later. In the second phase, which is mainly reported on here, we have concentrated on implementing three-dimensional NEPAL on a massively parallel machine, the Connection Machine CM-5, and have been able to obtain some 3D scattering results. In order to understand the parallelization of codes on the Connection Machine, we have also studied the parallelization of 3D finite-difference time-domain (FDTD) code with PML material absorbing boundary condition (ABC). We found that simple algorithms like the FDTD with material ABC can be parallelized very well allowing us to solve within a minute a problem of over a million nodes. In addition, we have studied the use of the fast multipole method and the ray-propagation fast multipole algorithm to expedite matrix-vector multiplication in a conjugate-gradient solution to integral equations of scattering. We find that these methods are faster than LU decomposition for one incident angle, but are slower than LU decomposition when many incident angles are needed as in the monostatic RCS calculations.

The crack problem for a nonhomogeneous plane

NASA Technical Reports Server (NTRS)

Delale, F.; Erdogan, F.

1982-01-01

The plane elasticity problem for a nonhomogeneous medium containing a crack is considered. It is assumed that the Poisson's ratio of the medium is constant and the Young's modulus E varies exponentially with the coordinate parallel to the crack. First the half plane problem is formulated and the solution is given for arbitrary tractions along the boundary. Then the integral equation for the crack problem is derived. It is shown that the integral equation having the derivative of the crack surface displacement as the density function has a simple Cauchy type kernel. Hence, its solution and the stresses around the crack tips have the conventional square root singularity. The solution is given for various loading conditions. The results show that the effect of the Poisson's ratio and consequently that of the thickness constraint on the stress intensity factors are rather negligible.

The crack problem for a nonhomogeneous plane

NASA Technical Reports Server (NTRS)

Delale, F.; Erdogan, F.

1983-01-01

The plane elasticity problem for a nonhomogeneous medium containing a crack is considered. It is assumed that the Poisson's ratio of the medium is constant and the Young's modulus E varies exponentially with the coordinate parallel to the crack. First the half plane problem is formulated and the solution is given for arbitrary tractions along the boundary. Then the integral equation for the crack problem is derived. It is shown that the integral equation having the derivative of the crack surface displacement as the density function has a simple Cauchy type kernel. Hence, its solution and the stresses around the crack tips have the conventional square root singularity. The solution is given for various loading conditions. The results show that the effect of the Poisson's ratio and consequently that of the thickness constraint on the stress intensity factors are rather negligible.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

NASA Astrophysics Data System (ADS)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A.; Oliveira, Micael J. T.; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G.; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A. L.

2012-06-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Optimizing transformations of stencil operations for parallel cache-based architectures

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

Bassetti, F.; Davis, K.

This paper describes a new technique for optimizing serial and parallel stencil- and stencil-like operations for cache-based architectures. This technique takes advantage of the semantic knowledge implicity in stencil-like computations. The technique is implemented as a source-to-source program transformation; because of its specificity it could not be expected of a conventional compiler. Empirical results demonstrate a uniform factor of two speedup. The experiments clearly show the benefits of this technique to be a consequence, as intended, of the reduction in cache misses. The test codes are based on a 5-point stencil obtained by the discretization of the Poisson equation andmore » applied to a two-dimensional uniform grid using the Jacobi method as an iterative solver. Results are presented for a 1-D tiling for a single processor, and in parallel using 1-D data partition. For the parallel case both blocking and non-blocking communication are tested. The same scheme of experiments has bee n performed for the 2-D tiling case. However, for the parallel case the 2-D partitioning is not discussed here, so the parallel case handled for 2-D is 2-D tiling with 1-D data partitioning.« less

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

PubMed

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A L

2012-06-13

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Development and Application of a Parallel LCAO Cluster Method

NASA Astrophysics Data System (ADS)

Patton, David C.

1997-08-01

CPU intensive steps in the SCF electronic structure calculations of clusters and molecules with a first-principles LCAO method have been fully parallelized via a message passing paradigm. Identification of the parts of the code that are composed of many independent compute-intensive steps is discussed in detail as they are the most readily parallelized. Most of the parallelization involves spatially decomposing numerical operations on a mesh. One exception is the solution of Poisson's equation which relies on distribution of the charge density and multipole methods. The method we use to parallelize this part of the calculation is quite novel and is covered in detail. We present a general method for dynamically load-balancing a parallel calculation and discuss how we use this method in our code. The results of benchmark calculations of the IR and Raman spectra of PAH molecules such as anthracene (C_14H_10) and tetracene (C_18H_12) are presented. These benchmark calculations were performed on an IBM SP2 and a SUN Ultra HPC server with both MPI and PVM. Scalability and speedup for these calculations is analyzed to determine the efficiency of the code. In addition, performance and usage issues for MPI and PVM are presented.

Adiabatic reduction of a model of stochastic gene expression with jump Markov process.

PubMed

Yvinec, Romain; Zhuge, Changjing; Lei, Jinzhi; Mackey, Michael C

2014-04-01

This paper considers adiabatic reduction in a model of stochastic gene expression with bursting transcription considered as a jump Markov process. In this model, the process of gene expression with auto-regulation is described by fast/slow dynamics. The production of mRNA is assumed to follow a compound Poisson process occurring at a rate depending on protein levels (the phenomena called bursting in molecular biology) and the production of protein is a linear function of mRNA numbers. When the dynamics of mRNA is assumed to be a fast process (due to faster mRNA degradation than that of protein) we prove that, with appropriate scalings in the burst rate, jump size or translational rate, the bursting phenomena can be transmitted to the slow variable. We show that, depending on the scaling, the reduced equation is either a stochastic differential equation with a jump Poisson process or a deterministic ordinary differential equation. These results are significant because adiabatic reduction techniques seem to have not been rigorously justified for a stochastic differential system containing a jump Markov process. We expect that the results can be generalized to adiabatic methods in more general stochastic hybrid systems.

Full particle simulations of quasi-perpendicular shocks

NASA Astrophysics Data System (ADS)

Lembège, B.

This tutorial-style review is dedicated to the different strategies and constraints used for analysing the dynamics of a collisionless shocks with full particle simulations. Main results obtained with such simulations can be found in published materials (recent references are provided in this text); these will be only quoted herein in order to illustrate a few aspects of these simulations. Thanks to the large improvement of super computers, full particle simulations reveal to be quite helpful for analyzing in details the dynamics of collisionless shocks. The main characteristics of such codes can be shortly reminded as follows: one resolves the full set of Poisson and Maxwell's equations without any approximation. Two approaches are commonly used for resolving this equation's set, more precisely the space derivatives: (i) the finite difference approach and (ii) the use of FFT's (Fast Fourier Transform). Two advantages of approach (ii) are that FFT's are highly optimized in supercomputers libraries, and these allow to separate all fields components into two groups: the longitudinal electrostatic component El (solution of Poisson equation) and the transverse electromagnetic components Et and Bt solutions of the Maxwell's equations (so called "fields pusher"). Such a separation is quite helpful in the post processing stage necessary for the data analysis, as will be explained in the presentation. both ions and electrons populations are treated as individual finite-size particles and suffer the effects of all fields via the Lorentz force, so called "particle pusher", which is applied to each particle. Because of the large number of particles commonly used, the particle pusher represents the most expensive part of the calculations on which most efforts of optimisation needs to be performed (in terms of "vectorisation" or of "parallelism"). Relativistic effects may be included in this force via the use of particle momemtum. Each particle has three velocity components (vx, vy, vz), but may have 1, 2 or 3 space coordinates (x, y, z) according to the dimension of the code of concern.

Multi-LED parallel transmission for long distance underwater VLC system with one SPAD receiver

NASA Astrophysics Data System (ADS)

Wang, Chao; Yu, Hong-Yi; Zhu, Yi-Jun; Wang, Tao; Ji, Ya-Wei

2018-03-01

In this paper, a multiple light emitting diode (LED) chips parallel transmission (Multi-LED-PT) scheme for underwater visible light communication system with one photon-counting single photon avalanche diode (SPAD) receiver is proposed. As the lamp always consists of multi-LED chips, the data rate could be improved when we drive these multi-LED chips parallel by using the interleaver-division-multiplexing technique. For each chip, the on-off-keying modulation is used to reduce the influence of clipping. Then a serial successive interference cancellation detection algorithm based on ideal Poisson photon-counting channel by the SPAD is proposed. Finally, compared to the SPAD-based direct current-biased optical orthogonal frequency division multiplexing system, the proposed Multi-LED-PT system could improve the error-rate performance and anti-nonlinearity performance significantly under the effects of absorption, scattering and weak turbulence-induced channel fading together.

Phosphoenolpyruvate carboxykinase 1 gene (Pck1) displays parallel evolution between Old World and New World fruit bats.

PubMed

Zhu, Lei; Yin, Qiuyuan; Irwin, David M; Zhang, Shuyi

2015-01-01

Bats are an ideal mammalian group for exploring adaptations to fasting due to their large variety of diets and because fasting is a regular part of their life cycle. Mammals fed on a carbohydrate-rich diet experience a rapid decrease in blood glucose levels during a fast, thus, the development of mechanisms to resist the consequences of regular fasts, experienced on a daily basis, must have been crucial in the evolution of frugivorous bats. Phosphoenolpyruvate carboxykinase 1 (PEPCK1, encoded by the Pck1 gene) is the rate-limiting enzyme in gluconeogenesis and is largely responsible for the maintenance of glucose homeostasis during fasting in fruit-eating bats. To test whether Pck1 has experienced adaptive evolution in frugivorous bats, we obtained Pck1 coding sequence from 20 species of bats, including five Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our molecular evolutionary analyses of these sequences revealed that Pck1 was under purifying selection in both Old World and New World fruit bats with no evidence of positive selection detected in either ancestral branch leading to fruit bats. Interestingly, however, six specific amino acid substitutions were detected on the ancestral lineage of OWFBs. In addition, we found considerable evidence for parallel evolution, at the amino acid level, between the PEPCK1 sequences of Old World fruit bats and New World fruit bats. Test for parallel evolution showed that four parallel substitutions (Q276R, R503H, I558V and Q593R) were driven by natural selection. Our study provides evidence that Pck1 underwent parallel evolution between Old World and New World fruit bats, two lineages of mammals that feed on a carbohydrate-rich diet and experience regular periods of fasting as part of their life cycle.

Phosphoenolpyruvate Carboxykinase 1 Gene (Pck1) Displays Parallel Evolution between Old World and New World Fruit Bats

PubMed Central

Irwin, David M.; Zhang, Shuyi

2015-01-01

Bats are an ideal mammalian group for exploring adaptations to fasting due to their large variety of diets and because fasting is a regular part of their life cycle. Mammals fed on a carbohydrate-rich diet experience a rapid decrease in blood glucose levels during a fast, thus, the development of mechanisms to resist the consequences of regular fasts, experienced on a daily basis, must have been crucial in the evolution of frugivorous bats. Phosphoenolpyruvate carboxykinase 1 (PEPCK1, encoded by the Pck1 gene) is the rate-limiting enzyme in gluconeogenesis and is largely responsible for the maintenance of glucose homeostasis during fasting in fruit-eating bats. To test whether Pck1 has experienced adaptive evolution in frugivorous bats, we obtained Pck1 coding sequence from 20 species of bats, including five Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our molecular evolutionary analyses of these sequences revealed that Pck1 was under purifying selection in both Old World and New World fruit bats with no evidence of positive selection detected in either ancestral branch leading to fruit bats. Interestingly, however, six specific amino acid substitutions were detected on the ancestral lineage of OWFBs. In addition, we found considerable evidence for parallel evolution, at the amino acid level, between the PEPCK1 sequences of Old World fruit bats and New World fruit bats. Test for parallel evolution showed that four parallel substitutions (Q276R, R503H, I558V and Q593R) were driven by natural selection. Our study provides evidence that Pck1 underwent parallel evolution between Old World and New World fruit bats, two lineages of mammals that feed on a carbohydrate-rich diet and experience regular periods of fasting as part of their life cycle. PMID:25807515

A fast sorting algorithm for a hypersonic rarefied flow particle simulation on the connection machine

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1989-01-01

The data parallel implementation of a particle simulation for hypersonic rarefied flow described by Dagum associates a single parallel data element with each particle in the simulation. The simulated space is divided into discrete regions called cells containing a variable and constantly changing number of particles. The implementation requires a global sort of the parallel data elements so as to arrange them in an order that allows immediate access to the information associated with cells in the simulation. Described here is a very fast algorithm for performing the necessary ranking of the parallel data elements. The performance of the new algorithm is compared with that of the microcoded instruction for ranking on the Connection Machine.

Extreme Performance Scalable Operating Systems Final Progress Report (July 1, 2008 - October 31, 2011)

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

Malony, Allen D; Shende, Sameer

This is the final progress report for the FastOS (Phase 2) (FastOS-2) project with Argonne National Laboratory and the University of Oregon (UO). The project started at UO on July 1, 2008 and ran until April 30, 2010, at which time a six-month no-cost extension began. The FastOS-2 work at UO delivered excellent results in all research work areas: * scalable parallel monitoring * kernel-level performance measurement * parallel I/0 system measurement * large-scale and hybrid application performance measurement * onlne scalable performance data reduction and analysis * binary instrumentation

Low-frequency surface waves on semi-bounded magnetized quantum plasma

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

Moradi, Afshin, E-mail: a.moradi@kut.ac.ir

2016-08-15

The propagation of low-frequency electrostatic surface waves on the interface between a vacuum and an electron-ion quantum plasma is studied in the direction perpendicular to an external static magnetic field which is parallel to the interface. A new dispersion equation is derived by employing both the quantum magnetohydrodynamic and Poisson equations. It is shown that the dispersion equations for forward and backward-going surface waves are different from each other.

The Arrow of Time in the Collapse of Collisionless Self-gravitating Systems: Non-validity of the Vlasov-Poisson Equation during Violent Relaxation

NASA Astrophysics Data System (ADS)

Beraldo e Silva, Leandro; de Siqueira Pedra, Walter; Sodré, Laerte; Perico, Eder L. D.; Lima, Marcos

2017-09-01

The collapse of a collisionless self-gravitating system, with the fast achievement of a quasi-stationary state, is driven by violent relaxation, with a typical particle interacting with the time-changing collective potential. It is traditionally assumed that this evolution is governed by the Vlasov-Poisson equation, in which case entropy must be conserved. We run N-body simulations of isolated self-gravitating systems, using three simulation codes, NBODY-6 (direct summation without softening), NBODY-2 (direct summation with softening), and GADGET-2 (tree code with softening), for different numbers of particles and initial conditions. At each snapshot, we estimate the Shannon entropy of the distribution function with three different techniques: Kernel, Nearest Neighbor, and EnBiD. For all simulation codes and estimators, the entropy evolution converges to the same limit as N increases. During violent relaxation, the entropy has a fast increase followed by damping oscillations, indicating that violent relaxation must be described by a kinetic equation other than the Vlasov-Poisson equation, even for N as large as that of astronomical structures. This indicates that violent relaxation cannot be described by a time-reversible equation, shedding some light on the so-called “fundamental paradox of stellar dynamics.” The long-term evolution is well-described by the orbit-averaged Fokker-Planck model, with Coulomb logarithm values in the expected range 10{--}12. By means of NBODY-2, we also study the dependence of the two-body relaxation timescale on the softening length. The approach presented in the current work can potentially provide a general method for testing any kinetic equation intended to describe the macroscopic evolution of N-body systems.

Fast hydrological model calibration based on the heterogeneous parallel computing accelerated shuffled complex evolution method

NASA Astrophysics Data System (ADS)

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Hong, Yang; Zuo, Depeng; Ren, Minglei; Lei, Tianjie; Liang, Ke

2018-01-01

Hydrological model calibration has been a hot issue for decades. The shuffled complex evolution method developed at the University of Arizona (SCE-UA) has been proved to be an effective and robust optimization approach. However, its computational efficiency deteriorates significantly when the amount of hydrometeorological data increases. In recent years, the rise of heterogeneous parallel computing has brought hope for the acceleration of hydrological model calibration. This study proposed a parallel SCE-UA method and applied it to the calibration of a watershed rainfall-runoff model, the Xinanjiang model. The parallel method was implemented on heterogeneous computing systems using OpenMP and CUDA. Performance testing and sensitivity analysis were carried out to verify its correctness and efficiency. Comparison results indicated that heterogeneous parallel computing-accelerated SCE-UA converged much more quickly than the original serial version and possessed satisfactory accuracy and stability for the task of fast hydrological model calibration.

SU-E-T-466: Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit

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

Ramos-Mendez, J; Faddegon, B; Perl, J

2015-06-15

Purpose: To develop and verify an extension to TOPAS for calculation of dose response models (TCP/NTCP). TOPAS wraps and extends Geant4. Methods: The TOPAS DICOM interface was extended to include structure contours, for subsequent calculation of DVH’s and TCP/NTCP. The following dose response models were implemented: Lyman-Kutcher-Burman (LKB), critical element (CE), population based critical volume (CV), parallel-serials, a sigmoid-based model of Niemierko for NTCP and TCP, and a Poisson-based model for TCP. For verification, results for the parallel-serial and Poisson models, with 6 MV x-ray dose distributions calculated with TOPAS and Pinnacle v9.2, were compared to data from the benchmarkmore » configuration of the AAPM Task Group 166 (TG166). We provide a benchmark configuration suitable for proton therapy along with results for the implementation of the Niemierko, CV and CE models. Results: The maximum difference in DVH calculated with Pinnacle and TOPAS was 2%. Differences between TG166 data and Monte Carlo calculations of up to 4.2%±6.1% were found for the parallel-serial model and up to 1.0%±0.7% for the Poisson model (including the uncertainty due to lack of knowledge of the point spacing in TG166). For CE, CV and Niemierko models, the discrepancies between the Pinnacle and TOPAS results are 74.5%, 34.8% and 52.1% when using 29.7 cGy point spacing, the differences being highly sensitive to dose spacing. On the other hand, with our proposed benchmark configuration, the largest differences were 12.05%±0.38%, 3.74%±1.6%, 1.57%±4.9% and 1.97%±4.6% for the CE, CV, Niemierko and LKB models, respectively. Conclusion: Several dose response models were successfully implemented with the extension module. Reference data was calculated for future benchmarking. Dose response calculated for the different models varied much more widely for the TG166 benchmark than for the proposed benchmark, which had much lower sensitivity to the choice of DVH dose points. This work was supported by National Cancer Institute Grant R01CA140735.« less

Research on the Application of Fast-steering Mirror in Stellar Interferometer

NASA Astrophysics Data System (ADS)

Mei, R.; Hu, Z. W.; Xu, T.; Sun, C. S.

2017-07-01

For a stellar interferometer, the fast-steering mirror (FSM) is widely utilized to correct wavefront tilt caused by atmospheric turbulence and internal instrumental vibration due to its high resolution and fast response frequency. In this study, the non-coplanar error between the FSM and actuator deflection axis introduced by manufacture, assembly, and adjustment is analyzed. Via a numerical method, the additional optical path difference (OPD) caused by above factors is studied, and its effects on tracking accuracy of stellar interferometer are also discussed. On the other hand, the starlight parallelism between the beams of two arms is one of the main factors of the loss of fringe visibility. By analyzing the influence of wavefront tilt caused by the atmospheric turbulence on fringe visibility, a simple and efficient real-time correction scheme of starlight parallelism is proposed based on a single array detector. The feasibility of this scheme is demonstrated by laboratory experiment. The results show that starlight parallelism meets the requirement of stellar interferometer in wavefront tilt preliminarily after the correction of fast-steering mirror.

Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi

PubMed Central

Li, Chuan; Li, Lin; Zhang, Jie; Alexov, Emil

2012-01-01

The Gauss-Seidel method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the Gauss-Seidel method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of CPUs. In contrast to other existing solutions, our method does not require any assumptions and is equally applicable for solving linear and nonlinear equations. This approach is implemented in the DelPhi program, which is a finite difference Poisson-Boltzmann equation solver to model electrostatics in molecular biology. This development makes the iterative procedure on obtaining the electrostatic potential distribution in the parallelized DelPhi several folds faster than that in the serial code. Further we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures. PMID:22674480

Fast I/O for Massively Parallel Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew T.

1996-01-01

The two primary goals for this report were the design, contruction and modeling of parallel disk arrays for scientific visualization and animation, and a study of the IO requirements of highly parallel applications. In addition, further work in parallel display systems required to project and animate the very high-resolution frames resulting from our supercomputing simulations in ocean circulation and compressible gas dynamics.

Solutions of large-scale electromagnetics problems involving dielectric objects with the parallel multilevel fast multipole algorithm.

PubMed

Ergül, Özgür

2011-11-01

Fast and accurate solutions of large-scale electromagnetics problems involving homogeneous dielectric objects are considered. Problems are formulated with the electric and magnetic current combined-field integral equation and discretized with the Rao-Wilton-Glisson functions. Solutions are performed iteratively by using the multilevel fast multipole algorithm (MLFMA). For the solution of large-scale problems discretized with millions of unknowns, MLFMA is parallelized on distributed-memory architectures using a rigorous technique, namely, the hierarchical partitioning strategy. Efficiency and accuracy of the developed implementation are demonstrated on very large problems involving as many as 100 million unknowns.

Shear-induced chaos

NASA Astrophysics Data System (ADS)

Lin, Kevin K.; Young, Lai-Sang

2008-05-01

Guided by a geometric understanding developed in earlier works of Wang and Young, we carry out numerical studies of shear-induced chaos in several parallel but different situations. The settings considered include periodic kicking of limit cycles, random kicks at Poisson times and continuous-time driving by white noise. The forcing of a quasi-periodic model describing two coupled oscillators is also investigated. In all cases, positive Lyapunov exponents are found in suitable parameter ranges when the forcing is suitably directed.

A Fast Solver for Implicit Integration of the Vlasov--Poisson System in the Eulerian Framework

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

Garrett, C. Kristopher; Hauck, Cory D.

In this paper, we present a domain decomposition algorithm to accelerate the solution of Eulerian-type discretizations of the linear, steady-state Vlasov equation. The steady-state solver then forms a key component in the implementation of fully implicit or nearly fully implicit temporal integrators for the nonlinear Vlasov--Poisson system. The solver relies on a particular decomposition of phase space that enables the use of sweeping techniques commonly used in radiation transport applications. The original linear system for the phase space unknowns is then replaced by a smaller linear system involving only unknowns on the boundary between subdomains, which can then be solvedmore » efficiently with Krylov methods such as GMRES. Steady-state solves are combined to form an implicit Runge--Kutta time integrator, and the Vlasov equation is coupled self-consistently to the Poisson equation via a linearized procedure or a nonlinear fixed-point method for the electric field. Finally, numerical results for standard test problems demonstrate the efficiency of the domain decomposition approach when compared to the direct application of an iterative solver to the original linear system.« less

Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment

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

Meng, Da; Zheng, Bin; Lin, Guang

2014-08-29

We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is themore » number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.« less

A Fast Solver for Implicit Integration of the Vlasov--Poisson System in the Eulerian Framework

DOE PAGES

Garrett, C. Kristopher; Hauck, Cory D.

2018-04-05

In this paper, we present a domain decomposition algorithm to accelerate the solution of Eulerian-type discretizations of the linear, steady-state Vlasov equation. The steady-state solver then forms a key component in the implementation of fully implicit or nearly fully implicit temporal integrators for the nonlinear Vlasov--Poisson system. The solver relies on a particular decomposition of phase space that enables the use of sweeping techniques commonly used in radiation transport applications. The original linear system for the phase space unknowns is then replaced by a smaller linear system involving only unknowns on the boundary between subdomains, which can then be solvedmore » efficiently with Krylov methods such as GMRES. Steady-state solves are combined to form an implicit Runge--Kutta time integrator, and the Vlasov equation is coupled self-consistently to the Poisson equation via a linearized procedure or a nonlinear fixed-point method for the electric field. Finally, numerical results for standard test problems demonstrate the efficiency of the domain decomposition approach when compared to the direct application of an iterative solver to the original linear system.« less

Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin

PubMed Central

Simakov, Nikolay A.

2010-01-01

A soft repulsion (SR) model of short range interactions between mobile ions and protein atoms is introduced in the framework of continuum representation of the protein and solvent. The Poisson-Nernst-Plank (PNP) theory of ion transport through biological channels is modified to incorporate this soft wall protein model. Two sets of SR parameters are introduced: the first is parameterized for all essential amino acid residues using all atom molecular dynamic simulations; the second is a truncated Lennard – Jones potential. We have further designed an energy based algorithm for the determination of the ion accessible volume, which is appropriate for a particular system discretization. The effects of these models of short-range interaction were tested by computing current-voltage characteristics of the α-hemolysin channel. The introduced SR potentials significantly improve prediction of channel selectivity. In addition, we studied the effect of choice of some space-dependent diffusion coefficient distributions on the predicted current-voltage properties. We conclude that the diffusion coefficient distributions largely affect total currents and have little effect on rectifications, selectivity or reversal potential. The PNP-SR algorithm is implemented in a new efficient parallel Poisson, Poisson-Boltzman and PNP equation solver, also incorporated in a graphical molecular modeling package HARLEM. PMID:21028776

Application of an Elongated Kelvin Model to Space Shuttle Foams

NASA Technical Reports Server (NTRS)

Sullivan, Roy M.; Ghosn, Louis J.; Lerch, Bradley A.

2009-01-01

The space shuttle foams are rigid closed-cell polyurethane foams. The two foams used most-extensively oil space shuttle external tank are BX-265 and NCFL4-124. Because of the foaming and rising process, the foam microstructures are elongated in the rise direction. As a result, these two foams exhibit a nonisotropic mechanical behavior. A detailed microstructural characterization of the two foams is presented. Key features of the foam cells are described and the average cell dimensions in the two foams are summarized. Experimental studies are also conducted to measure the room temperature mechanical response of the two foams in the two principal material directions (parallel to the rise and perpendicular to the rise). The measured elastic modulus, proportional limit stress, ultimate tensile strength, and Poisson's ratios are reported. The generalized elongated Kelvin foam model previously developed by the authors is reviewed and the equations which result from this model are summarized. Using the measured microstructural dimensions and the measured stiffness ratio, the foam tensile strength ratio and Poisson's ratios are predicted for both foams and are compared with the experimental data. The predicted tensile strength ratio is in close agreement with the measured strength ratio for both BX-265 and NCFI24-124. The comparison between the predicted Poisson's ratios and the measured values is not as favorable.

Performance of parallel computation using CUDA for solving the one-dimensional elasticity equations

NASA Astrophysics Data System (ADS)

Darmawan, J. B. B.; Mungkasi, S.

2017-01-01

In this paper, we investigate the performance of parallel computation in solving the one-dimensional elasticity equations. Elasticity equations are usually implemented in engineering science. Solving these equations fast and efficiently is desired. Therefore, we propose the use of parallel computation. Our parallel computation uses CUDA of the NVIDIA. Our research results show that parallel computation using CUDA has a great advantage and is powerful when the computation is of large scale.

Parallel MR imaging: a user's guide.

PubMed

Glockner, James F; Hu, Houchun H; Stanley, David W; Angelos, Lisa; King, Kevin

2005-01-01

Parallel imaging is a recently developed family of techniques that take advantage of the spatial information inherent in phased-array radiofrequency coils to reduce acquisition times in magnetic resonance imaging. In parallel imaging, the number of sampled k-space lines is reduced, often by a factor of two or greater, thereby significantly shortening the acquisition time. Parallel imaging techniques have only recently become commercially available, and the wide range of clinical applications is just beginning to be explored. The potential clinical applications primarily involve reduction in acquisition time, improved spatial resolution, or a combination of the two. Improvements in image quality can be achieved by reducing the echo train lengths of fast spin-echo and single-shot fast spin-echo sequences. Parallel imaging is particularly attractive for cardiac and vascular applications and will likely prove valuable as 3-T body and cardiovascular imaging becomes part of standard clinical practice. Limitations of parallel imaging include reduced signal-to-noise ratio and reconstruction artifacts. It is important to consider these limitations when deciding when to use these techniques. (c) RSNA, 2005.

FastID: Extremely Fast Forensic DNA Comparisons

DTIC Science & Technology

2017-05-19

FastID: Extremely Fast Forensic DNA Comparisons Darrell O. Ricke, PhD Bioengineering Systems & Technologies Massachusetts Institute of...Technology Lincoln Laboratory Lexington, MA USA Darrell.Ricke@ll.mit.edu Abstract—Rapid analysis of DNA forensic samples can have a critical impact on...time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

PubMed

Hung, Ling-Hong; Samudrala, Ram

2014-06-15

fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project. fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco. fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster) © The Author 2014. Published by Oxford University Press.

The use of ultrasonic properties of CR-39 track detectors in neutron dosimetry

NASA Astrophysics Data System (ADS)

Afifi, H.; El-Sersy, A.; Khaled, N.

2004-01-01

The longitudinal and shear wave ultrasonic velocities have been measured before and after exposing 5-mm thick CR-39 solid state nuclear track detectors to both a mixed field of gamma-rays and fast neutrons from an Am-Be source in the ranges from 0 to 10 4 mSv. The change in the intermolecular structure as caused by the fast neutron exposure was studied by the ultrasonic pulse echo method at a frequency of 2 MHz and at room temperature. The elastic coefficients, Poisson's ratio, microhardness, ultrasonic absorption coefficient and internal friction have been determined. The study shows that the gamma-ray irradiation had no effect on the ultrasonic properties of CR-39 at least at the used doses. However, all the ultrasonic properties are influenced by the fast neutrons at doses up to 10 4 mSv. Our experimental results confirmed that the ultrasonic technique is useful for fast neutron detection, by exploiting the differences in mechanical properties of CR-39.

Fast-ion stabilization of tokamak plasma turbulence

NASA Astrophysics Data System (ADS)

Di Siena, A.; Görler, T.; Doerk, H.; Poli, E.; Bilato, R.

2018-05-01

A significant reduction of the turbulence-induced anomalous heat transport has been observed in recent studies of magnetically confined plasmas in the presence of a significant fast-ion fractions. Therefore, the control of fast-ion populations with external heating might open the way to more optimistic scenarios for future fusion devices. However, little is known about the parameter range of relevance of these fast-ion effects which are often only highlighted in correlation with substantial electromagnetic fluctuations. Here, a significant fast ion induced stabilization is also found in both linear and nonlinear electrostatic gyrokinetic simulations which cannot be explained with the conventional assumptions based on pressure profile and dilution effects. Strong wave-fast particle resonant interactions are observed for realistic parameters where the fast particle trace approximation clearly failed and explained with the help of a reduced Vlasov model. In contrast to previous interpretations, fast particles can actively modify the Poisson field equation—even at low fast particle densities where dilution tends to be negligible and at relatively high temperatures, i.e. T  <  30T e . Further key parameters controlling the role of the fast ions are identified in the following and various ways of further optimizing their beneficial impact are explored. Finally, possible extensions into the electromagnetic regime are briefly discussed and the relevance of these findings for ITER standard scenarios is highlighted.

Convergence of highly parallel stray field calculation using the fast multipole method on irregular meshes

NASA Astrophysics Data System (ADS)

Palmesi, P.; Abert, C.; Bruckner, F.; Suess, D.

2018-05-01

Fast stray field calculation is commonly considered of great importance for micromagnetic simulations, since it is the most time consuming part of the simulation. The Fast Multipole Method (FMM) has displayed linear O(N) parallelization behavior on many cores. This article investigates the error of a recent FMM approach approximating sources using linear—instead of constant—finite elements in the singular integral for calculating the stray field and the corresponding potential. After measuring performance in an earlier manuscript, this manuscript investigates the convergence of the relative L2 error for several FMM simulation parameters. Various scenarios either calculating the stray field directly or via potential are discussed.

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

DOE PAGES

Li, Ruipeng; Saad, Yousef

2017-08-01

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

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

Li, Ruipeng; Saad, Yousef

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

POSTPROCESSING MIXED FINITE ELEMENT METHODS FOR SOLVING CAHN-HILLIARD EQUATION: METHODS AND ERROR ANALYSIS

PubMed Central

Wang, Wansheng; Chen, Long; Zhou, Jie

2015-01-01

A postprocessing technique for mixed finite element methods for the Cahn-Hilliard equation is developed and analyzed. Once the mixed finite element approximations have been computed at a fixed time on the coarser mesh, the approximations are postprocessed by solving two decoupled Poisson equations in an enriched finite element space (either on a finer grid or a higher-order space) for which many fast Poisson solvers can be applied. The nonlinear iteration is only applied to a much smaller size problem and the computational cost using Newton and direct solvers is negligible compared with the cost of the linear problem. The analysis presented here shows that this technique remains the optimal rate of convergence for both the concentration and the chemical potential approximations. The corresponding error estimate obtained in our paper, especially the negative norm error estimates, are non-trivial and different with the existing results in the literatures. PMID:27110063

SU-D-206-02: Evaluation of Partial Storage of the System Matrix for Cone Beam Computed Tomography Using a GPU Platform

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

Matenine, D; Cote, G; Mascolo-Fortin, J

2016-06-15

Purpose: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons’ trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. Methods: We propose an optimized implementation of the Siddon’s algorithm using graphics processing units (GPUs) with a novel data storage scheme. The algorithm computes a part of the system matrix on demand, typically, for one projection angle. The proposed method was enhanced with accelerating options: storage of larger subsets of themore » system matrix, systematic reuse of data via geometric symmetries, an arithmetic-rich parallel code and code configuration via machine learning. It was tested on geometries mimicking a cone beam CT acquisition of a human head. To realistically assess the execution time, the ray-tracing routines were integrated into a regularized Poisson-based reconstruction algorithm. The proposed scheme was also compared to a different approach, where the system matrix is fully pre-computed and loaded at reconstruction time. Results: Fast ray-tracing of realistic acquisition geometries, which often lack spatial symmetry properties, was enabled via the proposed method. Ray-tracing interleaved with projection and backprojection operations required significant additional time. In most cases, ray-tracing was shown to use about 66 % of the total reconstruction time. In absolute terms, tracing times varied from 3.6 s to 7.5 min, depending on the problem size. The presence of geometrical symmetries allowed for non-negligible ray-tracing and reconstruction time reduction. Arithmetic-rich parallel code and machine learning permitted a modest reconstruction time reduction, in the order of 1 %. Conclusion: Partial system matrix storage permitted the reconstruction of higher 3D image grid sizes and larger projection datasets at the cost of additional time, when compared to the fully pre-computed approach. This work was supported in part by the Fonds de recherche du Quebec - Nature et technologies (FRQ-NT). The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council of Canada (Grant No. 432290).« less

Large-scale trench-normal mantle flow beneath central South America

NASA Astrophysics Data System (ADS)

Reiss, M. C.; Rümpker, G.; Wölbern, I.

2018-01-01

We investigate the anisotropic properties of the fore-arc region of the central Andean margin between 17-25°S by analyzing shear-wave splitting from teleseismic and local earthquakes from the Nazca slab. With partly over ten years of recording time, the data set is uniquely suited to address the long-standing debate about the mantle flow field at the South American margin and in particular whether the flow field beneath the slab is parallel or perpendicular to the trench. Our measurements suggest two anisotropic layers located within the crust and mantle beneath the stations, respectively. The teleseismic measurements show a moderate change of fast polarizations from North to South along the trench ranging from parallel to subparallel to the absolute plate motion and, are oriented mostly perpendicular to the trench. Shear-wave splitting measurements from local earthquakes show fast polarizations roughly aligned trench-parallel but exhibit short-scale variations which are indicative of a relatively shallow origin. Comparisons between fast polarization directions from local earthquakes and the strike of the local fault systems yield a good agreement. To infer the parameters of the lower anisotropic layer we employ an inversion of the teleseismic waveforms based on two-layer models, where the anisotropy of the upper (crustal) layer is constrained by the results from the local splitting. The waveform inversion yields a mantle layer that is best characterized by a fast axis parallel to the absolute plate motion which is more-or-less perpendicular to the trench. This orientation is likely caused by a combination of the fossil crystallographic preferred orientation of olivine within the slab and entrained mantle flow beneath the slab. The anisotropy within the crust of the overriding continental plate is explained by the shape-preferred orientation of micro-cracks in relation to local fault zones which are oriented parallel to the overall strike of the Andean range. Our results do not provide any evidence for a significant contribution of trench-parallel mantle flow beneath the subducting slab.

Control of Structure in Turbulent Flows: Bifurcating and Blooming Jets.

DTIC Science & Technology

1987-10-10

injected through computational boundaries. (2) to satisfy no- slip boundary conditions or (3) during ’ grid " refinement when one element may be split...use of fast Poisson solvers on a mesh of M grid points, the operation count for this step can approach 0(M log M). Additional required steps are (1...consider s- three-dimensionai perturbations to the uart vortices. The linear stability calculations ot Pierrehumbert & Widnadl [101 are available for

The multigrid preconditioned conjugate gradient method

NASA Technical Reports Server (NTRS)

Tatebe, Osamu

1993-01-01

A multigrid preconditioned conjugate gradient method (MGCG method), which uses the multigrid method as a preconditioner of the PCG method, is proposed. The multigrid method has inherent high parallelism and improves convergence of long wavelength components, which is important in iterative methods. By using this method as a preconditioner of the PCG method, an efficient method with high parallelism and fast convergence is obtained. First, it is considered a necessary condition of the multigrid preconditioner in order to satisfy requirements of a preconditioner of the PCG method. Next numerical experiments show a behavior of the MGCG method and that the MGCG method is superior to both the ICCG method and the multigrid method in point of fast convergence and high parallelism. This fast convergence is understood in terms of the eigenvalue analysis of the preconditioned matrix. From this observation of the multigrid preconditioner, it is realized that the MGCG method converges in very few iterations and the multigrid preconditioner is a desirable preconditioner of the conjugate gradient method.

Calculations of the binding affinities of protein-protein complexes with the fast multipole method

NASA Astrophysics Data System (ADS)

Kim, Bongkeun; Song, Jiming; Song, Xueyu

2010-09-01

In this paper, we used a coarse-grained model at the residue level to calculate the binding free energies of three protein-protein complexes. General formulations to calculate the electrostatic binding free energy and the van der Waals free energy are presented by solving linearized Poisson-Boltzmann equations using the boundary element method in combination with the fast multipole method. The residue level model with the fast multipole method allows us to efficiently investigate how the mutations on the active site of the protein-protein interface affect the changes in binding affinities of protein complexes. Good correlations between the calculated results and the experimental ones indicate that our model can capture the dominant contributions to the protein-protein interactions. At the same time, additional effects on protein binding due to atomic details are also discussed in the context of the limitations of such a coarse-grained model.

Coupling Poisson rectangular pulse and multiplicative microcanonical random cascade models to generate sub-daily precipitation timeseries

NASA Astrophysics Data System (ADS)

Pohle, Ina; Niebisch, Michael; Müller, Hannes; Schümberg, Sabine; Zha, Tingting; Maurer, Thomas; Hinz, Christoph

2018-07-01

To simulate the impacts of within-storm rainfall variabilities on fast hydrological processes, long precipitation time series with high temporal resolution are required. Due to limited availability of observed data such time series are typically obtained from stochastic models. However, most existing rainfall models are limited in their ability to conserve rainfall event statistics which are relevant for hydrological processes. Poisson rectangular pulse models are widely applied to generate long time series of alternating precipitation events durations and mean intensities as well as interstorm period durations. Multiplicative microcanonical random cascade (MRC) models are used to disaggregate precipitation time series from coarse to fine temporal resolution. To overcome the inconsistencies between the temporal structure of the Poisson rectangular pulse model and the MRC model, we developed a new coupling approach by introducing two modifications to the MRC model. These modifications comprise (a) a modified cascade model ("constrained cascade") which preserves the event durations generated by the Poisson rectangular model by constraining the first and last interval of a precipitation event to contain precipitation and (b) continuous sigmoid functions of the multiplicative weights to consider the scale-dependency in the disaggregation of precipitation events of different durations. The constrained cascade model was evaluated in its ability to disaggregate observed precipitation events in comparison to existing MRC models. For that, we used a 20-year record of hourly precipitation at six stations across Germany. The constrained cascade model showed a pronounced better agreement with the observed data in terms of both the temporal pattern of the precipitation time series (e.g. the dry and wet spell durations and autocorrelations) and event characteristics (e.g. intra-event intermittency and intensity fluctuation within events). The constrained cascade model also slightly outperformed the other MRC models with respect to the intensity-frequency relationship. To assess the performance of the coupled Poisson rectangular pulse and constrained cascade model, precipitation events were stochastically generated by the Poisson rectangular pulse model and then disaggregated by the constrained cascade model. We found that the coupled model performs satisfactorily in terms of the temporal pattern of the precipitation time series, event characteristics and the intensity-frequency relationship.

Fast parallel algorithm for slicing STL based on pipeline

NASA Astrophysics Data System (ADS)

Ma, Xulong; Lin, Feng; Yao, Bo

2016-05-01

In Additive Manufacturing field, the current researches of data processing mainly focus on a slicing process of large STL files or complicated CAD models. To improve the efficiency and reduce the slicing time, a parallel algorithm has great advantages. However, traditional algorithms can't make full use of multi-core CPU hardware resources. In the paper, a fast parallel algorithm is presented to speed up data processing. A pipeline mode is adopted to design the parallel algorithm. And the complexity of the pipeline algorithm is analyzed theoretically. To evaluate the performance of the new algorithm, effects of threads number and layers number are investigated by a serial of experiments. The experimental results show that the threads number and layers number are two remarkable factors to the speedup ratio. The tendency of speedup versus threads number reveals a positive relationship which greatly agrees with the Amdahl's law, and the tendency of speedup versus layers number also keeps a positive relationship agreeing with Gustafson's law. The new algorithm uses topological information to compute contours with a parallel method of speedup. Another parallel algorithm based on data parallel is used in experiments to show that pipeline parallel mode is more efficient. A case study at last shows a suspending performance of the new parallel algorithm. Compared with the serial slicing algorithm, the new pipeline parallel algorithm can make full use of the multi-core CPU hardware, accelerate the slicing process, and compared with the data parallel slicing algorithm, the new slicing algorithm in this paper adopts a pipeline parallel model, and a much higher speedup ratio and efficiency is achieved.

Experimental verification of the role of electron pressure in fast magnetic reconnection with a guide field

DOE PAGES

Fox, W.; Sciortino, F.; v. Stechow, A.; ...

2017-03-21

We report detailed laboratory observations of the structure of a reconnection current sheet in a two-fluid plasma regime with a guide magnetic field. We observe and quantitatively analyze the quadrupolar electron pressure variation in the ion-diffusion region, as originally predicted by extended magnetohydrodynamics simulations. The projection of the electron pressure gradient parallel to the magnetic field contributes significantly to balancing the parallel electric field, and the resulting cross-field electron jets in the reconnection layer are diamagnetic in origin. Furthermore, these results demonstrate how parallel and perpendicular force balance are coupled in guide field reconnection and confirm basic theoretical models ofmore » the importance of electron pressure gradients for obtaining fast magnetic reconnection.« less

Automatic recognition of vector and parallel operations in a higher level language

NASA Technical Reports Server (NTRS)

Schneck, P. B.

1971-01-01

A compiler for recognizing statements of a FORTRAN program which are suited for fast execution on a parallel or pipeline machine such as Illiac-4, Star or ASC is described. The technique employs interval analysis to provide flow information to the vector/parallel recognizer. Where profitable the compiler changes scalar variables to subscripted variables. The output of the compiler is an extension to FORTRAN which shows parallel and vector operations explicitly.

A regularized vortex-particle mesh method for large eddy simulation

NASA Astrophysics Data System (ADS)

Spietz, H. J.; Walther, J. H.; Hejlesen, M. M.

2017-11-01

We present recent developments of the remeshed vortex particle-mesh method for simulating incompressible fluid flow. The presented method relies on a parallel higher-order FFT based solver for the Poisson equation. Arbitrary high order is achieved through regularization of singular Green's function solutions to the Poisson equation and recently we have derived novel high order solutions for a mixture of open and periodic domains. With this approach the simulated variables may formally be viewed as the approximate solution to the filtered Navier Stokes equations, hence we use the method for Large Eddy Simulation by including a dynamic subfilter-scale model based on test-filters compatible with the aforementioned regularization functions. Further the subfilter-scale model uses Lagrangian averaging, which is a natural candidate in light of the Lagrangian nature of vortex particle methods. A multiresolution variation of the method is applied to simulate the benchmark problem of the flow past a square cylinder at Re = 22000 and the obtained results are compared to results from the literature.

A Parallel Implementation of Multilevel Recursive Spectral Bisection for Application to Adaptive Unstructured Meshes. Chapter 1

NASA Technical Reports Server (NTRS)

Barnard, Stephen T.; Simon, Horst; Lasinski, T. A. (Technical Monitor)

1994-01-01

The design of a parallel implementation of multilevel recursive spectral bisection is described. The goal is to implement a code that is fast enough to enable dynamic repartitioning of adaptive meshes.

Dual Roles for Spike Signaling in Cortical Neural Populations

PubMed Central

Ballard, Dana H.; Jehee, Janneke F. M.

2011-01-01

A prominent feature of signaling in cortical neurons is that of randomness in the action potential. The output of a typical pyramidal cell can be well fit with a Poisson model, and variations in the Poisson rate repeatedly have been shown to be correlated with stimuli. However while the rate provides a very useful characterization of neural spike data, it may not be the most fundamental description of the signaling code. Recent data showing γ frequency range multi-cell action potential correlations, together with spike timing dependent plasticity, are spurring a re-examination of the classical model, since precise timing codes imply that the generation of spikes is essentially deterministic. Could the observed Poisson randomness and timing determinism reflect two separate modes of communication, or do they somehow derive from a single process? We investigate in a timing-based model whether the apparent incompatibility between these probabilistic and deterministic observations may be resolved by examining how spikes could be used in the underlying neural circuits. The crucial component of this model draws on dual roles for spike signaling. In learning receptive fields from ensembles of inputs, spikes need to behave probabilistically, whereas for fast signaling of individual stimuli, the spikes need to behave deterministically. Our simulations show that this combination is possible if deterministic signals using γ latency coding are probabilistically routed through different members of a cortical cell population at different times. This model exhibits standard features characteristic of Poisson models such as orientation tuning and exponential interval histograms. In addition, it makes testable predictions that follow from the γ latency coding. PMID:21687798

A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids

PubMed Central

Boschitsch, Alexander H.; Fenley, Marcia O.

2011-01-01

An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann Equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged multi-biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and multi-biomolecule assemblies, the total number of grid-points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward, fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid-dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for: (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent – analytical solutions are available for this case, thus allowing rigorous assessment of the solution accuracy; (ii) a pair of low dielectric charged spheres embedded in a ionic solvent to compute electrostatic interaction free energies as a function of the distance between sphere centers; (iii) surface potentials of proteins, nucleic acids and their larger-scale assemblies such as ribosomes; and (iv) electrostatic solvation free energies and their salt sensitivities – obtained with both linear and nonlinear Poisson-Boltzmann equation – for a large set of proteins. These latter results along with timings can serve as benchmarks for comparing the performance of different PBE solvers. PMID:21984876

Optimal Matched Filter in the Low-number Count Poisson Noise Regime and Implications for X-Ray Source Detection

NASA Astrophysics Data System (ADS)

Ofek, Eran O.; Zackay, Barak

2018-04-01

Detection of templates (e.g., sources) embedded in low-number count Poisson noise is a common problem in astrophysics. Examples include source detection in X-ray images, γ-rays, UV, neutrinos, and search for clusters of galaxies and stellar streams. However, the solutions in the X-ray-related literature are sub-optimal in some cases by considerable factors. Using the lemma of Neyman–Pearson, we derive the optimal statistics for template detection in the presence of Poisson noise. We demonstrate that, for known template shape (e.g., point sources), this method provides higher completeness, for a fixed false-alarm probability value, compared with filtering the image with the point-spread function (PSF). In turn, we find that filtering by the PSF is better than filtering the image using the Mexican-hat wavelet (used by wavdetect). For some background levels, our method improves the sensitivity of source detection by more than a factor of two over the popular Mexican-hat wavelet filtering. This filtering technique can also be used for fast PSF photometry and flare detection; it is efficient and straightforward to implement. We provide an implementation in MATLAB. The development of a complete code that works on real data, including the complexities of background subtraction and PSF variations, is deferred for future publication.

Combined inverse-forward artificial neural networks for fast and accurate estimation of the diffusion coefficients of cartilage based on multi-physics models.

PubMed

Arbabi, Vahid; Pouran, Behdad; Weinans, Harrie; Zadpoor, Amir A

2016-09-06

Analytical and numerical methods have been used to extract essential engineering parameters such as elastic modulus, Poisson׳s ratio, permeability and diffusion coefficient from experimental data in various types of biological tissues. The major limitation associated with analytical techniques is that they are often only applicable to problems with simplified assumptions. Numerical multi-physics methods, on the other hand, enable minimizing the simplified assumptions but require substantial computational expertise, which is not always available. In this paper, we propose a novel approach that combines inverse and forward artificial neural networks (ANNs) which enables fast and accurate estimation of the diffusion coefficient of cartilage without any need for computational modeling. In this approach, an inverse ANN is trained using our multi-zone biphasic-solute finite-bath computational model of diffusion in cartilage to estimate the diffusion coefficient of the various zones of cartilage given the concentration-time curves. Robust estimation of the diffusion coefficients, however, requires introducing certain levels of stochastic variations during the training process. Determining the required level of stochastic variation is performed by coupling the inverse ANN with a forward ANN that receives the diffusion coefficient as input and returns the concentration-time curve as output. Combined together, forward-inverse ANNs enable computationally inexperienced users to obtain accurate and fast estimation of the diffusion coefficients of cartilage zones. The diffusion coefficients estimated using the proposed approach are compared with those determined using direct scanning of the parameter space as the optimization approach. It has been shown that both approaches yield comparable results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Motion streaks in fast motion rivalry cause orientation-selective suppression.

PubMed

Apthorp, Deborah; Wenderoth, Peter; Alais, David

2009-05-14

We studied binocular rivalry between orthogonally translating arrays of random Gaussian blobs and measured the strength of rivalry suppression for static oriented probes. Suppression depth was quantified by expressing monocular probe thresholds during dominance relative to thresholds during suppression. Rivalry between two fast motions or two slow motions was compared in order to test the suggestion that fast-moving objects leave oriented "motion streaks" due to temporal integration (W. S. Geisler, 1999). If fast motions do produce motion streaks, then fast motion rivalry might also entail rivalry between the orthogonal streak orientations. We tested this using a static oriented probe that was aligned either parallel to the motion trajectory (hence collinear with the "streaks") or was orthogonal to the trajectory, predicting that rivalry suppression would be greater for parallel probes, and only for rivalry between fast motions. Results confirmed that suppression depth did depend on probe orientation for fast motion but not for slow motion. Further experiments showed that threshold elevations for the oriented probe during suppression exhibited clear orientation tuning. However, orientation-tuned elevations were also present during dominance, suggesting within-channel masking as the basis of the extra-deep suppression. In sum, the presence of orientation-dependent suppression in fast motion rivalry is consistent with the "motion streaks" hypothesis.

Novel Optical Processor for Phased Array Antenna.

DTIC Science & Technology

1992-10-20

parallel glass slide into the signal beam optical loop. The parallel glass acts like a variable phase shifter to the signal beam simulating phase drift...A list of possible designs are given as follows , _ _ Velocity fa (100dB/cm) Lumit Wavelength I M2I1 TeO2 Longi 4.2 /m/ns about 3 GHz 1.4 4m 34 Fast...subject to achievable acoustic frequency, the preferred materials are the slow shear wave in TeO2 , the fast shear wave in TeO2 or the shear waves in

Poisson denoising on the sphere: application to the Fermi gamma ray space telescope

NASA Astrophysics Data System (ADS)

Schmitt, J.; Starck, J. L.; Casandjian, J. M.; Fadili, J.; Grenier, I.

2010-07-01

The Large Area Telescope (LAT), the main instrument of the Fermi gamma-ray Space telescope, detects high energy gamma rays with energies from 20 MeV to more than 300 GeV. The two main scientific objectives, the study of the Milky Way diffuse background and the detection of point sources, are complicated by the lack of photons. That is why we need a powerful Poisson noise removal method on the sphere which is efficient on low count Poisson data. This paper presents a new multiscale decomposition on the sphere for data with Poisson noise, called multi-scale variance stabilizing transform on the sphere (MS-VSTS). This method is based on a variance stabilizing transform (VST), a transform which aims to stabilize a Poisson data set such that each stabilized sample has a quasi constant variance. In addition, for the VST used in the method, the transformed data are asymptotically Gaussian. MS-VSTS consists of decomposing the data into a sparse multi-scale dictionary like wavelets or curvelets, and then applying a VST on the coefficients in order to get almost Gaussian stabilized coefficients. In this work, we use the isotropic undecimated wavelet transform (IUWT) and the curvelet transform as spherical multi-scale transforms. Then, binary hypothesis testing is carried out to detect significant coefficients, and the denoised image is reconstructed with an iterative algorithm based on hybrid steepest descent (HSD). To detect point sources, we have to extract the Galactic diffuse background: an extension of the method to background separation is then proposed. In contrary, to study the Milky Way diffuse background, we remove point sources with a binary mask. The gaps have to be interpolated: an extension to inpainting is then proposed. The method, applied on simulated Fermi LAT data, proves to be adaptive, fast and easy to implement.

Design of fast signal processing readout front-end electronics implemented in CMOS 40 nm technology

NASA Astrophysics Data System (ADS)

Kleczek, Rafal

2016-12-01

The author presents considerations on the design of fast readout front-end electronics implemented in a CMOS 40 nm technology with an emphasis on the system dead time, noise performance and power dissipation. The designed processing channel consists of a charge sensitive amplifier with different feedback types (Krummenacher, resistive and constant current blocks), a threshold setting block, a discriminator and a counter with logic circuitry. The results of schematic and post-layout simulations with randomly generated input pulses in a time domain according to the Poisson distribution are presented and analyzed. Dead time below 20 ns is possible while keeping noise ENC ≈ 90 e- for a detector capacitance CDET = 160 fF.

Bit-parallel arithmetic in a massively-parallel associative processor

NASA Technical Reports Server (NTRS)

Scherson, Isaac D.; Kramer, David A.; Alleyne, Brian D.

1992-01-01

A simple but powerful new architecture based on a classical associative processor model is presented. Algorithms for performing the four basic arithmetic operations both for integer and floating point operands are described. For m-bit operands, the proposed architecture makes it possible to execute complex operations in O(m) cycles as opposed to O(m exp 2) for bit-serial machines. A word-parallel, bit-parallel, massively-parallel computing system can be constructed using this architecture with VLSI technology. The operation of this system is demonstrated for the fast Fourier transform and matrix multiplication.

Modular time division multiplexer: Efficient simultaneous characterization of fast and slow transients in multiple samples

NASA Astrophysics Data System (ADS)

Kim, Stephan D.; Luo, Jiajun; Buchholz, D. Bruce; Chang, R. P. H.; Grayson, M.

2016-09-01

A modular time division multiplexer (MTDM) device is introduced to enable parallel measurement of multiple samples with both fast and slow decay transients spanning from millisecond to month-long time scales. This is achieved by dedicating a single high-speed measurement instrument for rapid data collection at the start of a transient, and by multiplexing a second low-speed measurement instrument for slow data collection of several samples in parallel for the later transients. The MTDM is a high-level design concept that can in principle measure an arbitrary number of samples, and the low cost implementation here allows up to 16 samples to be measured in parallel over several months, reducing the total ensemble measurement duration and equipment usage by as much as an order of magnitude without sacrificing fidelity. The MTDM was successfully demonstrated by simultaneously measuring the photoconductivity of three amorphous indium-gallium-zinc-oxide thin films with 20 ms data resolution for fast transients and an uninterrupted parallel run time of over 20 days. The MTDM has potential applications in many areas of research that manifest response times spanning many orders of magnitude, such as photovoltaics, rechargeable batteries, amorphous semiconductors such as silicon and amorphous indium-gallium-zinc-oxide.

Modular time division multiplexer: Efficient simultaneous characterization of fast and slow transients in multiple samples.

PubMed

Kim, Stephan D; Luo, Jiajun; Buchholz, D Bruce; Chang, R P H; Grayson, M

2016-09-01

A modular time division multiplexer (MTDM) device is introduced to enable parallel measurement of multiple samples with both fast and slow decay transients spanning from millisecond to month-long time scales. This is achieved by dedicating a single high-speed measurement instrument for rapid data collection at the start of a transient, and by multiplexing a second low-speed measurement instrument for slow data collection of several samples in parallel for the later transients. The MTDM is a high-level design concept that can in principle measure an arbitrary number of samples, and the low cost implementation here allows up to 16 samples to be measured in parallel over several months, reducing the total ensemble measurement duration and equipment usage by as much as an order of magnitude without sacrificing fidelity. The MTDM was successfully demonstrated by simultaneously measuring the photoconductivity of three amorphous indium-gallium-zinc-oxide thin films with 20 ms data resolution for fast transients and an uninterrupted parallel run time of over 20 days. The MTDM has potential applications in many areas of research that manifest response times spanning many orders of magnitude, such as photovoltaics, rechargeable batteries, amorphous semiconductors such as silicon and amorphous indium-gallium-zinc-oxide.

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

Shi, E. L.; Hammett, G. W.; Stoltzfus-Dueck, T.

Here, five-dimensional gyrokinetic continuum simulations of electrostatic plasma turbulence in a straight, open-field-line geometry have been performed using a full- discontinuous-Galerkin approach implemented in the Gkeyll code. While various simplifications have been used for now, such as long-wavelength approximations in the gyrokinetic Poisson equation and the Hamiltonian, these simulations include the basic elements of a fusion-device scrape-off layer: localised sources to model plasma outflow from the core, cross-field turbulent transport, parallel flow along magnetic field lines, and parallel losses at the limiter or divertor with sheath-model boundary conditions. The set of sheath-model boundary conditions used in the model allows currentsmore » to flow through the walls. In addition to details of the numerical approach, results from numerical simulations of turbulence in the Large Plasma Device, a linear device featuring straight magnetic field lines, are presented.« less

Progress with the COGENT Edge Kinetic Code: Collision operator options

DOE PAGES

Dorf, M. A.; Cohen, R. H.; Compton, J. C.; ...

2012-06-27

In this study, COGENT is a continuum gyrokinetic code for edge plasmas being developed by the Edge Simulation Laboratory collaboration. The code is distinguished by application of the fourth order conservative discretization, and mapped multiblock grid technology to handle the geometric complexity of the tokamak edge. It is written in v∥-μ (parallel velocity – magnetic moment) velocity coordinates, and making use of the gyrokinetic Poisson equation for the calculation of a self-consistent electric potential. In the present manuscript we report on the implementation and initial testing of a succession of increasingly detailed collision operator options, including a simple drag-diffusion operatormore » in the parallel velocity space, Lorentz collisions, and a linearized model Fokker-Planck collision operator conserving momentum and energy (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)« less

Fast-Food Environments and Family Fast-Food Intake in Nonmetropolitan Areas

PubMed Central

Longacre, Meghan R.; Drake, Keith M.; MacKenzie, Todd A.; Gibson, Lucinda; Owens, Peter; Titus, Linda J.; Beach, Michael L.; Dalton, Madeline A.

2012-01-01

Background Little is known about the influence of in-town fast-food availability on family-level fast-food intake in nonmetropolitan areas. Purpose The purpose of the current study was to determine whether the presence of chain fast-food outlets was associated with fast-food intake among adolescents and parents, and to assess whether this relationship was moderated by family access to motor vehicles. Methods Telephone surveys were conducted with 1547 adolescent–parent dyads in 32 New Hampshire and Vermont communities between 2007 and 2008. Fast-food intake in the past week was measured through self-report. In-town fast-food outlets were located and enumerated using an onsite audit. Family motor vehicle access was categorized based on the number of vehicles per licensed drivers in the household. Poisson regression was used to determine unadjusted and adjusted risk ratios (RRs). Analyses were conducted in 2011. Results About half (52.1%) of adolescents and 34.7% of parents consumed fast food at least once in the past week. Adolescents and parents who lived in towns with five or more fast-food outlets were about 30% more likely to eat fast food compared to those in towns with no fast-food outlets, even after adjusting for individual, family, and town characteristics (RR=1.29, 95% CI= 1.10, 1.51; RR=1.32, 95% CI=1.07,1.62, respectively). Interaction models demonstrated that the influence of in-town fast-food outlets on fast-food intake was strongest among families with low motor vehicle access. Conclusions In nonmetropolitan areas, household transportation should be considered as an important moderator of the relationship between in-town fast-food outlets and family intake. PMID:22608373

Fast-food environments and family fast-food intake in nonmetropolitan areas.

PubMed

Longacre, Meghan R; Drake, Keith M; MacKenzie, Todd A; Gibson, Lucinda; Owens, Peter; Titus, Linda J; Beach, Michael L; Dalton, Madeline A

2012-06-01

Little is known about the influence of in-town fast-food availability on family-level fast-food intake in nonmetropolitan areas. The purpose of the current study was to determine whether the presence of chain fast-food outlets was associated with fast-food intake among adolescents and parents, and to assess whether this relationship was moderated by family access to motor vehicles. Telephone surveys were conducted with 1547 adolescent-parent dyads in 32 New Hampshire and Vermont communities between 2007 and 2008. Fast-food intake in the past week was measured through self-report. In-town fast-food outlets were located and enumerated using an onsite audit. Family motor vehicle access was categorized based on the number of vehicles per licensed drivers in the household. Poisson regression was used to determine unadjusted and adjusted risk ratios (RRs). Analyses were conducted in 2011. About half (52.1%) of adolescents and 34.7% of parents consumed fast food at least once in the past week. Adolescents and parents who lived in towns with five or more fast-food outlets were about 30% more likely to eat fast food compared to those in towns with no fast-food outlets, even after adjusting for individual, family, and town characteristics (RR=1.29, 95% CI= 1.10, 1.51; RR=1.32, 95% CI=1.07, 1.62, respectively). Interaction models demonstrated that the influence of in-town fast-food outlets on fast-food intake was strongest among families with low motor vehicle access. In nonmetropolitan areas, household transportation should be considered as an important moderator of the relationship between in-town fast-food outlets and family intake. Copyright © 2012 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

A new Green's function Monte Carlo algorithm for the solution of the two-dimensional nonlinear Poisson-Boltzmann equation: Application to the modeling of the communication breakdown problem in space vehicles during re-entry

NASA Astrophysics Data System (ADS)

Chatterjee, Kausik; Roadcap, John R.; Singh, Surendra

2014-11-01

The objective of this paper is the exposition of a recently-developed, novel Green's function Monte Carlo (GFMC) algorithm for the solution of nonlinear partial differential equations and its application to the modeling of the plasma sheath region around a cylindrical conducting object, carrying a potential and moving at low speeds through an otherwise neutral medium. The plasma sheath is modeled in equilibrium through the GFMC solution of the nonlinear Poisson-Boltzmann (NPB) equation. The traditional Monte Carlo based approaches for the solution of nonlinear equations are iterative in nature, involving branching stochastic processes which are used to calculate linear functionals of the solution of nonlinear integral equations. Over the last several years, one of the authors of this paper, K. Chatterjee has been developing a philosophically-different approach, where the linearization of the equation of interest is not required and hence there is no need for iteration and the simulation of branching processes. Instead, an approximate expression for the Green's function is obtained using perturbation theory, which is used to formulate the random walk equations within the problem sub-domains where the random walker makes its walks. However, as a trade-off, the dimensions of these sub-domains have to be restricted by the limitations imposed by perturbation theory. The greatest advantage of this approach is the ease and simplicity of parallelization stemming from the lack of the need for iteration, as a result of which the parallelization procedure is identical to the parallelization procedure for the GFMC solution of a linear problem. The application area of interest is in the modeling of the communication breakdown problem during a space vehicle's re-entry into the atmosphere. However, additional application areas are being explored in the modeling of electromagnetic propagation through the atmosphere/ionosphere in UHF/GPS applications.

A finite-difference method for the variable coefficient Poisson equation on hierarchical Cartesian meshes

NASA Astrophysics Data System (ADS)

Raeli, Alice; Bergmann, Michel; Iollo, Angelo

2018-02-01

We consider problems governed by a linear elliptic equation with varying coefficients across internal interfaces. The solution and its normal derivative can undergo significant variations through these internal boundaries. We present a compact finite-difference scheme on a tree-based adaptive grid that can be efficiently solved using a natively parallel data structure. The main idea is to optimize the truncation error of the discretization scheme as a function of the local grid configuration to achieve second-order accuracy. Numerical illustrations are presented in two and three-dimensional configurations.

Fast solution of elliptic partial differential equations using linear combinations of plane waves.

PubMed

Pérez-Jordá, José M

2016-02-01

Given an arbitrary elliptic partial differential equation (PDE), a procedure for obtaining its solution is proposed based on the method of Ritz: the solution is written as a linear combination of plane waves and the coefficients are obtained by variational minimization. The PDE to be solved is cast as a system of linear equations Ax=b, where the matrix A is not sparse, which prevents the straightforward application of standard iterative methods in order to solve it. This sparseness problem can be circumvented by means of a recursive bisection approach based on the fast Fourier transform, which makes it possible to implement fast versions of some stationary iterative methods (such as Gauss-Seidel) consuming O(NlogN) memory and executing an iteration in O(Nlog(2)N) time, N being the number of plane waves used. In a similar way, fast versions of Krylov subspace methods and multigrid methods can also be implemented. These procedures are tested on Poisson's equation expressed in adaptive coordinates. It is found that the best results are obtained with the GMRES method using a multigrid preconditioner with Gauss-Seidel relaxation steps.

Fast-food exposure around schools in urban Adelaide.

PubMed

Coffee, Neil T; Kennedy, Hannah P; Niyonsenga, Theo

2016-12-01

To assess whether exposure to fast-food outlets around schools differed depending on socio-economic status (SES). Binary logistic regression was used to investigate the presence and zero-inflated Poisson regression was used for the count (due to the excess of zeroes) of fast food within 1000 m and 15000 m road network buffers around schools. The low and middle SES tertiles were combined due to a lack of significant variation as the 'disadvantaged' group and compared with the high SES tertile as the 'advantaged' group. School SES was expressed using the 2011 Australian Bureau of Statistics, socio-economic indices for areas, index of relative socio-economic disadvantage. Fast-food data included independent takeaway food outlets and major fast-food chains. Metropolitan Adelaide, South Australia. A total of 459 schools were geocoded to the street address and 1000 m and 1500 m road network distance buffers calculated. There was a 1·6 times greater risk of exposure to fast food within 1000 m (OR=1·634; 95 % 1·017, 2·625) and a 9·5 times greater risk of exposure to a fast food within 1500 m (OR=9·524; 95 % CI 3·497, 25·641) around disadvantaged schools compared with advantaged schools. Disadvantaged schools were exposed to more fast food, with more than twice the number of disadvantaged schools exposed to fast food. The higher exposure to fast food near more disadvantaged schools may reflect lower commercial land cost in low-SES areas, potentially creating more financially desirable investments for fast-food developers.

Large-scale trench-perpendicular mantle flow beneath northern Chile

NASA Astrophysics Data System (ADS)

Reiss, M. C.; Rumpker, G.; Woelbern, I.

2017-12-01

We investigate the anisotropic properties of the forearc region of the central Andean margin by analyzing shear-wave splitting from teleseismic and local earthquakes from the Nazca slab. The data stems from the Integrated Plate boundary Observatory Chile (IPOC) located in northern Chile, covering an approximately 120 km wide coastal strip between 17°-25° S with an average station spacing of 60 km. With partly over ten years of data, this data set is uniquely suited to address the long-standing debate about the mantle flow field at the South American margin and in particular whether the flow field beneath the slab is parallel or perpendicular to the trench. Our measurements yield two distinct anisotropic layers. The teleseismic measurements show a change of fast polarizations directions from North to South along the trench ranging from parallel to subparallel to the absolute plate motion and, given the geometry of absolute plate motion and strike of the trench, mostly perpendicular to the trench. Shear-wave splitting from local earthquakes shows fast polarizations roughly aligned trench-parallel but exhibit short-scale variations which are indicative of a relatively shallow source. Comparisons between fast polarization directions and the strike of the local fault systems yield a good agreement. We use forward modelling to test the influence of the upper layer on the teleseismic measurements. We show that the observed variations of teleseismic measurements along the trench are caused by the anisotropy in the upper layer. Accordingly, the mantle layer is best characterized by an anisotropic fast axes parallel to the absolute plate motion which is roughly trench-perpendicular. This anisotropy is likely caused by a combination of crystallographic preferred orientation of the mantle mineral olivine as fossilized anisotropy in the slab and entrained flow beneath the slab. We interpret the upper anisotropic layer to be confined to the crust of the overriding continental plate. This is explained by the shape-preferred orientation of micro-cracks in relation to local fault zones which are oriented parallel the overall strike of the Andean range. Our results do not provide any evidence for a significant contribution of trench-parallel mantle flow beneath the subducting slab to the measurements.

Solution of elliptic partial differential equations by fast Poisson solvers using a local relaxation factor. 2: Two-step method

NASA Technical Reports Server (NTRS)

Chang, S. C.

1986-01-01

A two-step semidirect procedure is developed to accelerate the one-step procedure described in NASA TP-2529. For a set of constant coefficient model problems, the acceleration factor increases from 1 to 2 as the one-step procedure convergence rate decreases from + infinity to 0. It is also shown numerically that the two-step procedure can substantially accelerate the convergence of the numerical solution of many partial differential equations (PDE's) with variable coefficients.

[CMACPAR an modified parallel neuro-controller for control processes].

PubMed

Ramos, E; Surós, R

1999-01-01

CMACPAR is a Parallel Neurocontroller oriented to real time systems as for example Control Processes. Its characteristics are mainly a fast learning algorithm, a reduced number of calculations, great generalization capacity, local learning and intrinsic parallelism. This type of neurocontroller is used in real time applications required by refineries, hydroelectric centers, factories, etc. In this work we present the analysis and the parallel implementation of a modified scheme of the Cerebellar Model CMAC for the n-dimensional space projection using a mean granularity parallel neurocontroller. The proposed memory management allows for a significant memory reduction in training time and required memory size.

Stability of parallel electroosmotic flow subject to an axial modulated electric field

NASA Astrophysics Data System (ADS)

Suresh, Vinod; Homsy, George

2001-11-01

The stability of parallel electroosmotic flow in a micro-channel subjected to an AC electric field is studied. A spatially uniform time harmonic electric field is applied along the length of a two-dimensional micro-channel containing a dilute electrolytic solution, resulting in a time periodic parallel flow. The top and bottom walls of the channel are maintained at constant potential. The base state ion concentrations and double layer potential are determined using the Poisson-Boltzmann equation in the Debye-Hückel approximation. Experiments by other workers (Santiago et. al., unpublished) have shown that such a system can exhibit instabilities that take the form of mixing motion occurring in the bulk flow outside the double layer. It is shown that such instabilities can potentially result from the coupling of disturbances in the ion concentrations or electric potential to the base state velocity or ion concentrations, respectively. The stability boundary of the system is determined using Floquet theory and its dependence on the modulation frequency and amplitude of the axial electric field is studied.

MPI parallelization of Vlasov codes for the simulation of nonlinear laser-plasma interactions

NASA Astrophysics Data System (ADS)

Savchenko, V.; Won, K.; Afeyan, B.; Decyk, V.; Albrecht-Marc, M.; Ghizzo, A.; Bertrand, P.

2003-10-01

The simulation of optical mixing driven KEEN waves [1] and electron plasma waves [1] in laser-produced plasmas require nonlinear kinetic models and massive parallelization. We use Massage Passing Interface (MPI) libraries and Appleseed [2] to solve the Vlasov Poisson system of equations on an 8 node dual processor MAC G4 cluster. We use the semi-Lagrangian time splitting method [3]. It requires only row-column exchanges in the global data redistribution, minimizing the total number of communications between processors. Recurrent communication patterns for 2D FFTs involves global transposition. In the Vlasov-Maxwell case, we use splitting into two 1D spatial advections and a 2D momentum advection [4]. Discretized momentum advection equations have a double loop structure with the outer index being assigned to different processors. We adhere to a code structure with separate routines for calculations and data management for parallel computations. [1] B. Afeyan et al., IFSA 2003 Conference Proceedings, Monterey, CA [2] V. K. Decyk, Computers in Physics, 7, 418 (1993) [3] Sonnendrucker et al., JCP 149, 201 (1998) [4] Begue et al., JCP 151, 458 (1999)

Summer Proceedings 2016: The Center for Computing Research at Sandia National Laboratories

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

Carleton, James Brian; Parks, Michael L.

Solving sparse linear systems from the discretization of elliptic partial differential equations (PDEs) is an important building block in many engineering applications. Sparse direct solvers can solve general linear systems, but are usually slower and use much more memory than effective iterative solvers. To overcome these two disadvantages, a hierarchical solver (LoRaSp) based on H2-matrices was introduced in [22]. Here, we have developed a parallel version of the algorithm in LoRaSp to solve large sparse matrices on distributed memory machines. On a single processor, the factorization time of our parallel solver scales almost linearly with the problem size for three-dimensionalmore » problems, as opposed to the quadratic scalability of many existing sparse direct solvers. Moreover, our solver leads to almost constant numbers of iterations, when used as a preconditioner for Poisson problems. On more than one processor, our algorithm has significant speedups compared to sequential runs. With this parallel algorithm, we are able to solve large problems much faster than many existing packages as demonstrated by the numerical experiments.« less

Externally Calibrated Parallel Imaging for 3D Multispectral Imaging Near Metallic Implants Using Broadband Ultrashort Echo Time Imaging

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Reeder, Scott B.

2017-01-01

Purpose To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. Theory and Methods A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Results Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. Conclusion A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. PMID:27403613

Probabilistic structural analysis methods for improving Space Shuttle engine reliability

NASA Technical Reports Server (NTRS)

Boyce, L.

1989-01-01

Probabilistic structural analysis methods are particularly useful in the design and analysis of critical structural components and systems that operate in very severe and uncertain environments. These methods have recently found application in space propulsion systems to improve the structural reliability of Space Shuttle Main Engine (SSME) components. A computer program, NESSUS, based on a deterministic finite-element program and a method of probabilistic analysis (fast probability integration) provides probabilistic structural analysis for selected SSME components. While computationally efficient, it considers both correlated and nonnormal random variables as well as an implicit functional relationship between independent and dependent variables. The program is used to determine the response of a nickel-based superalloy SSME turbopump blade. Results include blade tip displacement statistics due to the variability in blade thickness, modulus of elasticity, Poisson's ratio or density. Modulus of elasticity significantly contributed to blade tip variability while Poisson's ratio did not. Thus, a rational method for choosing parameters to be modeled as random is provided.

Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT.

PubMed

Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten

2016-08-09

The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.

FAST TRACK COMMUNICATION: Shear coordinate description of the quantized versal unfolding of a D4 singularity

NASA Astrophysics Data System (ADS)

Chekhov, Leonid; Mazzocco, Marta

2010-11-01

In this communication, by using Teichmüller theory of a sphere with four holes/orbifold points, we obtain a system of flat coordinates on the general affine cubic surface having a D4 singularity at the origin. We show that the Goldman bracket on the geodesic functions on the four-holed/orbifold sphere coincides with the Etingof-Ginzburg Poisson bracket on the affine D4 cubic. We prove that this bracket is the image under the Riemann-Hilbert map of the Poisson-Lie bracket on \\oplus _{1}^3\\mathfrak {sl}^\\ast (2,{{\\bb C}}) . We realize the action of the mapping class group by the action of the braid group on the geodesic functions. This action coincides with the procedure of analytic continuation of solutions of the sixth Painlevé equation. Finally, we produce the explicit quantization of the Goldman bracket on the geodesic functions on the four-holed/orbifold sphere and of the braid group action.

Parallel fast multipole boundary element method applied to computational homogenization

NASA Astrophysics Data System (ADS)

Ptaszny, Jacek

2018-01-01

In the present work, a fast multipole boundary element method (FMBEM) and a parallel computer code for 3D elasticity problem is developed and applied to the computational homogenization of a solid containing spherical voids. The system of equation is solved by using the GMRES iterative solver. The boundary of the body is dicretized by using the quadrilateral serendipity elements with an adaptive numerical integration. Operations related to a single GMRES iteration, performed by traversing the corresponding tree structure upwards and downwards, are parallelized by using the OpenMP standard. The assignment of tasks to threads is based on the assumption that the tree nodes at which the moment transformations are initialized can be partitioned into disjoint sets of equal or approximately equal size and assigned to the threads. The achieved speedup as a function of number of threads is examined.

Electron Cooling and Isotropization during Magnetotail Current Sheet Thinning: Implications for Parallel Electric Fields

NASA Astrophysics Data System (ADS)

Lu, San; Artemyev, A. V.; Angelopoulos, V.

2017-11-01

Magnetotail current sheet thinning is a distinctive feature of substorm growth phase, during which magnetic energy is stored in the magnetospheric lobes. Investigation of charged particle dynamics in such thinning current sheets is believed to be important for understanding the substorm energy storage and the current sheet destabilization responsible for substorm expansion phase onset. We use Time History of Events and Macroscale Interactions during Substorms (THEMIS) B and C observations in 2008 and 2009 at 18 - 25 RE to show that during magnetotail current sheet thinning, the electron temperature decreases (cooling), and the parallel temperature decreases faster than the perpendicular temperature, leading to a decrease of the initially strong electron temperature anisotropy (isotropization). This isotropization cannot be explained by pure adiabatic cooling or by pitch angle scattering. We use test particle simulations to explore the mechanism responsible for the cooling and isotropization. We find that during the thinning, a fast decrease of a parallel electric field (directed toward the Earth) can speed up the electron parallel cooling, causing it to exceed the rate of perpendicular cooling, and thus lead to isotropization, consistent with observation. If the parallel electric field is too small or does not change fast enough, the electron parallel cooling is slower than the perpendicular cooling, so the parallel electron anisotropy grows, contrary to observation. The same isotropization can also be accomplished by an increasing parallel electric field directed toward the equatorial plane. Our study reveals the existence of a large-scale parallel electric field, which plays an important role in magnetotail particle dynamics during the current sheet thinning process.

Fast Food and Neighborhood Stroke Risk

PubMed Central

Morgenstern, Lewis B.; Escobar, James D.; Sánchez, Brisa N.; Hughes, Rebecca; Zuniga, Belinda G.; Garcia, Nelda; Lisabeth, Lynda D.

2009-01-01

Objective To investigate the association between the number of fast food restaurants and ischemic stroke in neighborhoods. Methods This work was a pre-specified part of the Brain Attack in Corpus Christi (BASIC) project. Ischemic stroke cases were prospectively ascertained in Nueces County, Texas. Home addresses were geocoded and used to establish the census tract for each stroke case. Census tracts were used as proxies for neighborhoods (n=64). Using a standard definition, fast food restaurants were identified from a commercial list. Poisson regression was used to study the association between the number of fast food restaurants in the neighborhood, using a 1-mile buffer around each census tract, and the risk of stroke in the neighborhood. Models were adjusted for demographics and neighborhood socioeconomic status (SES). Results There were 1,247 completed ischemic strokes from January 2000 through June 2003 and 262 fast food restaurants. The median number of fast food restaurants per census tract including buffer was 22 (IQR 12–33). Adjusting for neighborhood demographics and SES, the association of fast food restaurants with stroke was significant (p=0.02). The association suggested that the risk of stroke in a neighborhood increased by 1% for every fast food restaurant (RR 1.01 95% CI: 1.00–1.01). The relative risk of stroke comparing neighborhoods in the 75th to the 25th percentile of the distribution of fast food restaurants was 1.13 (95% CI: 1.02–1.25). Interpretation Controlling for demographic and SES factors, there was a significant association between fast food restaurants and stroke risk in neighborhoods in this community-based study. PMID:19743456

Gyrokinetic continuum simulation of turbulence in a straight open-field-line plasma

DOE PAGES

Shi, E. L.; Hammett, G. W.; Stoltzfus-Dueck, T.; ...

2017-05-29

Here, five-dimensional gyrokinetic continuum simulations of electrostatic plasma turbulence in a straight, open-field-line geometry have been performed using a full- discontinuous-Galerkin approach implemented in the Gkeyll code. While various simplifications have been used for now, such as long-wavelength approximations in the gyrokinetic Poisson equation and the Hamiltonian, these simulations include the basic elements of a fusion-device scrape-off layer: localised sources to model plasma outflow from the core, cross-field turbulent transport, parallel flow along magnetic field lines, and parallel losses at the limiter or divertor with sheath-model boundary conditions. The set of sheath-model boundary conditions used in the model allows currentsmore » to flow through the walls. In addition to details of the numerical approach, results from numerical simulations of turbulence in the Large Plasma Device, a linear device featuring straight magnetic field lines, are presented.« less

Expansion of Non-Quasi-Neutral Limited Plasmas Driven by Two-Temperature Electron Clouds

NASA Astrophysics Data System (ADS)

Murakami, Masakatsu; Honrubia, Javier

2017-10-01

Fast heating of an isolated solid mass, under irradiation of ultra-intense ultra-short laser pulse, to averaged temperatures of order of keV is theoretically studied. Achievable maximum ion temperatures are determined as a consequence of the interplay of the electron-to-ion energy deposition and nonrelativistic plasma expansion, where fast ion emission plays an important role in the energy balance. To describe the plasma expansion, we develop a self-similar solution, in which the plasma is composed of three fluids, i.e., ions and two-temperature electrons. Under the condition of isothermal electron expansion in cylindrical geometry, such a fluid system, self-consistently incorporated with the Poisson equation, is fully solved. The charge separation and resultant accelerated ion population due to the induced electrostatic field are quantitatively presented. The analytical model is compared with two-dimensional hydrodynamic simulations to provide practical working windows for the target and laser parameters for the fast heating.

Parallel heuristics for scalable community detection

DOE PAGES

Lu, Hao; Halappanavar, Mahantesh; Kalyanaraman, Ananth

2015-08-14

Community detection has become a fundamental operation in numerous graph-theoretic applications. Despite its potential for application, there is only limited support for community detection on large-scale parallel computers, largely owing to the irregular and inherently sequential nature of the underlying heuristics. In this paper, we present parallelization heuristics for fast community detection using the Louvain method as the serial template. The Louvain method is an iterative heuristic for modularity optimization. Originally developed in 2008, the method has become increasingly popular owing to its ability to detect high modularity community partitions in a fast and memory-efficient manner. However, the method ismore » also inherently sequential, thereby limiting its scalability. Here, we observe certain key properties of this method that present challenges for its parallelization, and consequently propose heuristics that are designed to break the sequential barrier. For evaluation purposes, we implemented our heuristics using OpenMP multithreading, and tested them over real world graphs derived from multiple application domains. Compared to the serial Louvain implementation, our parallel implementation is able to produce community outputs with a higher modularity for most of the inputs tested, in comparable number or fewer iterations, while providing real speedups of up to 16x using 32 threads.« less

The Mercury System: Embedding Computation into Disk Drives

DTIC Science & Technology

2004-08-20

enabling technologies to build extremely fast data search engines . We do this by moving the search closer to the data, and performing it in hardware...engine searches in parallel across a disk or disk surface 2. System Parallelism: Searching is off-loaded to search engines and main processor can

Accurate analytical modeling of junctionless DG-MOSFET by green's function approach

NASA Astrophysics Data System (ADS)

Nandi, Ashutosh; Pandey, Nilesh

2017-11-01

An accurate analytical model of Junctionless double gate MOSFET (JL-DG-MOSFET) in the subthreshold regime of operation is developed in this work using green's function approach. The approach considers 2-D mixed boundary conditions and multi-zone techniques to provide an exact analytical solution to 2-D Poisson's equation. The Fourier coefficients are calculated correctly to derive the potential equations that are further used to model the channel current and subthreshold slope of the device. The threshold voltage roll-off is computed from parallel shifts of Ids-Vgs curves between the long channel and short-channel devices. It is observed that the green's function approach of solving 2-D Poisson's equation in both oxide and silicon region can accurately predict channel potential, subthreshold current (Isub), threshold voltage (Vt) roll-off and subthreshold slope (SS) of both long & short channel devices designed with different doping concentrations and higher as well as lower tsi/tox ratio. All the analytical model results are verified through comparisons with TCAD Sentaurus simulation results. It is observed that the model matches quite well with TCAD device simulations.

Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

NASA Technical Reports Server (NTRS)

Sun, Xian-He

1997-01-01

Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm and Reduced Parallel Diagonal Dominant (RPDD) algorithm have been carefully studied on different parallel platforms for different applications, and a NASA simulation code developed by Man M. Rai and his colleagues has been parallelized and implemented based on data dependency analysis. These achievements are addressed in detail in the paper.

A fast, parallel algorithm for distant-dependent calculation of crystal properties

NASA Astrophysics Data System (ADS)

Stein, Matthew

2017-12-01

A fast, parallel algorithm for distant-dependent calculation and simulation of crystal properties is presented along with speedup results and methods of application. An illustrative example is used to compute the Lennard-Jones lattice constants up to 32 significant figures for 4 ≤ p ≤ 30 in the simple cubic, face-centered cubic, body-centered cubic, hexagonal-close-pack, and diamond lattices. In most cases, the known precision of these constants is more than doubled, and in some cases, corrected from previously published figures. The tools and strategies to make this computation possible are detailed along with application to other potentials, including those that model defects.

Effects of ATC automation on precision approaches to closely space parallel runways

NASA Technical Reports Server (NTRS)

Slattery, R.; Lee, K.; Sanford, B.

1995-01-01

Improved navigational technology (such as the Microwave Landing System and the Global Positioning System) installed in modern aircraft will enable air traffic controllers to better utilize available airspace. Consequently, arrival traffic can fly approaches to parallel runways separated by smaller distances than are currently allowed. Previous simulation studies of advanced navigation approaches have found that controller workload is increased when there is a combination of aircraft that are capable of following advanced navigation routes and aircraft that are not. Research into Air Traffic Control automation at Ames Research Center has led to the development of the Center-TRACON Automation System (CTAS). The Final Approach Spacing Tool (FAST) is the component of the CTAS used in the TRACON area. The work in this paper examines, via simulation, the effects of FAST used for aircraft landing on closely spaced parallel runways. The simulation contained various combinations of aircraft, equipped and unequipped with advanced navigation systems. A set of simulations was run both manually and with an augmented set of FAST advisories to sequence aircraft, assign runways, and avoid conflicts. The results of the simulations are analyzed, measuring the airport throughput, aircraft delay, loss of separation, and controller workload.

Distributed Function Mining for Gene Expression Programming Based on Fast Reduction.

PubMed

Deng, Song; Yue, Dong; Yang, Le-chan; Fu, Xiong; Feng, Ya-zhou

2016-01-01

For high-dimensional and massive data sets, traditional centralized gene expression programming (GEP) or improved algorithms lead to increased run-time and decreased prediction accuracy. To solve this problem, this paper proposes a new improved algorithm called distributed function mining for gene expression programming based on fast reduction (DFMGEP-FR). In DFMGEP-FR, fast attribution reduction in binary search algorithms (FAR-BSA) is proposed to quickly find the optimal attribution set, and the function consistency replacement algorithm is given to solve integration of the local function model. Thorough comparative experiments for DFMGEP-FR, centralized GEP and the parallel gene expression programming algorithm based on simulated annealing (parallel GEPSA) are included in this paper. For the waveform, mushroom, connect-4 and musk datasets, the comparative results show that the average time-consumption of DFMGEP-FR drops by 89.09%%, 88.85%, 85.79% and 93.06%, respectively, in contrast to centralized GEP and by 12.5%, 8.42%, 9.62% and 13.75%, respectively, compared with parallel GEPSA. Six well-studied UCI test data sets demonstrate the efficiency and capability of our proposed DFMGEP-FR algorithm for distributed function mining.

Fast data reconstructed method of Fourier transform imaging spectrometer based on multi-core CPU

NASA Astrophysics Data System (ADS)

Yu, Chunchao; Du, Debiao; Xia, Zongze; Song, Li; Zheng, Weijian; Yan, Min; Lei, Zhenggang

2017-10-01

Imaging spectrometer can gain two-dimensional space image and one-dimensional spectrum at the same time, which shows high utility in color and spectral measurements, the true color image synthesis, military reconnaissance and so on. In order to realize the fast reconstructed processing of the Fourier transform imaging spectrometer data, the paper designed the optimization reconstructed algorithm with OpenMP parallel calculating technology, which was further used for the optimization process for the HyperSpectral Imager of `HJ-1' Chinese satellite. The results show that the method based on multi-core parallel computing technology can control the multi-core CPU hardware resources competently and significantly enhance the calculation of the spectrum reconstruction processing efficiency. If the technology is applied to more cores workstation in parallel computing, it will be possible to complete Fourier transform imaging spectrometer real-time data processing with a single computer.

Potential Application of a Graphical Processing Unit to Parallel Computations in the NUBEAM Code

NASA Astrophysics Data System (ADS)

Payne, J.; McCune, D.; Prater, R.

2010-11-01

NUBEAM is a comprehensive computational Monte Carlo based model for neutral beam injection (NBI) in tokamaks. NUBEAM computes NBI-relevant profiles in tokamak plasmas by tracking the deposition and the slowing of fast ions. At the core of NUBEAM are vector calculations used to track fast ions. These calculations have recently been parallelized to run on MPI clusters. However, cost and interlink bandwidth limit the ability to fully parallelize NUBEAM on an MPI cluster. Recent implementation of double precision capabilities for Graphical Processing Units (GPUs) presents a cost effective and high performance alternative or complement to MPI computation. Commercially available graphics cards can achieve up to 672 GFLOPS double precision and can handle hundreds of thousands of threads. The ability to execute at least one thread per particle simultaneously could significantly reduce the execution time and the statistical noise of NUBEAM. Progress on implementation on a GPU will be presented.

Ex-vessel neutron dosimetry analysis for westinghouse 4-loop XL pressurized water reactor plant using the RadTrack{sup TM} Code System with the 3D parallel discrete ordinates code RAPTOR-M3G

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

Chen, J.; Alpan, F. A.; Fischer, G.A.

2011-07-01

Traditional two-dimensional (2D)/one-dimensional (1D) SYNTHESIS methodology has been widely used to calculate fast neutron (>1.0 MeV) fluence exposure to reactor pressure vessel in the belt-line region. However, it is expected that this methodology cannot provide accurate fast neutron fluence calculation at elevations far above or below the active core region. A three-dimensional (3D) parallel discrete ordinates calculation for ex-vessel neutron dosimetry on a Westinghouse 4-Loop XL Pressurized Water Reactor has been done. It shows good agreement between the calculated results and measured results. Furthermore, the results show very different fast neutron flux values at some of the former plate locationsmore » and elevations above and below an active core than those calculated by a 2D/1D SYNTHESIS method. This indicates that for certain irregular reactor internal structures, where the fast neutron flux has a very strong local effect, it is required to use a 3D transport method to calculate accurate fast neutron exposure. (authors)« less

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

fastBMA: scalable network inference and transitive reduction.

PubMed

Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

2017-10-01

Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

Pronounced zonation of seismic anisotropy in the Western Hellenic subduction zone and its geodynamic significance

NASA Astrophysics Data System (ADS)

Olive, Jean-Arthur; Pearce, Frederick; Rondenay, Stéphane; Behn, Mark D.

2014-04-01

Many subduction zones exhibit significant retrograde motion of their arc and trench. The observation of fast shear-wave velocities parallel to the trench in such settings has been inferred to represent trench-parallel mantle flow beneath a retreating slab. Here, we investigate this process by measuring seismic anisotropy in the shallow Aegean mantle. We carry out shear-wave splitting analysis on a dense array of seismometers across the Western Hellenic Subduction Zone, and find a pronounced zonation of anisotropy at the scale of the subduction zone. Fast SKS splitting directions subparallel to the trench-retreat direction dominate the region nearest to the trench. Fast splitting directions abruptly transition to trench-parallel above the corner of the mantle wedge, and rotate back to trench-normal over the back-arc. We argue that the trench-normal anisotropy near the trench is explained by entrainment of an asthenospheric layer beneath the shallow-dipping portion of the slab. Toward the volcanic arc this signature is overprinted by trench-parallel anisotropy in the mantle wedge, likely caused by a layer of strained serpentine immediately above the slab. Arcward steepening of the slab and horizontal divergence of mantle flow due to rollback may generate an additional component of sub-slab trench-parallel anisotropy in this region. Poloidal flow above the retreating slab is likely the dominant source of back-arc trench-normal anisotropy. We hypothesize that trench-normal anisotropy associated with significant entrainment of the asthenospheric mantle near the trench may be widespread but only observable at shallow-dipping subduction zones where stations nearest the trench do not overlie the mantle wedge.

Efficient Parallel Levenberg-Marquardt Model Fitting towards Real-Time Automated Parametric Imaging Microscopy

PubMed Central

Zhu, Xiang; Zhang, Dianwen

2013-01-01

We present a fast, accurate and robust parallel Levenberg-Marquardt minimization optimizer, GPU-LMFit, which is implemented on graphics processing unit for high performance scalable parallel model fitting processing. GPU-LMFit can provide a dramatic speed-up in massive model fitting analyses to enable real-time automated pixel-wise parametric imaging microscopy. We demonstrate the performance of GPU-LMFit for the applications in superresolution localization microscopy and fluorescence lifetime imaging microscopy. PMID:24130785

A distributed parallel storage architecture and its potential application within EOSDIS

NASA Technical Reports Server (NTRS)

Johnston, William E.; Tierney, Brian; Feuquay, Jay; Butzer, Tony

1994-01-01

We describe the architecture, implementation, use of a scalable, high performance, distributed-parallel data storage system developed in the ARPA funded MAGIC gigabit testbed. A collection of wide area distributed disk servers operate in parallel to provide logical block level access to large data sets. Operated primarily as a network-based cache, the architecture supports cooperation among independently owned resources to provide fast, large-scale, on-demand storage to support data handling, simulation, and computation.

Engine-start Control Strategy of P2 Parallel Hybrid Electric Vehicle

NASA Astrophysics Data System (ADS)

Xiangyang, Xu; Siqi, Zhao; Peng, Dong

2017-12-01

A smooth and fast engine-start process is important to parallel hybrid electric vehicles with an electric motor mounted in front of the transmission. However, there are some challenges during the engine-start control. Firstly, the electric motor must simultaneously provide a stable driving torque to ensure the drivability and a compensative torque to drag the engine before ignition. Secondly, engine-start time is a trade-off control objective because both fast start and smooth start have to be considered. To solve these problems, this paper first analyzed the resistance of the engine start process, and established a physic model in MATLAB/Simulink. Then a model-based coordinated control strategy among engine, motor and clutch was developed. Two basic control strategy during fast start and smooth start process were studied. Simulation results showed that the control objectives were realized by applying given control strategies, which can meet different requirement from the driver.

GASOLINE: Smoothed Particle Hydrodynamics (SPH) code

NASA Astrophysics Data System (ADS)

N-Body Shop

2017-10-01

Gasoline solves the equations of gravity and hydrodynamics in astrophysical problems, including simulations of planets, stars, and galaxies. It uses an SPH method that features correct mixing behavior in multiphase fluids and minimal artificial viscosity. This method is identical to the SPH method used in the ChaNGa code (ascl:1105.005), allowing users to extend results to problems requiring >100,000 cores. Gasoline uses a fast, memory-efficient O(N log N) KD-Tree to solve Poisson's Equation for gravity and avoids artificial viscosity in non-shocking compressive flows.

Adaptive multiple super fast simulated annealing for stochastic microstructure reconstruction

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

Ryu, Seun; Lin, Guang; Sun, Xin

2013-01-01

Fast image reconstruction from statistical information is critical in image fusion from multimodality chemical imaging instrumentation to create high resolution image with large domain. Stochastic methods have been used widely in image reconstruction from two point correlation function. The main challenge is to increase the efficiency of reconstruction. A novel simulated annealing method is proposed for fast solution of image reconstruction. Combining the advantage of very fast cooling schedules, dynamic adaption and parallelization, the new simulation annealing algorithm increases the efficiencies by several orders of magnitude, making the large domain image fusion feasible.

Evaluation and utilization of preassembled frozen commercial fast real-time qPCR master mixes for detection of cytomegalovirus and BK virus.

PubMed

Glover, William A; Atienza, Ederlyn E; Nesbitt, Shannon; Kim, Woo J; Castor, Jared; Cook, Linda; Jerome, Keith R

2016-01-01

Quantitative DNA detection of cytomegalovirus (CMV) and BK virus (BKV) is critical in the management of transplant patients. Quantitative laboratory-developed procedures for CMV and BKV have been described in which much of the processing is automated, resulting in rapid, reproducible, and high-throughput testing of transplant patients. To increase the efficiency of such assays, the performance and stability of four commercial preassembled frozen fast qPCR master mixes (Roche FastStart Universal Probe Master Mix with Rox, Bio-Rad SsoFast Probes Supermix with Rox, Life Technologies TaqMan FastAdvanced Master Mix, and Life Technologies Fast Universal PCR Master Mix), in combination with in-house designed primers and probes, was evaluated using controls and standards from standard CMV and BK assays. A subsequent parallel evaluation using patient samples was performed comparing the performance of freshly prepared assay mixes versus aliquoted frozen master mixes made with two of the fast qPCR mixes (Life Technologies TaqMan FastAdvanced Master Mix, and Bio-Rad SsoFast Probes Supermix with Rox), chosen based on their performance and compatibility with existing PCR cycling conditions. The data demonstrate that the frozen master mixes retain excellent performance over a period of at least 10 weeks. During the parallel testing using clinical specimens, no difference in quantitative results was observed between the preassembled frozen master mixes and freshly prepared master mixes. Preassembled fast real-time qPCR frozen master mixes perform well and represent an additional strategy laboratories can implement to reduce assay preparation times, and to minimize technical errors and effort necessary to perform clinical PCR. © 2015 Wiley Periodicals, Inc.

Investigating adolescents' sweetened beverage consumption and Western fast food restaurant visits in China, 2006-2011.

PubMed

Lee, Yen-Han; Chiang, Timothy C; Liu, Ching-Ti; Chang, Yen-Chang

2018-05-25

Background China has undergone rapid Westernization and established dramatic social reforms since the early 21st century. However, health issues led to challenges in the lives of the Chinese residents. Western fast food and sweetened beverages, two food options associated with chronic diseases and obesity, have played key roles to alter adolescents' dietary patterns. This study aims to examine the association between adolescents' visits to Western fast food restaurants and sweetened beverage consumption. Methods Applying three waves of the China Health and Nutrition Study (CHNS) between 2006 and 2011 (n = 1063), we used generalized Poisson regression (GPR) to investigate the association between adolescents' Western fast food restaurant visits and sweetened beverage consumption, as the popularity of fast food and sweetened beverages has skyrocketed among adolescents in contemporary China. A linear-by-linear association test was used as a trend test to study general patterns between sweetened beverage consumption and Western fast food restaurant visits. We adjusted all models with sweetened beverage consumption frequency, four food preferences (fast food, salty snacks, fruits and vegetables), school status, gross household income, provinces, rural/urban regions, age and gender. Results From the results of the trend test, frequent sweetened beverage consumption was highly associated with more Western fast food restaurant visits among Chinese adolescents in the three waves (p < 0.001). Furthermore, we observed that adolescents, who had less than monthly sweetened beverage consumption or did not drink them at all, had much less likelihood of visiting Western fast food restaurants (p < 0.05), compared with those daily consumers. Conclusion Adolescents' sweetened beverage consumption was highly associated with Western fast food restaurant visits in contemporary China. Further actions are needed from the Chinese central government to create a healthier dietary environment for adolescents.

Are Fast Radio Bursts the Birthmark of Magnetars?

NASA Astrophysics Data System (ADS)

Lieu, Richard

2017-01-01

A model of fast radio bursts, which enlists young, short period extragalactic magnetars satisfying B/P > 2 × 1016 G s-1 (1 G = 1 statvolt cm-1) as the source, is proposed. When the parallel component {{\\boldsymbol{E}}}\\parallel of the surface electric field (under the scenario of a vacuum magnetosphere) of such pulsars approaches 5% of the critical field {E}c={m}e2{c}3/(e{\\hslash }), in strength, the field can readily decay via the Schwinger mechanism into electron-positron pairs, the back reaction of which causes {{\\boldsymbol{E}}}\\parallel to oscillate on a characteristic timescale smaller than the development of a spark gap. Thus, under this scenario, the open field line region of the pulsar magnetosphere is controlled by Schwinger pairs, and their large creation and acceleration rates enable the escaping pairs to coherently emit radio waves directly from the polar cap. The majority of the energy is emitted at frequencies ≲ 1 {GHz} where the coherent radiation has the highest yield, at a rate large enough to cause the magnetar to lose spin significantly over a timescale ≈ a few × {10}-3 s, the duration of a fast radio burst. Owing to the circumstellar environment of a young magnetar, however, the ≲1 GHz radiation is likely to be absorbed or reflected by the overlying matter. It is shown that the brightness of the remaining (observable) frequencies of ≈ 1 {GHz} and above are on a par with a typical fast radio burst. Unless some spin-up mechanism is available to recover the original high rotation rate that triggered the Schwinger mechanism, the fast radio burst will not be repeated again in the same magnetar.

Fast, Parallel and Secure Cryptography Algorithm Using Lorenz's Attractor

NASA Astrophysics Data System (ADS)

Marco, Anderson Gonçalves; Martinez, Alexandre Souto; Bruno, Odemir Martinez

A novel cryptography method based on the Lorenz's attractor chaotic system is presented. The proposed algorithm is secure and fast, making it practical for general use. We introduce the chaotic operation mode, which provides an interaction among the password, message and a chaotic system. It ensures that the algorithm yields a secure codification, even if the nature of the chaotic system is known. The algorithm has been implemented in two versions: one sequential and slow and the other, parallel and fast. Our algorithm assures the integrity of the ciphertext (we know if it has been altered, which is not assured by traditional algorithms) and consequently its authenticity. Numerical experiments are presented, discussed and show the behavior of the method in terms of security and performance. The fast version of the algorithm has a performance comparable to AES, a popular cryptography program used commercially nowadays, but it is more secure, which makes it immediately suitable for general purpose cryptography applications. An internet page has been set up, which enables the readers to test the algorithm and also to try to break into the cipher.

Components of action potential repolarization in cerebellar parallel fibres.

PubMed

Pekala, Dobromila; Baginskas, Armantas; Szkudlarek, Hanna J; Raastad, Morten

2014-11-15

Repolarization of the presynaptic action potential is essential for transmitter release, excitability and energy expenditure. Little is known about repolarization in thin, unmyelinated axons forming en passant synapses, which represent the most common type of axons in the mammalian brain's grey matter.We used rat cerebellar parallel fibres, an example of typical grey matter axons, to investigate the effects of K(+) channel blockers on repolarization. We show that repolarization is composed of a fast tetraethylammonium (TEA)-sensitive component, determining the width and amplitude of the spike, and a slow margatoxin (MgTX)-sensitive depolarized after-potential (DAP). These two components could be recorded at the granule cell soma as antidromic action potentials and from the axons with a newly developed miniaturized grease-gap method. A considerable proportion of fast repolarization remained in the presence of TEA, MgTX, or both. This residual was abolished by the addition of quinine. The importance of proper control of fast repolarization was demonstrated by somatic recordings of antidromic action potentials. In these experiments, the relatively broad K(+) channel blocker 4-aminopyridine reduced the fast repolarization, resulting in bursts of action potentials forming on top of the DAP. We conclude that repolarization of the action potential in parallel fibres is supported by at least three groups of K(+) channels. Differences in their temporal profiles allow relatively independent control of the spike and the DAP, whereas overlap of their temporal profiles provides robust control of axonal bursting properties.

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

PubMed

Li, Wenyuan; Gong, Ke; Li, Qingjiao; Alber, Frank; Zhou, Xianghong Jasmine

2015-03-15

Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability-the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency-the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed-the parallel version can run very fast on multiple computing nodes with limited local memory. The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http://zhoulab.usc.edu/Hi-Corrector/. © The Author 2014. Published by Oxford University Press.

Massively Parallel Processing for Fast and Accurate Stamping Simulations

NASA Astrophysics Data System (ADS)

Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

2005-08-01

The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

Ordered fast fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1989-01-01

Design alternatives for ordered Fast Fourier Transformation (FFT) algorithms were examined on massively parallel hypercube multiprocessors such as the Connection Machine. Particular emphasis is placed on reducing communication which is known to dominate the overall computing time. To this end, the order and computational phases of the FFT were combined, and the sequence to processor maps that reduce communication were used. The class of ordered transforms is expanded to include any FFT in which the order of the transform is the same as that of the input sequence. Two such orderings are examined, namely, standard-order and A-order which can be implemented with equal ease on the Connection Machine where orderings are determined by geometries and priorities. If the sequence has N = 2 exp r elements and the hypercube has P = 2 exp d processors, then a standard-order FFT can be implemented with d + r/2 + 1 parallel transmissions. An A-order sequence can be transformed with 2d - r/2 parallel transmissions which is r - d + 1 fewer than the standard order. A parallel method for computing the trigonometric coefficients is presented that does not use trigonometric functions or interprocessor communication. A performance of 0.9 GFLOPS was obtained for an A-order transform on the Connection Machine.

Parallel processing in the honeybee olfactory pathway: structure, function, and evolution.

PubMed

Rössler, Wolfgang; Brill, Martin F

2013-11-01

Animals face highly complex and dynamic olfactory stimuli in their natural environments, which require fast and reliable olfactory processing. Parallel processing is a common principle of sensory systems supporting this task, for example in visual and auditory systems, but its role in olfaction remained unclear. Studies in the honeybee focused on a dual olfactory pathway. Two sets of projection neurons connect glomeruli in two antennal-lobe hemilobes via lateral and medial tracts in opposite sequence with the mushroom bodies and lateral horn. Comparative studies suggest that this dual-tract circuit represents a unique adaptation in Hymenoptera. Imaging studies indicate that glomeruli in both hemilobes receive redundant sensory input. Recent simultaneous multi-unit recordings from projection neurons of both tracts revealed widely overlapping response profiles strongly indicating parallel olfactory processing. Whereas lateral-tract neurons respond fast with broad (generalistic) profiles, medial-tract neurons are odorant specific and respond slower. In analogy to "what-" and "where" subsystems in visual pathways, this suggests two parallel olfactory subsystems providing "what-" (quality) and "when" (temporal) information. Temporal response properties may support across-tract coincidence coding in higher centers. Parallel olfactory processing likely enhances perception of complex odorant mixtures to decode the diverse and dynamic olfactory world of a social insect.

Turbomachinery CFD on parallel computers

NASA Technical Reports Server (NTRS)

Blech, Richard A.; Milner, Edward J.; Quealy, Angela; Townsend, Scott E.

1992-01-01

The role of multistage turbomachinery simulation in the development of propulsion system models is discussed. Particularly, the need for simulations with higher fidelity and faster turnaround time is highlighted. It is shown how such fast simulations can be used in engineering-oriented environments. The use of parallel processing to achieve the required turnaround times is discussed. Current work by several researchers in this area is summarized. Parallel turbomachinery CFD research at the NASA Lewis Research Center is then highlighted. These efforts are focused on implementing the average-passage turbomachinery model on MIMD, distributed memory parallel computers. Performance results are given for inviscid, single blade row and viscous, multistage applications on several parallel computers, including networked workstations.

Matrix-Free Polynomial-Based Nonlinear Least Squares Optimized Preconditioning and its Application to Discontinuous Galerkin Discretizations of the Euler Equations

DTIC Science & Technology

2015-06-01

cient parallel code for applying the operator. Our method constructs a polynomial preconditioner using a nonlinear least squares (NLLS) algorithm. We show...apply the underlying operator. Such a preconditioner can be very attractive in scenarios where one has a highly efficient parallel code for applying...repeatedly solve a large system of linear equations where one has an extremely fast parallel code for applying an underlying fixed linear operator

Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units

PubMed Central

Anandakrishnan, Ramu; Scogland, Tom R. W.; Fenley, Andrew T.; Gordon, John C.; Feng, Wu-chun; Onufriev, Alexey V.

2010-01-01

Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multiscale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone. PMID:20452792

[Metabolic study of the initial period of fasting in the king penguin chick].

PubMed

Cherel, Y; Le Maho, Y

1985-01-01

There is an 80% decrease in the specific daily change in body mass (dm/m dt) during the first 5-6 days of fasting in king penguin chicks, which characterizes period I of fasting. Parallel decreases in plasma alanine and uric acid concentrations suggest an important reduction in protein degradation. Plasma concentration of beta-hydroxybutyrate and glucose are high, respectively 1.3 and 12.5 mmol X 1(-1), and do not change significantly.

Implementation of High Time Delay Accuracy of Ultrasonic Phased Array Based on Interpolation CIC Filter

PubMed Central

Liu, Peilu; Li, Xinghua; Li, Haopeng; Su, Zhikun; Zhang, Hongxu

2017-01-01

In order to improve the accuracy of ultrasonic phased array focusing time delay, analyzing the original interpolation Cascade-Integrator-Comb (CIC) filter, an 8× interpolation CIC filter parallel algorithm was proposed, so that interpolation and multichannel decomposition can simultaneously process. Moreover, we summarized the general formula of arbitrary multiple interpolation CIC filter parallel algorithm and established an ultrasonic phased array focusing time delay system based on 8× interpolation CIC filter parallel algorithm. Improving the algorithmic structure, 12.5% of addition and 29.2% of multiplication was reduced, meanwhile the speed of computation is still very fast. Considering the existing problems of the CIC filter, we compensated the CIC filter; the compensated CIC filter’s pass band is flatter, the transition band becomes steep, and the stop band attenuation increases. Finally, we verified the feasibility of this algorithm on Field Programming Gate Array (FPGA). In the case of system clock is 125 MHz, after 8× interpolation filtering and decomposition, time delay accuracy of the defect echo becomes 1 ns. Simulation and experimental results both show that the algorithm we proposed has strong feasibility. Because of the fast calculation, small computational amount and high resolution, this algorithm is especially suitable for applications with high time delay accuracy and fast detection. PMID:29023385

Implementation of High Time Delay Accuracy of Ultrasonic Phased Array Based on Interpolation CIC Filter.

PubMed

Liu, Peilu; Li, Xinghua; Li, Haopeng; Su, Zhikun; Zhang, Hongxu

2017-10-12

In order to improve the accuracy of ultrasonic phased array focusing time delay, analyzing the original interpolation Cascade-Integrator-Comb (CIC) filter, an 8× interpolation CIC filter parallel algorithm was proposed, so that interpolation and multichannel decomposition can simultaneously process. Moreover, we summarized the general formula of arbitrary multiple interpolation CIC filter parallel algorithm and established an ultrasonic phased array focusing time delay system based on 8× interpolation CIC filter parallel algorithm. Improving the algorithmic structure, 12.5% of addition and 29.2% of multiplication was reduced, meanwhile the speed of computation is still very fast. Considering the existing problems of the CIC filter, we compensated the CIC filter; the compensated CIC filter's pass band is flatter, the transition band becomes steep, and the stop band attenuation increases. Finally, we verified the feasibility of this algorithm on Field Programming Gate Array (FPGA). In the case of system clock is 125 MHz, after 8× interpolation filtering and decomposition, time delay accuracy of the defect echo becomes 1 ns. Simulation and experimental results both show that the algorithm we proposed has strong feasibility. Because of the fast calculation, small computational amount and high resolution, this algorithm is especially suitable for applications with high time delay accuracy and fast detection.

FastQuery: A Parallel Indexing System for Scientific Data

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

Chou, Jerry; Wu, Kesheng; Prabhat,

2011-07-29

Modern scientific datasets present numerous data management and analysis challenges. State-of-the- art index and query technologies such as FastBit can significantly improve accesses to these datasets by augmenting the user data with indexes and other secondary information. However, a challenge is that the indexes assume the relational data model but the scientific data generally follows the array data model. To match the two data models, we design a generic mapping mechanism and implement an efficient input and output interface for reading and writing the data and their corresponding indexes. To take advantage of the emerging many-core architectures, we also developmore » a parallel strategy for indexing using threading technology. This approach complements our on-going MPI-based parallelization efforts. We demonstrate the flexibility of our software by applying it to two of the most commonly used scientific data formats, HDF5 and NetCDF. We present two case studies using data from a particle accelerator model and a global climate model. We also conducted a detailed performance study using these scientific datasets. The results show that FastQuery speeds up the query time by a factor of 2.5x to 50x, and it reduces the indexing time by a factor of 16 on 24 cores.« less

Quasi-parallel precession diffraction: Alignment method for scanning transmission electron microscopes.

PubMed

Plana-Ruiz, S; Portillo, J; Estradé, S; Peiró, F; Kolb, Ute; Nicolopoulos, S

2018-06-06

A general method to set illuminating conditions for selectable beam convergence and probe size is presented in this work for Transmission Electron Microscopes (TEM) fitted with µs/pixel fast beam scanning control, (S)TEM, and an annular dark field detector. The case of interest of beam convergence and probe size, which enables diffraction pattern indexation, is then used as a starting point in this work to add 100 Hz precession to the beam while imaging the specimen at a fast rate and keeping the projector system in diffraction mode. The described systematic alignment method for the adjustment of beam precession on the specimen plane while scanning at fast rates is mainly based on the sharpness of the precessed STEM image. The complete alignment method for parallel condition and precession, Quasi-Parallel PED-STEM, is presented in block diagram scheme, as it has been tested on a variety of instruments. The immediate application of this methodology is that it renders the TEM column ready for the acquisition of Precessed Electron Diffraction Tomographies (EDT) as well as for the acquisition of slow Precessed Scanning Nanometer Electron Diffraction (SNED). Examples of the quality of the Precessed Electron Diffraction (PED) patterns and PED-STEM alignment images are presented with corresponding probe sizes and convergence angles. Copyright © 2018. Published by Elsevier B.V.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

PubMed

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

2011-06-03

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

SELF-GRAVITATIONAL FORCE CALCULATION OF SECOND-ORDER ACCURACY FOR INFINITESIMALLY THIN GASEOUS DISKS IN POLAR COORDINATES

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

Wang, Hsiang-Hsu; Taam, Ronald E.; Yen, David C. C., E-mail: yen@math.fju.edu.tw

Investigating the evolution of disk galaxies and the dynamics of proto-stellar disks can involve the use of both a hydrodynamical and a Poisson solver. These systems are usually approximated as infinitesimally thin disks using two-dimensional Cartesian or polar coordinates. In Cartesian coordinates, the calculations of the hydrodynamics and self-gravitational forces are relatively straightforward for attaining second-order accuracy. However, in polar coordinates, a second-order calculation of self-gravitational forces is required for matching the second-order accuracy of hydrodynamical schemes. We present a direct algorithm for calculating self-gravitational forces with second-order accuracy without artificial boundary conditions. The Poisson integral in polar coordinates ismore » expressed in a convolution form and the corresponding numerical complexity is nearly linear using a fast Fourier transform. Examples with analytic solutions are used to verify that the truncated error of this algorithm is of second order. The kernel integral around the singularity is applied to modify the particle method. The use of a softening length is avoided and the accuracy of the particle method is significantly improved.« less

Atomic Charge Parameters for the Finite Difference Poisson-Boltzmann Method Using Electronegativity Neutralization.

PubMed

Yang, Qingyi; Sharp, Kim A

2006-07-01

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.

In the linear quadratic model, the Poisson approximation and the Zaider-Minerbo formula agree on the ranking of tumor control probabilities, up to a critical cell birth rate.

PubMed

Ballhausen, Hendrik; Belka, Claus

2017-03-01

To provide a rule for the agreement or disagreement of the Poisson approximation (PA) and the Zaider-Minerbo formula (ZM) on the ranking of treatment alternatives in terms of tumor control probability (TCP) in the linear quadratic model. A general criterion involving a critical cell birth rate was formally derived. For demonstration, the criterion was applied to a distinct radiobiological model of fast growing head and neck tumors and a respective range of 22 conventional and nonconventional head and neck schedules. There is a critical cell birth rate b crit below which PA and ZM agree on which one out of two alternative treatment schemes with single-cell survival curves S'(t) and S''(t) offers better TCP: [Formula: see text] For cell birth rates b above this critical cell birth rate, PA and ZM disagree if and only if b >b crit > 0. In case of the exemplary head and neck schedules, out of 231 possible combinations, only 16 or 7% were found where PA and ZM disagreed. In all 231 cases the prediction of the criterion was numerically confirmed, and cell birth rates at crossovers between schedules matched the calculated critical cell birth rates. TCP estimated by PA and ZM almost never numerically coincide. Still, in many cases both formulas at least agree about which one out of two alternative fractionation schemes offers better TCP. In case of fast growing tumors featuring a high cell birth rate, however, ZM may suggest a re-evaluation of treatment options.

Normal forms for Poisson maps and symplectic groupoids around Poisson transversals

NASA Astrophysics Data System (ADS)

Frejlich, Pedro; Mărcuț, Ioan

2018-03-01

Poisson transversals are submanifolds in a Poisson manifold which intersect all symplectic leaves transversally and symplectically. In this communication, we prove a normal form theorem for Poisson maps around Poisson transversals. A Poisson map pulls a Poisson transversal back to a Poisson transversal, and our first main result states that simultaneous normal forms exist around such transversals, for which the Poisson map becomes transversally linear, and intertwines the normal form data of the transversals. Our second result concerns symplectic integrations. We prove that a neighborhood of a Poisson transversal is integrable exactly when the Poisson transversal itself is integrable, and in that case we prove a normal form theorem for the symplectic groupoid around its restriction to the Poisson transversal, which puts all structure maps in normal form. We conclude by illustrating our results with examples arising from Lie algebras.

Normal forms for Poisson maps and symplectic groupoids around Poisson transversals.

PubMed

Frejlich, Pedro; Mărcuț, Ioan

2018-01-01

Poisson transversals are submanifolds in a Poisson manifold which intersect all symplectic leaves transversally and symplectically. In this communication, we prove a normal form theorem for Poisson maps around Poisson transversals. A Poisson map pulls a Poisson transversal back to a Poisson transversal, and our first main result states that simultaneous normal forms exist around such transversals, for which the Poisson map becomes transversally linear, and intertwines the normal form data of the transversals. Our second result concerns symplectic integrations. We prove that a neighborhood of a Poisson transversal is integrable exactly when the Poisson transversal itself is integrable, and in that case we prove a normal form theorem for the symplectic groupoid around its restriction to the Poisson transversal, which puts all structure maps in normal form. We conclude by illustrating our results with examples arising from Lie algebras.

Fast animation of lightning using an adaptive mesh.

PubMed

Kim, Theodore; Lin, Ming C

2007-01-01

We present a fast method for simulating, animating, and rendering lightning using adaptive grids. The "dielectric breakdown model" is an elegant algorithm for electrical pattern formation that we extend to enable animation of lightning. The simulation can be slow, particularly in 3D, because it involves solving a large Poisson problem. Losasso et al. recently proposed an octree data structure for simulating water and smoke, and we show that this discretization can be applied to the problem of lightning simulation as well. However, implementing the incomplete Cholesky conjugate gradient (ICCG) solver for this problem can be daunting, so we provide an extensive discussion of implementation issues. ICCG solvers can usually be accelerated using "Eisenstat's trick," but the trick cannot be directly applied to the adaptive case. Fortunately, we show that an "almost incomplete Cholesky" factorization can be computed so that Eisenstat's trick can still be used. We then present a fast rendering method based on convolution that is competitive with Monte Carlo ray tracing but orders of magnitude faster, and we also show how to further improve the visual results using jittering.

FleCSPH - a parallel and distributed SPH implementation based on the FleCSI framework

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

Junghans, Christoph; Loiseau, Julien

2017-06-20

FleCSPH is a multi-physics compact application that exercises FleCSI parallel data structures for tree-based particle methods. In particular, FleCSPH implements a smoothed-particle hydrodynamics (SPH) solver for the solution of Lagrangian problems in astrophysics and cosmology. FleCSPH includes support for gravitational forces using the fast multipole method (FMM).

Solar Wind Proton Temperature Anisotropy: Linear Theory and WIND/SWE Observations

NASA Technical Reports Server (NTRS)

Hellinger, P.; Travnicek, P.; Kasper, J. C.; Lazarus, A. J.

2006-01-01

We present a comparison between WIND/SWE observations (Kasper et al., 2006) of beta parallel to p and T perpendicular to p/T parallel to p (where beta parallel to p is the proton parallel beta and T perpendicular to p and T parallel to p are the perpendicular and parallel proton are the perpendicular and parallel proton temperatures, respectively; here parallel and perpendicular indicate directions with respect to the ambient magnetic field) and predictions of the Vlasov linear theory. In the slow solar wind, the observed proton temperature anisotropy seems to be constrained by oblique instabilities, by the mirror one and the oblique fire hose, contrary to the results of the linear theory which predicts a dominance of the proton cyclotron instability and the parallel fire hose. The fast solar wind core protons exhibit an anticorrelation between beta parallel to c and T perpendicular to c/T parallel to c (where beta parallel to c is the core proton parallel beta and T perpendicular to c and T parallel to c are the perpendicular and parallel core proton temperatures, respectively) similar to that observed in the HELIOS data (Marsch et al., 2004).

A FAST ITERATIVE METHOD FOR SOLVING THE EIKONAL EQUATION ON TRIANGULATED SURFACES*

PubMed Central

Fu, Zhisong; Jeong, Won-Ki; Pan, Yongsheng; Kirby, Robert M.; Whitaker, Ross T.

2012-01-01

This paper presents an efficient, fine-grained parallel algorithm for solving the Eikonal equation on triangular meshes. The Eikonal equation, and the broader class of Hamilton–Jacobi equations to which it belongs, have a wide range of applications from geometric optics and seismology to biological modeling and analysis of geometry and images. The ability to solve such equations accurately and efficiently provides new capabilities for exploring and visualizing parameter spaces and for solving inverse problems that rely on such equations in the forward model. Efficient solvers on state-of-the-art, parallel architectures require new algorithms that are not, in many cases, optimal, but are better suited to synchronous updates of the solution. In previous work [W. K. Jeong and R. T. Whitaker, SIAM J. Sci. Comput., 30 (2008), pp. 2512–2534], the authors proposed the fast iterative method (FIM) to efficiently solve the Eikonal equation on regular grids. In this paper we extend the fast iterative method to solve Eikonal equations efficiently on triangulated domains on the CPU and on parallel architectures, including graphics processors. We propose a new local update scheme that provides solutions of first-order accuracy for both architectures. We also propose a novel triangle-based update scheme and its corresponding data structure for efficient irregular data mapping to parallel single-instruction multiple-data (SIMD) processors. We provide detailed descriptions of the implementations on a single CPU, a multicore CPU with shared memory, and SIMD architectures with comparative results against state-of-the-art Eikonal solvers. PMID:22641200

Fast Fourier Transform algorithm design and tradeoffs

NASA Technical Reports Server (NTRS)

Kamin, Ray A., III; Adams, George B., III

1988-01-01

The Fast Fourier Transform (FFT) is a mainstay of certain numerical techniques for solving fluid dynamics problems. The Connection Machine CM-2 is the target for an investigation into the design of multidimensional Single Instruction Stream/Multiple Data (SIMD) parallel FFT algorithms for high performance. Critical algorithm design issues are discussed, necessary machine performance measurements are identified and made, and the performance of the developed FFT programs are measured. Fast Fourier Transform programs are compared to the currently best Cray-2 FFT program.

Efficient Levenberg-Marquardt minimization of the maximum likelihood estimator for Poisson deviates

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

Laurence, T; Chromy, B

2009-11-10

Histograms of counted events are Poisson distributed, but are typically fitted without justification using nonlinear least squares fitting. The more appropriate maximum likelihood estimator (MLE) for Poisson distributed data is seldom used. We extend the use of the Levenberg-Marquardt algorithm commonly used for nonlinear least squares minimization for use with the MLE for Poisson distributed data. In so doing, we remove any excuse for not using this more appropriate MLE. We demonstrate the use of the algorithm and the superior performance of the MLE using simulations and experiments in the context of fluorescence lifetime imaging. Scientists commonly form histograms ofmore » counted events from their data, and extract parameters by fitting to a specified model. Assuming that the probability of occurrence for each bin is small, event counts in the histogram bins will be distributed according to the Poisson distribution. We develop here an efficient algorithm for fitting event counting histograms using the maximum likelihood estimator (MLE) for Poisson distributed data, rather than the non-linear least squares measure. This algorithm is a simple extension of the common Levenberg-Marquardt (L-M) algorithm, is simple to implement, quick and robust. Fitting using a least squares measure is most common, but it is the maximum likelihood estimator only for Gaussian-distributed data. Non-linear least squares methods may be applied to event counting histograms in cases where the number of events is very large, so that the Poisson distribution is well approximated by a Gaussian. However, it is not easy to satisfy this criterion in practice - which requires a large number of events. It has been well-known for years that least squares procedures lead to biased results when applied to Poisson-distributed data; a recent paper providing extensive characterization of these biases in exponential fitting is given. The more appropriate measure based on the maximum likelihood estimator (MLE) for the Poisson distribution is also well known, but has not become generally used. This is primarily because, in contrast to non-linear least squares fitting, there has been no quick, robust, and general fitting method. In the field of fluorescence lifetime spectroscopy and imaging, there have been some efforts to use this estimator through minimization routines such as Nelder-Mead optimization, exhaustive line searches, and Gauss-Newton minimization. Minimization based on specific one- or multi-exponential models has been used to obtain quick results, but this procedure does not allow the incorporation of the instrument response, and is not generally applicable to models found in other fields. Methods for using the MLE for Poisson-distributed data have been published by the wider spectroscopic community, including iterative minimization schemes based on Gauss-Newton minimization. The slow acceptance of these procedures for fitting event counting histograms may also be explained by the use of the ubiquitous, fast Levenberg-Marquardt (L-M) fitting procedure for fitting non-linear models using least squares fitting (simple searches obtain {approx}10000 references - this doesn't include those who use it, but don't know they are using it). The benefits of L-M include a seamless transition between Gauss-Newton minimization and downward gradient minimization through the use of a regularization parameter. This transition is desirable because Gauss-Newton methods converge quickly, but only within a limited domain of convergence; on the other hand the downward gradient methods have a much wider domain of convergence, but converge extremely slowly nearer the minimum. L-M has the advantages of both procedures: relative insensitivity to initial parameters and rapid convergence. Scientists, when wanting an answer quickly, will fit data using L-M, get an answer, and move on. Only those that are aware of the bias issues will bother to fit using the more appropriate MLE for Poisson deviates. However, since there is a simple, analytical formula for the appropriate MLE measure for Poisson deviates, it is inexcusable that least squares estimators are used almost exclusively when fitting event counting histograms. There have been ways found to use successive non-linear least squares fitting to obtain similarly unbiased results, but this procedure is justified by simulation, must be re-tested when conditions change significantly, and requires two successive fits. There is a great need for a fitting routine for the MLE estimator for Poisson deviates that has convergence domains and rates comparable to the non-linear least squares L-M fitting. We show in this report that a simple way to achieve that goal is to use the L-M fitting procedure not to minimize the least squares measure, but the MLE for Poisson deviates.« less

Tempest Neoclassical Simulation of Fusion Edge Plasmas

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Cohen, B. I.; Cohen, R. H.; Dorr, M.; Hittinger, J.; Kerbel, G. D.; Nevins, W. M.; Rognlien, T. D.

2006-04-01

We are developing a continuum gyrokinetic full-F code, TEMPEST, to simulate edge plasmas. The geometry is that of a fully diverted tokamak and so includes boundary conditions for both closed magnetic flux surfaces and open field lines. The code, presently 4-dimensional (2D2V), includes kinetic ions and electrons, a gyrokinetic Poisson solver for electric field, and the nonlinear Fokker-Planck collision operator. Here we present the simulation results of neoclassical transport with Boltzmann electrons. In a large aspect ratio circular geometry, excellent agreement is found for neoclassical equilibrium with parallel flows in the banana regime without a temperature gradient. In divertor geometry, it is found that the endloss of particles and energy induces pedestal-like density and temperature profiles inside the magnetic separatrix and parallel flow stronger than the neoclassical predictions in the SOL. The impact of the X-point divertor geometry on the self-consistent electric field and geo-acoustic oscillations will be reported. We will also discuss the status of extending TEMPEST into a 5-D code.

Parallel processing data network of master and slave transputers controlled by a serial control network

DOEpatents

Crosetto, D.B.

1996-12-31

The present device provides for a dynamically configurable communication network having a multi-processor parallel processing system having a serial communication network and a high speed parallel communication network. The serial communication network is used to disseminate commands from a master processor to a plurality of slave processors to effect communication protocol, to control transmission of high density data among nodes and to monitor each slave processor`s status. The high speed parallel processing network is used to effect the transmission of high density data among nodes in the parallel processing system. Each node comprises a transputer, a digital signal processor, a parallel transfer controller, and two three-port memory devices. A communication switch within each node connects it to a fast parallel hardware channel through which all high density data arrives or leaves the node. 6 figs.

Parallel processing data network of master and slave transputers controlled by a serial control network

DOEpatents

Crosetto, Dario B.

1996-01-01

The present device provides for a dynamically configurable communication network having a multi-processor parallel processing system having a serial communication network and a high speed parallel communication network. The serial communication network is used to disseminate commands from a master processor (100) to a plurality of slave processors (200) to effect communication protocol, to control transmission of high density data among nodes and to monitor each slave processor's status. The high speed parallel processing network is used to effect the transmission of high density data among nodes in the parallel processing system. Each node comprises a transputer (104), a digital signal processor (114), a parallel transfer controller (106), and two three-port memory devices. A communication switch (108) within each node (100) connects it to a fast parallel hardware channel (70) through which all high density data arrives or leaves the node.

A discrimination-association model for decomposing component processes of the implicit association test.

PubMed

Stefanutti, Luca; Robusto, Egidio; Vianello, Michelangelo; Anselmi, Pasquale

2013-06-01

A formal model is proposed that decomposes the implicit association test (IAT) effect into three process components: stimuli discrimination, automatic association, and termination criterion. Both response accuracy and reaction time are considered. Four independent and parallel Poisson processes, one for each of the four label categories of the IAT, are assumed. The model parameters are the rate at which information accrues on the counter of each process and the amount of information that is needed before a response is given. The aim of this study is to present the model and an illustrative application in which the process components of a Coca-Pepsi IAT are decomposed.

Ca/Na selectivity coefficients from the Poisson-Boltzmann theory

NASA Astrophysics Data System (ADS)

Hedström, Magnus; Karnland, Ola

As a model for ion equilibrium in montmorillonite, the Poisson-Boltzmann (PB) equation was solved for two parallel charged surfaces in contact with an external NaCl/CaCl 2 mixed solution. The ion concentration profiles in the montmorillonite interlayer were obtained from the PB equation and integration of those gave the occupancy of Na + and Ca 2+ in the clay. That information together with the composition of the external electrolyte were then used for the calculation of the Gaines-Thomas selectivity coefficient K GT. The predictions from the model were compared to experimental data from batch as well as compacted conditions, and the agreement was generally good. With a surface layer-charge density of one unit charge per 145 Å 2, which is close to the value for Wyoming-type montmorillonite, the calculated selectivity coefficients were found to vary from about 4 in batch to 8 in compacted montmorillonite with dry density ∼1700 kg/m 3. From the point of view of assessing the evolution, with regard to sodium-calcium ion exchange, of the bentonite buffer in a repository for spent nuclear fuel, these results justify the use of data obtained in batch experiments.

Protein biomarker discovery and fast monitoring for the identification and detection of Anisakids by parallel reaction monitoring (PRM) mass spectrometry.

PubMed

Carrera, Mónica; Gallardo, José M; Pascual, Santiago; González, Ángel F; Medina, Isabel

2016-06-16

Anisakids are fish-borne parasites that are responsible for a large number of human infections and allergic reactions around the world. World health organizations and food safety authorities aim to control and prevent this emerging health problem. In the present work, a new method for the fast monitoring of these parasites is described. The strategy is divided in three steps: (i) purification of thermostable proteins from fish-borne parasites (Anisakids), (ii) in-solution HIFU trypsin digestion and (iii) monitoring of several peptide markers by parallel reaction monitoring (PRM) mass spectrometry. This methodology allows the fast detection of Anisakids in <2h. An affordable assay utilizing this methodology will facilitate testing for regulatory and safety applications. The work describes for the first time, the Protein Biomarker Discovery and the Fast Monitoring for the identification and detection of Anisakids in fishery products. The strategy is based on the purification of thermostable proteins, the use of accelerated in-solution trypsin digestions under an ultrasonic field provided by High-Intensity Focused Ultrasound (HIFU) and the monitoring of several peptide biomarkers by Parallel Reaction Monitoring (PRM) Mass Spectrometry in a linear ion trap mass spectrometer. The workflow allows the unequivocal detection of Anisakids, in <2h. The present strategy constitutes the fastest method for Anisakids detection, whose application in the food quality control area, could provide to the authorities an effective and rapid method to guarantee the safety to the consumers. Copyright © 2016 Elsevier B.V. All rights reserved.

Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

NASA Astrophysics Data System (ADS)

Yokota, Rio; Barba, L. A.; Narumi, Tetsu; Yasuoka, Kenji

2013-03-01

This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on GPU hardware using single precision. The simulations use a vortex particle method to solve the Navier-Stokes equations, with a highly parallel fast multipole method (FMM) as numerical engine, and match the current record in mesh size for this application, a cube of 40963 computational points solved with a spectral method. The standard numerical approach used in this field is the pseudo-spectral method, relying on the FFT algorithm as the numerical engine. The particle-based simulations presented in this paper quantitatively match the kinetic energy spectrum obtained with a pseudo-spectral method, using a trusted code. In terms of parallel performance, weak scaling results show the FMM-based vortex method achieving 74% parallel efficiency on 4096 processes (one GPU per MPI process, 3 GPUs per node of the TSUBAME-2.0 system). The FFT-based spectral method is able to achieve just 14% parallel efficiency on the same number of MPI processes (using only CPU cores), due to the all-to-all communication pattern of the FFT algorithm. The calculation time for one time step was 108 s for the vortex method and 154 s for the spectral method, under these conditions. Computing with 69 billion particles, this work exceeds by an order of magnitude the largest vortex-method calculations to date.

Zeroth Poisson Homology, Foliated Cohomology and Perfect Poisson Manifolds

NASA Astrophysics Data System (ADS)

Martínez-Torres, David; Miranda, Eva

2018-01-01

We prove that, for compact regular Poisson manifolds, the zeroth homology group is isomorphic to the top foliated cohomology group, and we give some applications. In particular, we show that, for regular unimodular Poisson manifolds, top Poisson and foliated cohomology groups are isomorphic. Inspired by the symplectic setting, we define what a perfect Poisson manifold is. We use these Poisson homology computations to provide families of perfect Poisson manifolds.

Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

PubMed

Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

2015-01-01

To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

Fast disk array for image storage

NASA Astrophysics Data System (ADS)

Feng, Dan; Zhu, Zhichun; Jin, Hai; Zhang, Jiangling

1997-01-01

A fast disk array is designed for the large continuous image storage. It includes a high speed data architecture and the technology of data striping and organization on the disk array. The high speed data path which is constructed by two dual port RAM and some control circuit is configured to transfer data between a host system and a plurality of disk drives. The bandwidth can be more than 100 MB/s if the data path based on PCI (peripheral component interconnect). The organization of data stored on the disk array is similar to RAID 4. Data are striped on a plurality of disk, and each striping unit is equal to a track. I/O instructions are performed in parallel on the disk drives. An independent disk is used to store the parity information in the fast disk array architecture. By placing the parity generation circuit directly on the SCSI (or SCSI 2) bus, the parity information can be generated on the fly. It will affect little on the data writing in parallel on the other disks. The fast disk array architecture designed in the paper can meet the demands of the image storage.

Fast MPEG-CDVS Encoder With GPU-CPU Hybrid Computing

NASA Astrophysics Data System (ADS)

Duan, Ling-Yu; Sun, Wei; Zhang, Xinfeng; Wang, Shiqi; Chen, Jie; Yin, Jianxiong; See, Simon; Huang, Tiejun; Kot, Alex C.; Gao, Wen

2018-05-01

The compact descriptors for visual search (CDVS) standard from ISO/IEC moving pictures experts group (MPEG) has succeeded in enabling the interoperability for efficient and effective image retrieval by standardizing the bitstream syntax of compact feature descriptors. However, the intensive computation of CDVS encoder unfortunately hinders its widely deployment in industry for large-scale visual search. In this paper, we revisit the merits of low complexity design of CDVS core techniques and present a very fast CDVS encoder by leveraging the massive parallel execution resources of GPU. We elegantly shift the computation-intensive and parallel-friendly modules to the state-of-the-arts GPU platforms, in which the thread block allocation and the memory access are jointly optimized to eliminate performance loss. In addition, those operations with heavy data dependence are allocated to CPU to resolve the extra but non-necessary computation burden for GPU. Furthermore, we have demonstrated the proposed fast CDVS encoder can work well with those convolution neural network approaches which has harmoniously leveraged the advantages of GPU platforms, and yielded significant performance improvements. Comprehensive experimental results over benchmarks are evaluated, which has shown that the fast CDVS encoder using GPU-CPU hybrid computing is promising for scalable visual search.

Direct measurement of sub-Debye-length attraction between oppositely charged surfaces.

PubMed

Kampf, Nir; Ben-Yaakov, Dan; Andelman, David; Safran, S A; Klein, Jacob

2009-09-11

Using a surface force balance with fast video analysis, we have measured directly the attractive forces between oppositely charged solid surfaces (charge densities sigma(+), sigma(-)) across water over the entire range of interaction, in particular, at surface separations D below the Debye screening length lambda(S). At very low salt concentration we find a long-ranged attraction between the surfaces (onset ca. 100 nm), whose variation at D

Comment on ‘A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-square deconvolution with Laguerre expansion’

NASA Astrophysics Data System (ADS)

Zhang, Yongliang; Day-Uei Li, David

2017-02-01

This comment is to clarify that Poisson noise instead of Gaussian noise shall be included to assess the performances of least-squares deconvolution with Laguerre expansion (LSD-LE) for analysing fluorescence lifetime imaging data obtained from time-resolved systems. Moreover, we also corrected an equation in the paper. As the LSD-LE method is rapid and has the potential to be widely applied not only for diagnostic but for wider bioimaging applications, it is desirable to have precise noise models and equations.

Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer.

PubMed

Suplatov, Dmitry; Popova, Nina; Zhumatiy, Sergey; Voevodin, Vladimir; Švedas, Vytas

2016-04-01

Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads - one for task management and communication, and another for subtask execution - are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .

Effect of parallel electric fields on the ponderomotive stabilization of MHD instabilities

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

Litwin, C.; Hershkowitz, N.

The contribution of the wave electric field component E/sub parallel/, parallel to the magnetic field, to the ponderomotive stabilization of curvature driven instabilities is evaluated and compared to the transverse component contribution. For the experimental density range, in which the stability is primarily determined by the m = 1 magnetosonic wave, this contribution is found to be the dominant and stabilizing when the electron temperature is neglected. For sufficiently high electron temperatures the dominant fast wave is found to be axially evanescent. In the same limit, E/sub parallel/ becomes radially oscillating. It is concluded that the increased electron temperature nearmore » the plasma surface reduces the magnitude of ponderomotive effects.« less

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

PubMed Central

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

2011-01-01

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

Very fast motion planning for highly dexterous-articulated robots

NASA Technical Reports Server (NTRS)

Challou, Daniel J.; Gini, Maria; Kumar, Vipin

1994-01-01

Due to the inherent danger of space exploration, the need for greater use of teleoperated and autonomous robotic systems in space-based applications has long been apparent. Autonomous and semi-autonomous robotic devices have been proposed for carrying out routine functions associated with scientific experiments aboard the shuttle and space station. Finally, research into the use of such devices for planetary exploration continues. To accomplish their assigned tasks, all such autonomous and semi-autonomous devices will require the ability to move themselves through space without hitting themselves or the objects which surround them. In space it is important to execute the necessary motions correctly when they are first attempted because repositioning is expensive in terms of both time and resources (e.g., fuel). Finally, such devices will have to function in a variety of different environments. Given these constraints, a means for fast motion planning to insure the correct movement of robotic devices would be ideal. Unfortunately, motion planning algorithms are rarely used in practice because of their computational complexity. Fast methods have been developed for detecting imminent collisions, but the more general problem of motion planning remains computationally intractable. However, in this paper we show how the use of multicomputers and appropriate parallel algorithms can substantially reduce the time required to synthesize paths for dexterous articulated robots with a large number of joints. We have developed a parallel formulation of the Randomized Path Planner proposed by Barraquand and Latombe. We have shown that our parallel formulation is capable of formulating plans in a few seconds or less on various parallel architectures including: the nCUBE2 multicomputer with up to 1024 processors (nCUBE2 is a registered trademark of the nCUBE corporation), and a network of workstations.

Seismic anisotropy in the vicinity of the Alpine fault, New Zealand, estimated by seismic interferometry

NASA Astrophysics Data System (ADS)

Takagi, R.; Okada, T.; Yoshida, K.; Townend, J.; Boese, C. M.; Baratin, L. M.; Chamberlain, C. J.; Savage, M. K.

2016-12-01

We estimate shear wave velocity anisotropy in shallow crust near the Alpine fault using seismic interferometry of borehole vertical arrays. We utilized four borehole observations: two sensors are deployed in two boreholes of the Deep Fault Drilling Project in the hanging wall side, and the other two sites are located in the footwall side. Surface sensors deployed just above each borehole are used to make vertical arrays. Crosscorrelating rotated horizontal seismograms observed by the borehole and surface sensors, we extracted polarized shear waves propagating from the bottom to the surface of each borehole. The extracted shear waves show polarization angle dependence of travel time, indicating shear wave anisotropy between the two sensors. In the hanging wall side, the estimated fast shear wave directions are parallel to the Alpine fault. Strong anisotropy of 20% is observed at the site within 100 m from the Alpine fault. The hanging wall consists of mylonite and schist characterized by fault parallel foliation. In addition, an acoustic borehole imaging reveals fractures parallel to the Alpine fault. The fault parallel anisotropy suggest structural anisotropy is predominant in the hanging wall, demonstrating consistency of geological and seismological observations. In the footwall side, on the other hand, the angle between the fast direction and the strike of the Alpine fault is 33-40 degrees. Since the footwall is composed of granitoid that may not have planar structure, stress induced anisotropy is possibly predominant. The direction of maximum horizontal stress (SHmax) estimated by focal mechanisms of regional earthquakes is 55 degrees of the Alpine fault. Possible interpretation of the difference between the fast direction and SHmax direction is depth rotation of stress field near the Alpine fault. Similar depth rotation of stress field is also observed in the SAFOD borehole at the San Andreas fault.

Computational simulations of supersonic magnetohydrodynamic flow control, power and propulsion systems

NASA Astrophysics Data System (ADS)

Wan, Tian

This work is motivated by the lack of fully coupled computational tool that solves successfully the turbulent chemically reacting Navier-Stokes equation, the electron energy conservation equation and the electric current Poisson equation. In the present work, the abovementioned equations are solved in a fully coupled manner using fully implicit parallel GMRES methods. The system of Navier-Stokes equations are solved using a GMRES method with combined Schwarz and ILU(0) preconditioners. The electron energy equation and the electric current Poisson equation are solved using a GMRES method with combined SOR and Jacobi preconditioners. The fully coupled method has also been implemented successfully in an unstructured solver, US3D, and convergence test results were presented. This new method is shown two to five times faster than the original DPLR method. The Poisson solver is validated with analytic test problems. Then, four problems are selected; two of them are computed to explore the possibility of onboard MHD control and power generation, and the other two are simulation of experiments. First, the possibility of onboard reentry shock control by a magnetic field is explored. As part of a previous project, MHD power generation onboard a re-entry vehicle is also simulated. Then, the MHD acceleration experiments conducted at NASA Ames research center are simulated. Lastly, the MHD power generation experiments known as the HVEPS project are simulated. For code validation, the scramjet experiments at University of Queensland are simulated first. The generator section of the HVEPS test facility is computed then. The main conclusion is that the computational tool is accurate for different types of problems and flow conditions, and its accuracy and efficiency are necessary when the flow complexity increases.

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet-Neumann boundary conditions

NASA Astrophysics Data System (ADS)

Reimer, Ashton S.; Cheviakov, Alexei F.

2013-03-01

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Catalogue identifier: AENQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 102793 No. of bytes in distributed program, including test data, etc.: 369378 Distribution format: tar.gz Programming language: Matlab 2010a. Computer: PC, Macintosh. Operating system: Windows, OSX, Linux. RAM: 8 GB (8, 589, 934, 592 bytes) Classification: 4.3. Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions. Solution method: Finite difference with mesh refinement. Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D. Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement. Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.

Fast Computation and Assessment Methods in Power System Analysis

NASA Astrophysics Data System (ADS)

Nagata, Masaki

Power system analysis is essential for efficient and reliable power system operation and control. Recently, online security assessment system has become of importance, as more efficient use of power networks is eagerly required. In this article, fast power system analysis techniques such as contingency screening, parallel processing and intelligent systems application are briefly surveyed from the view point of their application to online dynamic security assessment.

DISCRETE COMPOUND POISSON PROCESSES AND TABLES OF THE GEOMETRIC POISSON DISTRIBUTION.

DTIC Science & Technology

A concise summary of the salient properties of discrete Poisson processes , with emphasis on comparing the geometric and logarithmic Poisson processes . The...the geometric Poisson process are given for 176 sets of parameter values. New discrete compound Poisson processes are also introduced. These...processes have properties that are particularly relevant when the summation of several different Poisson processes is to be analyzed. This study provides the

The Anisotropic Structure of South China Sea: Using OBS Data to Constrain Mantle Flow

NASA Astrophysics Data System (ADS)

Li, L.; Xue, M.; Yang, T.; Liu, C.; Hua, Q.; Xia, S.; Huang, H.; Le, B. M.; Huo, D.; Pan, M.

2015-12-01

The dynamic mechanism of the formation of South China Sea (SCS) has been debated for decades. The anisotropic structure can provide useful insight into the complex evolution of SCS by indicating its mantle flow direction and strength. In this study, we employ shear wave splitting methods on two half-year seismic data collected from 10 and 6 passive source Ocean Bottom Seismometers (OBS) respectively. These OBSs were deployed along both sides of the extinct ridge in the central basin of SCS by Tongji University in 2012 and 2013 respectively, which were then successfully recovered in 2013 and 2015 respectively. Through processing and inspecting the global and regional earthquakes (with local events being processing) of the 2012 dataset, measurements are made for 2 global events and 24 regional events at 5 OBSs using the tangential energy minimization, the smallest eigenvalue minimization, as well as the correlation methods. We also implement cluster analysis on the splitting results obtained for different time windows as well as filtered at different frequency bands. For teleseismic core phases like SKS and PKS, we find the fast polarization direction beneath the central basin is approximately NE-SW, nearly parallel to the extinct ridge in the central basin of SCS. Whereas for regional events, the splitting analysis on S, PS and ScS phases shows much more complicated fast directions as the ray path varies for different phases. The fast directions observed can be divided into three groups: (1) for the events from the Eurasia plate, a gradual rotation of the fast polarization direction from NNE-SSW to NEE-SWW along the path from the inner Eurasia plate to the central SCS is observed, implying the mantle flow is controlled by the India-Eurasia collision; (2) for the events located at the junction of Pacific plate and Philippine plate, the dominant fast direction is NW-SE, almost perpendicular to Ryukyu Trench as well as sub-parallel to the absolute direction of Philippine plate; (3) for the events occurred in the SE direction near the Philippine Fault zone, the observed NE-SW fast direction is sub-parallel to the subduction direction of the Philippine plate.

JSD: Parallel Job Accounting on the IBM SP2

NASA Technical Reports Server (NTRS)

Saphir, William; Jones, James Patton; Walter, Howard (Technical Monitor)

1995-01-01

The IBM SP2 is one of the most promising parallel computers for scientific supercomputing - it is fast and usually reliable. One of its biggest problems is a lack of robust and comprehensive system software. Among other things, this software allows a collection of Unix processes to be treated as a single parallel application. It does not, however, provide accounting for parallel jobs other than what is provided by AIX for the individual process components. Without parallel job accounting, it is not possible to monitor system use, measure the effectiveness of system administration strategies, or identify system bottlenecks. To address this problem, we have written jsd, a daemon that collects accounting data for parallel jobs. jsd records information in a format that is easily machine- and human-readable, allowing us to extract the most important accounting information with very little effort. jsd also notifies system administrators in certain cases of system failure.

Aerodynamic simulation on massively parallel systems

NASA Technical Reports Server (NTRS)

Haeuser, Jochem; Simon, Horst D.

1992-01-01

This paper briefly addresses the computational requirements for the analysis of complete configurations of aircraft and spacecraft currently under design to be used for advanced transportation in commercial applications as well as in space flight. The discussion clearly shows that massively parallel systems are the only alternative which is both cost effective and on the other hand can provide the necessary TeraFlops, needed to satisfy the narrow design margins of modern vehicles. It is assumed that the solution of the governing physical equations, i.e., the Navier-Stokes equations which may be complemented by chemistry and turbulence models, is done on multiblock grids. This technique is situated between the fully structured approach of classical boundary fitted grids and the fully unstructured tetrahedra grids. A fully structured grid best represents the flow physics, while the unstructured grid gives best geometrical flexibility. The multiblock grid employed is structured within a block, but completely unstructured on the block level. While a completely unstructured grid is not straightforward to parallelize, the above mentioned multiblock grid is inherently parallel, in particular for multiple instruction multiple datastream (MIMD) machines. In this paper guidelines are provided for setting up or modifying an existing sequential code so that a direct parallelization on a massively parallel system is possible. Results are presented for three parallel systems, namely the Intel hypercube, the Ncube hypercube, and the FPS 500 system. Some preliminary results for an 8K CM2 machine will also be mentioned. The code run is the two dimensional grid generation module of Grid, which is a general two dimensional and three dimensional grid generation code for complex geometries. A system of nonlinear Poisson equations is solved. This code is also a good testcase for complex fluid dynamics codes, since the same datastructures are used. All systems provided good speedups, but message passing MIMD systems seem to be best suited for large miltiblock applications.

Deformation and fracture of explosion-welded Ti/Al plates: A synchrotron-based study

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

E, J. C.; Huang, J. Y.; Bie, B. X.

Here, explosion-welded Ti/Al plates are characterized with energy dispersive spectroscopy and x-ray computed tomography, and exhibit smooth, well-jointed, interface. We perform dynamic and quasi-static uniaxial tension experiments on Ti/Al with the loading direction either perpendicular or parallel to the Ti/Al interface, using a mini split Hopkinson tension bar and a material testing system in conjunction with time-resolved synchrotron x-ray imaging. X-ray imaging and strain-field mapping reveal different deformation mechanisms responsible for anisotropic bulk-scale responses, including yield strength, ductility and rate sensitivity. Deformation and fracture are achieved predominantly in Al layer for perpendicular loading, but both Ti and Al layers asmore » well as the interface play a role for parallel loading. The rate sensitivity of Ti/Al follows those of the constituent metals. For perpendicular loading, single deformation band develops in Al layer under quasi-static loading, while multiple deformation bands nucleate simultaneously under dynamic loading, leading to a higher dynamic fracture strain. For parallel loading, the interface impedes the growth of deformation and results in increased ductility of Ti/Al under quasi-static loading, while interface fracture occurs under dynamic loading due to the disparity in Poisson's contraction.« less

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.

PubMed

Anandakrishnan, Ramu; Scogland, Tom R W; Fenley, Andrew T; Gordon, John C; Feng, Wu-chun; Onufriev, Alexey V

2010-06-01

Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson-Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multi-scale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Deformation and fracture of explosion-welded Ti/Al plates: A synchrotron-based study

DOE PAGES

E, J. C.; Huang, J. Y.; Bie, B. X.; ...

2016-08-02

Here, explosion-welded Ti/Al plates are characterized with energy dispersive spectroscopy and x-ray computed tomography, and exhibit smooth, well-jointed, interface. We perform dynamic and quasi-static uniaxial tension experiments on Ti/Al with the loading direction either perpendicular or parallel to the Ti/Al interface, using a mini split Hopkinson tension bar and a material testing system in conjunction with time-resolved synchrotron x-ray imaging. X-ray imaging and strain-field mapping reveal different deformation mechanisms responsible for anisotropic bulk-scale responses, including yield strength, ductility and rate sensitivity. Deformation and fracture are achieved predominantly in Al layer for perpendicular loading, but both Ti and Al layers asmore » well as the interface play a role for parallel loading. The rate sensitivity of Ti/Al follows those of the constituent metals. For perpendicular loading, single deformation band develops in Al layer under quasi-static loading, while multiple deformation bands nucleate simultaneously under dynamic loading, leading to a higher dynamic fracture strain. For parallel loading, the interface impedes the growth of deformation and results in increased ductility of Ti/Al under quasi-static loading, while interface fracture occurs under dynamic loading due to the disparity in Poisson's contraction.« less

Performance of a parallel algebraic multilevel preconditioner for stabilized finite element semiconductor device modeling

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

Lin, Paul T.; Shadid, John N.; Sala, Marzio

In this study results are presented for the large-scale parallel performance of an algebraic multilevel preconditioner for solution of the drift-diffusion model for semiconductor devices. The preconditioner is the key numerical procedure determining the robustness, efficiency and scalability of the fully-coupled Newton-Krylov based, nonlinear solution method that is employed for this system of equations. The coupled system is comprised of a source term dominated Poisson equation for the electric potential, and two convection-diffusion-reaction type equations for the electron and hole concentration. The governing PDEs are discretized in space by a stabilized finite element method. Solution of the discrete system ismore » obtained through a fully-implicit time integrator, a fully-coupled Newton-based nonlinear solver, and a restarted GMRES Krylov linear system solver. The algebraic multilevel preconditioner is based on an aggressive coarsening graph partitioning of the nonzero block structure of the Jacobian matrix. Representative performance results are presented for various choices of multigrid V-cycles and W-cycles and parameter variations for smoothers based on incomplete factorizations. Parallel scalability results are presented for solution of up to 10{sup 8} unknowns on 4096 processors of a Cray XT3/4 and an IBM POWER eServer system.« less

Fast Face-Recognition Optical Parallel Correlator Using High Accuracy Correlation Filter

NASA Astrophysics Data System (ADS)

Watanabe, Eriko; Kodate, Kashiko

2005-11-01

We designed and fabricated a fully automatic fast face recognition optical parallel correlator [E. Watanabe and K. Kodate: Appl. Opt. 44 (2005) 5666] based on the VanderLugt principle. The implementation of an as-yet unattained ultra high-speed system was aided by reconfiguring the system to make it suitable for easier parallel processing, as well as by composing a higher accuracy correlation filter and high-speed ferroelectric liquid crystal-spatial light modulator (FLC-SLM). In running trial experiments using this system (dubbed FARCO), we succeeded in acquiring remarkably low error rates of 1.3% for false match rate (FMR) and 2.6% for false non-match rate (FNMR). Given the results of our experiments, the aim of this paper is to examine methods of designing correlation filters and arranging database image arrays for even faster parallel correlation, underlining the issues of calculation technique, quantization bit rate, pixel size and shift from optical axis. The correlation filter has proved its excellent performance and higher precision than classical correlation and joint transform correlator (JTC). Moreover, arrangement of multi-object reference images leads to 10-channel correlation signals, as sharply marked as those of a single channel. This experiment result demonstrates great potential for achieving the process speed of 10000 face/s.

Bit error rate tester using fast parallel generation of linear recurring sequences

DOEpatents

Pierson, Lyndon G.; Witzke, Edward L.; Maestas, Joseph H.

2003-05-06

A fast method for generating linear recurring sequences by parallel linear recurring sequence generators (LRSGs) with a feedback circuit optimized to balance minimum propagation delay against maximal sequence period. Parallel generation of linear recurring sequences requires decimating the sequence (creating small contiguous sections of the sequence in each LRSG). A companion matrix form is selected depending on whether the LFSR is right-shifting or left-shifting. The companion matrix is completed by selecting a primitive irreducible polynomial with 1's most closely grouped in a corner of the companion matrix. A decimation matrix is created by raising the companion matrix to the (n*k).sup.th power, where k is the number of parallel LRSGs and n is the number of bits to be generated at a time by each LRSG. Companion matrices with 1's closely grouped in a corner will yield sparse decimation matrices. A feedback circuit comprised of XOR logic gates implements the decimation matrix in hardware. Sparse decimation matrices can be implemented with minimum number of XOR gates, and therefore a minimum propagation delay through the feedback circuit. The LRSG of the invention is particularly well suited to use as a bit error rate tester on high speed communication lines because it permits the receiver to synchronize to the transmitted pattern within 2n bits.

Parallel Demand-Withdraw Processes in Family Therapy for Adolescent Drug Abuse

PubMed Central

Rynes, Kristina N.; Rohrbaugh, Michael J.; Lebensohn-Chialvo, Florencia; Shoham, Varda

2013-01-01

Isomorphism, or parallel process, occurs in family therapy when patterns of therapist-client interaction replicate problematic interaction patterns within the family. This study investigated parallel demand-withdraw processes in Brief Strategic Family Therapy (BSFT) for adolescent drug abuse, hypothesizing that therapist-demand/adolescent-withdraw interaction (TD/AW) cycles observed early in treatment would predict poor adolescent outcomes at follow-up for families who exhibited entrenched parent-demand/adolescent-withdraw interaction (PD/AW) before treatment began. Participants were 91 families who received at least 4 sessions of BSFT in a multi-site clinical trial on adolescent drug abuse (Robbins et al., 2011). Prior to receiving therapy, families completed videotaped family interaction tasks from which trained observers coded PD/AW. Another team of raters coded TD/AW during two early BSFT sessions. The main dependent variable was the number of drug use days that adolescents reported in Timeline Follow-Back interviews 7 to 12 months after family therapy began. Zero-inflated Poisson (ZIP) regression analyses supported the main hypothesis, showing that PD/AW and TD/AW interacted to predict adolescent drug use at follow-up. For adolescents in high PD/AW families, higher levels of TD/AW predicted significant increases in drug use at follow-up, whereas for low PD/AW families, TD/AW and follow-up drug use were unrelated. Results suggest that attending to parallel demand-withdraw processes in parent/adolescent and therapist/adolescent dyads may be useful in family therapy for substance-using adolescents. PMID:23438248

Anomaly Detection in Dynamic Networks

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

Turcotte, Melissa

2014-10-14

Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. Amore » second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behavior inherent in communication networks. This seasonal behavior is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the change points over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don’t fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the communication counts. In a sequential analysis, anomalous behavior is then identified from outlying behavior with respect to the fitted predictive probability models. Seasonality is again incorporated into the model and is treated as a changepoint model on the transition probabilities of a discrete time Markov process. Second stage analytics are then developed which combine anomalous edges to identify anomalous substructures in the network.« less

Efficient implementation of parallel three-dimensional FFT on clusters of PCs

NASA Astrophysics Data System (ADS)

Takahashi, Daisuke

2003-05-01

In this paper, we propose a high-performance parallel three-dimensional fast Fourier transform (FFT) algorithm on clusters of PCs. The three-dimensional FFT algorithm can be altered into a block three-dimensional FFT algorithm to reduce the number of cache misses. We show that the block three-dimensional FFT algorithm improves performance by utilizing the cache memory effectively. We use the block three-dimensional FFT algorithm to implement the parallel three-dimensional FFT algorithm. We succeeded in obtaining performance of over 1.3 GFLOPS on an 8-node dual Pentium III 1 GHz PC SMP cluster.

Method for resonant measurement

DOEpatents

Rhodes, G.W.; Migliori, A.; Dixon, R.D.

1996-03-05

A method of measurement of objects to determine object flaws, Poisson`s ratio ({sigma}) and shear modulus ({mu}) is shown and described. First, the frequency for expected degenerate responses is determined for one or more input frequencies and then splitting of degenerate resonant modes are observed to identify the presence of flaws in the object. Poisson`s ratio and the shear modulus can be determined by identification of resonances dependent only on the shear modulus, and then using that shear modulus to find Poisson`s ratio using other modes dependent on both the shear modulus and Poisson`s ratio. 1 fig.

A stochastical event-based continuous time step rainfall generator based on Poisson rectangular pulse and microcanonical random cascade models

NASA Astrophysics Data System (ADS)

Pohle, Ina; Niebisch, Michael; Zha, Tingting; Schümberg, Sabine; Müller, Hannes; Maurer, Thomas; Hinz, Christoph

2017-04-01

Rainfall variability within a storm is of major importance for fast hydrological processes, e.g. surface runoff, erosion and solute dissipation from surface soils. To investigate and simulate the impacts of within-storm variabilities on these processes, long time series of rainfall with high resolution are required. Yet, observed precipitation records of hourly or higher resolution are in most cases available only for a small number of stations and only for a few years. To obtain long time series of alternating rainfall events and interstorm periods while conserving the statistics of observed rainfall events, the Poisson model can be used. Multiplicative microcanonical random cascades have been widely applied to disaggregate rainfall time series from coarse to fine temporal resolution. We present a new coupling approach of the Poisson rectangular pulse model and the multiplicative microcanonical random cascade model that preserves the characteristics of rainfall events as well as inter-storm periods. In the first step, a Poisson rectangular pulse model is applied to generate discrete rainfall events (duration and mean intensity) and inter-storm periods (duration). The rainfall events are subsequently disaggregated to high-resolution time series (user-specified, e.g. 10 min resolution) by a multiplicative microcanonical random cascade model. One of the challenges of coupling these models is to parameterize the cascade model for the event durations generated by the Poisson model. In fact, the cascade model is best suited to downscale rainfall data with constant time step such as daily precipitation data. Without starting from a fixed time step duration (e.g. daily), the disaggregation of events requires some modifications of the multiplicative microcanonical random cascade model proposed by Olsson (1998): Firstly, the parameterization of the cascade model for events of different durations requires continuous functions for the probabilities of the multiplicative weights, which we implemented through sigmoid functions. Secondly, the branching of the first and last box is constrained to preserve the rainfall event durations generated by the Poisson rectangular pulse model. The event-based continuous time step rainfall generator has been developed and tested using 10 min and hourly rainfall data of four stations in North-Eastern Germany. The model performs well in comparison to observed rainfall in terms of event durations and mean event intensities as well as wet spell and dry spell durations. It is currently being tested using data from other stations across Germany and in different climate zones. Furthermore, the rainfall event generator is being applied in modelling approaches aimed at understanding the impact of rainfall variability on hydrological processes. Reference Olsson, J.: Evaluation of a scaling cascade model for temporal rainfall disaggregation, Hydrology and Earth System Sciences, 2, 19.30

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

Effects of imbalanced currents on large-format LiFePO4/graphite batteries systems connected in parallel

NASA Astrophysics Data System (ADS)

Shi, Wei; Hu, Xiaosong; Jin, Chao; Jiang, Jiuchun; Zhang, Yanru; Yip, Tony

2016-05-01

With the development and popularization of electric vehicles, it is urgent and necessary to develop effective management and diagnosis technology for battery systems. In this work, we design a parallel battery model, according to equivalent circuits of parallel voltage and branch current, to study effects of imbalanced currents on parallel large-format LiFePO4/graphite battery systems. Taking a 60 Ah LiFePO4/graphite battery system manufactured by ATL (Amperex Technology Limited, China) as an example, causes of imbalanced currents in the parallel connection are analyzed using our model, and the associated effect mechanisms on long-term stability of each single battery are examined. Theoretical and experimental results show that continuously increasing imbalanced currents during cycling are mainly responsible for the capacity fade of LiFePO4/graphite parallel batteries. It is thus a good way to avoid fast performance fade of parallel battery systems by suppressing variations of branch currents.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

PubMed

Procacci, Piero

2016-06-27

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

Transport Equations Resolution By N-BEE Anti-Dissipative Scheme In 2D Model Of Low Pressure Glow Discharge

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

Kraloua, B.; Hennad, A.

The aim of this paper is to determine electric and physical properties by 2D modelling of glow discharge low pressure in continuous regime maintained by term constant source. This electric discharge is confined in reactor plan-parallel geometry. This reactor is filled by Argon monatomic gas. Our continuum model the order two is composed the first three moments the Boltzmann's equations coupled with Poisson's equation by self consistent method. These transport equations are discretized by the finite volumes method. The equations system is resolved by a new technique, it is about the N-BEE explicit scheme using the time splitting method.

The effect of model uncertainty on some optimal routing problems

NASA Technical Reports Server (NTRS)

Mohanty, Bibhu; Cassandras, Christos G.

1991-01-01

The effect of model uncertainties on optimal routing in a system of parallel queues is examined. The uncertainty arises in modeling the service time distribution for the customers (jobs, packets) to be served. For a Poisson arrival process and Bernoulli routing, the optimal mean system delay generally depends on the variance of this distribution. However, as the input traffic load approaches the system capacity the optimal routing assignment and corresponding mean system delay are shown to converge to a variance-invariant point. The implications of these results are examined in the context of gradient-based routing algorithms. An example of a model-independent algorithm using online gradient estimation is also included.

Fast Poisson noise removal by biorthogonal Haar domain hypothesis testing

NASA Astrophysics Data System (ADS)

Zhang, B.; Fadili, M. J.; Starck, J.-L.; Digel, S. W.

2008-07-01

Methods based on hypothesis tests (HTs) in the Haar domain are widely used to denoise Poisson count data. Facing large datasets or real-time applications, Haar-based denoisers have to use the decimated transform to meet limited-memory or computation-time constraints. Unfortunately, for regular underlying intensities, decimation yields discontinuous estimates and strong “staircase” artifacts. In this paper, we propose to combine the HT framework with the decimated biorthogonal Haar (Bi-Haar) transform instead of the classical Haar. The Bi-Haar filter bank is normalized such that the p-values of Bi-Haar coefficients (p) provide good approximation to those of Haar (pH) for high-intensity settings or large scales; for low-intensity settings and small scales, we show that p are essentially upper-bounded by pH. Thus, we may apply the Haar-based HTs to Bi-Haar coefficients to control a prefixed false positive rate. By doing so, we benefit from the regular Bi-Haar filter bank to gain a smooth estimate while always maintaining a low computational complexity. A Fisher-approximation-based threshold implementing the HTs is also established. The efficiency of this method is illustrated on an example of hyperspectral-source-flux estimation.

An efficient parallel algorithm for matrix-vector multiplication

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

Hendrickson, B.; Leland, R.; Plimpton, S.

The multiplication of a vector by a matrix is the kernel computation of many algorithms in scientific computation. A fast parallel algorithm for this calculation is therefore necessary if one is to make full use of the new generation of parallel supercomputers. This paper presents a high performance, parallel matrix-vector multiplication algorithm that is particularly well suited to hypercube multiprocessors. For an n x n matrix on p processors, the communication cost of this algorithm is O(n/[radical]p + log(p)), independent of the matrix sparsity pattern. The performance of the algorithm is demonstrated by employing it as the kernel in themore » well-known NAS conjugate gradient benchmark, where a run time of 6.09 seconds was observed. This is the best published performance on this benchmark achieved to date using a massively parallel supercomputer.« less

A sequential vesicle pool model with a single release sensor and a Ca(2+)-dependent priming catalyst effectively explains Ca(2+)-dependent properties of neurosecretion.

PubMed

Walter, Alexander M; Pinheiro, Paulo S; Verhage, Matthijs; Sørensen, Jakob B

2013-01-01

Neurotransmitter release depends on the fusion of secretory vesicles with the plasma membrane and the release of their contents. The final fusion step displays higher-order Ca(2+) dependence, but also upstream steps depend on Ca(2+). After deletion of the Ca(2+) sensor for fast release - synaptotagmin-1 - slower Ca(2+)-dependent release components persist. These findings have provoked working models involving parallel releasable vesicle pools (Parallel Pool Models, PPM) driven by alternative Ca(2+) sensors for release, but no slow release sensor acting on a parallel vesicle pool has been identified. We here propose a Sequential Pool Model (SPM), assuming a novel Ca(2+)-dependent action: a Ca(2+)-dependent catalyst that accelerates both forward and reverse priming reactions. While both models account for fast fusion from the Readily-Releasable Pool (RRP) under control of synaptotagmin-1, the origins of slow release differ. In the SPM the slow release component is attributed to the Ca(2+)-dependent refilling of the RRP from a Non-Releasable upstream Pool (NRP), whereas the PPM attributes slow release to a separate slowly-releasable vesicle pool. Using numerical integration we compared model predictions to data from mouse chromaffin cells. Like the PPM, the SPM explains biphasic release, Ca(2+)-dependence and pool sizes in mouse chromaffin cells. In addition, the SPM accounts for the rapid recovery of the fast component after strong stimulation, where the PPM fails. The SPM also predicts the simultaneous changes in release rate and amplitude seen when mutating the SNARE-complex. Finally, it can account for the loss of fast- and the persistence of slow release in the synaptotagmin-1 knockout by assuming that the RRP is depleted, leading to slow and Ca(2+)-dependent fusion from the NRP. We conclude that the elusive 'alternative Ca(2+) sensor' for slow release might be the upstream priming catalyst, and that a sequential model effectively explains Ca(2+)-dependent properties of secretion without assuming parallel pools or sensors.

A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca2+-Dependent Priming Catalyst Effectively Explains Ca2+-Dependent Properties of Neurosecretion

PubMed Central

Walter, Alexander M.; Pinheiro, Paulo S.; Verhage, Matthijs; Sørensen, Jakob B.

2013-01-01

Neurotransmitter release depends on the fusion of secretory vesicles with the plasma membrane and the release of their contents. The final fusion step displays higher-order Ca2+ dependence, but also upstream steps depend on Ca2+. After deletion of the Ca2+ sensor for fast release – synaptotagmin-1 – slower Ca2+-dependent release components persist. These findings have provoked working models involving parallel releasable vesicle pools (Parallel Pool Models, PPM) driven by alternative Ca2+ sensors for release, but no slow release sensor acting on a parallel vesicle pool has been identified. We here propose a Sequential Pool Model (SPM), assuming a novel Ca2+-dependent action: a Ca2+-dependent catalyst that accelerates both forward and reverse priming reactions. While both models account for fast fusion from the Readily-Releasable Pool (RRP) under control of synaptotagmin-1, the origins of slow release differ. In the SPM the slow release component is attributed to the Ca2+-dependent refilling of the RRP from a Non-Releasable upstream Pool (NRP), whereas the PPM attributes slow release to a separate slowly-releasable vesicle pool. Using numerical integration we compared model predictions to data from mouse chromaffin cells. Like the PPM, the SPM explains biphasic release, Ca2+-dependence and pool sizes in mouse chromaffin cells. In addition, the SPM accounts for the rapid recovery of the fast component after strong stimulation, where the PPM fails. The SPM also predicts the simultaneous changes in release rate and amplitude seen when mutating the SNARE-complex. Finally, it can account for the loss of fast- and the persistence of slow release in the synaptotagmin-1 knockout by assuming that the RRP is depleted, leading to slow and Ca2+-dependent fusion from the NRP. We conclude that the elusive ‘alternative Ca2+ sensor’ for slow release might be the upstream priming catalyst, and that a sequential model effectively explains Ca2+-dependent properties of secretion without assuming parallel pools or sensors. PMID:24339761

Properties of the Bivariate Delayed Poisson Process

DTIC Science & Technology

1974-07-01

and Lewis (1972) in their Berkeley Symposium paper and here their analysis of the bivariate Poisson processes (without Poisson noise) is carried... Poisson processes . They cannot, however, be independent Poisson processes because their events are associated in pairs by the displace- ment centres...process because its marginal processes for events of each type are themselves (univariate) Poisson processes . Cox and Lewis (1972) assumed a

Development of fast parallel multi-technique scanning X-ray imaging at Synchrotron Soleil

NASA Astrophysics Data System (ADS)

Medjoubi, K.; Leclercq, N.; Langlois, F.; Buteau, A.; Lé, S.; Poirier, S.; Mercère, P.; Kewish, C. M.; Somogyi, A.

2013-10-01

A fast multimodal scanning X-ray imaging scheme is prototyped at Soleil Synchrotron. It permits the simultaneous acquisition of complementary information on the sample structure, composition and chemistry by measuring transmission, differential phase contrast, small-angle scattering, and X-ray fluorescence by dedicated detectors with ms dwell time per pixel. The results of the proof of principle experiments are presented in this paper.

Quantum gas in the fast forward scheme of adiabatically expanding cavities: Force and equation of state

NASA Astrophysics Data System (ADS)

Babajanova, Gulmira; Matrasulov, Jasur; Nakamura, Katsuhiro

2018-04-01

With use of the scheme of fast forward which realizes quasistatic or adiabatic dynamics in shortened timescale, we investigate a thermally isolated ideal quantum gas confined in a rapidly dilating one-dimensional (1D) cavity with the time-dependent size L =L (t ) . In the fast-forward variants of equation of states, i.e., Bernoulli's formula and Poisson's adiabatic equation, the force or 1D analog of pressure can be expressed as a function of the velocity (L ˙) and acceleration (L ̈) of L besides rapidly changing state variables like effective temperature (T ) and L itself. The force is now a sum of nonadiabatic (NAD) and adiabatic contributions with the former caused by particles moving synchronously with kinetics of L and the latter by ideal bulk particles insensitive to such a kinetics. The ratio of NAD and adiabatic contributions does not depend on the particle number (N ) in the case of the soft-wall confinement, whereas such a ratio is controllable in the case of hard-wall confinement. We also reveal the condition when the NAD contribution overwhelms the adiabatic one and thoroughly changes the standard form of the equilibrium equation of states.

Operator induced multigrid algorithms using semirefinement

NASA Technical Reports Server (NTRS)

Decker, Naomi; Vanrosendale, John

1989-01-01

A variant of multigrid, based on zebra relaxation, and a new family of restriction/prolongation operators is described. Using zebra relaxation in combination with an operator-induced prolongation leads to fast convergence, since the coarse grid can correct all error components. The resulting algorithms are not only fast, but are also robust, in the sense that the convergence rate is insensitive to the mesh aspect ratio. This is true even though line relaxation is performed in only one direction. Multigrid becomes a direct method if an operator-induced prolongation is used, together with the induced coarse grid operators. Unfortunately, this approach leads to stencils which double in size on each coarser grid. The use of an implicit three point restriction can be used to factor these large stencils, in order to retain the usual five or nine point stencils, while still achieving fast convergence. This algorithm achieves a V-cycle convergence rate of 0.03 on Poisson's equation, using 1.5 zebra sweeps per level, while the convergence rate improves to 0.003 if optimal nine point stencils are used. Numerical results for two and three dimensional model problems are presented, together with a two level analysis explaining these results.

Fast MPEG-CDVS Encoder With GPU-CPU Hybrid Computing.

PubMed

Duan, Ling-Yu; Sun, Wei; Zhang, Xinfeng; Wang, Shiqi; Chen, Jie; Yin, Jianxiong; See, Simon; Huang, Tiejun; Kot, Alex C; Gao, Wen

2018-05-01

The compact descriptors for visual search (CDVS) standard from ISO/IEC moving pictures experts group has succeeded in enabling the interoperability for efficient and effective image retrieval by standardizing the bitstream syntax of compact feature descriptors. However, the intensive computation of a CDVS encoder unfortunately hinders its widely deployment in industry for large-scale visual search. In this paper, we revisit the merits of low complexity design of CDVS core techniques and present a very fast CDVS encoder by leveraging the massive parallel execution resources of graphics processing unit (GPU). We elegantly shift the computation-intensive and parallel-friendly modules to the state-of-the-arts GPU platforms, in which the thread block allocation as well as the memory access mechanism are jointly optimized to eliminate performance loss. In addition, those operations with heavy data dependence are allocated to CPU for resolving the extra but non-necessary computation burden for GPU. Furthermore, we have demonstrated the proposed fast CDVS encoder can work well with those convolution neural network approaches which enables to leverage the advantages of GPU platforms harmoniously, and yield significant performance improvements. Comprehensive experimental results over benchmarks are evaluated, which has shown that the fast CDVS encoder using GPU-CPU hybrid computing is promising for scalable visual search.

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics.

PubMed

Kelly, Benjamin J; Fitch, James R; Hu, Yangqiu; Corsmeier, Donald J; Zhong, Huachun; Wetzel, Amy N; Nordquist, Russell D; Newsom, David L; White, Peter

2015-01-20

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

Parallel processing in a host plus multiple array processor system for radar

NASA Technical Reports Server (NTRS)

Barkan, B. Z.

1983-01-01

Host plus multiple array processor architecture is demonstrated to yield a modular, fast, and cost-effective system for radar processing. Software methodology for programming such a system is developed. Parallel processing with pipelined data flow among the host, array processors, and discs is implemented. Theoretical analysis of performance is made and experimentally verified. The broad class of problems to which the architecture and methodology can be applied is indicated.

Fast Whole-Engine Stirling Analysis

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

2006-01-01

This presentation discusses the simulation approach to whole-engine for physical consistency, REV regenerator modeling, grid layering for smoothness, and quality, conjugate heat transfer method adjustment, high-speed low cost parallel cluster, and debugging.

Shot noise enhancement from non-equilibrium plasmons in Luttinger liquid junctions.

PubMed

Kim, Jaeuk U; Kinaret, Jari M; Choi, Mahn-Soo

2005-06-29

We consider a quantum wire double junction system with each wire segment described by a spinless Luttinger model, and study theoretically shot noise in this system in the sequential tunnelling regime. We find that the non-equilibrium plasmonic excitations in the central wire segment give rise to qualitatively different behaviour compared to the case with equilibrium plasmons. In particular, shot noise is greatly enhanced by them, and exceeds the Poisson limit. We show that the enhancement can be explained by the emergence of several current-carrying processes, and that the effect disappears if the channels effectively collapse to one because of fast plasmon relaxation processes, for example.

Simulations of Coulomb systems confined by polarizable surfaces using periodic Green functions.

PubMed

Dos Santos, Alexandre P; Girotto, Matheus; Levin, Yan

2017-11-14

We present an efficient approach for simulating Coulomb systems confined by planar polarizable surfaces. The method is based on the solution of the Poisson equation using periodic Green functions. It is shown that the electrostatic energy arising from the surface polarization can be decoupled from the energy due to the direct Coulomb interaction between the ions. This allows us to combine an efficient Ewald summation method, or any other fast method for summing over the replicas, with the polarization contribution calculated using Green function techniques. We apply the method to calculate density profiles of ions confined between the charged dielectric and metal surfaces.

Shot noise enhancement from non-equilibrium plasmons in Luttinger liquid junctions

NASA Astrophysics Data System (ADS)

Kim, Jaeuk U.; Kinaret, Jari M.; Choi, Mahn-Soo

2005-06-01

We consider a quantum wire double junction system with each wire segment described by a spinless Luttinger model, and study theoretically shot noise in this system in the sequential tunnelling regime. We find that the non-equilibrium plasmonic excitations in the central wire segment give rise to qualitatively different behaviour compared to the case with equilibrium plasmons. In particular, shot noise is greatly enhanced by them, and exceeds the Poisson limit. We show that the enhancement can be explained by the emergence of several current-carrying processes, and that the effect disappears if the channels effectively collapse to one because of fast plasmon relaxation processes, for example.

Parallel Cartesian grid refinement for 3D complex flow simulations

NASA Astrophysics Data System (ADS)

Angelidis, Dionysios; Sotiropoulos, Fotis

2013-11-01

A second order accurate method for discretizing the Navier-Stokes equations on 3D unstructured Cartesian grids is presented. Although the grid generator is based on the oct-tree hierarchical method, fully unstructured data-structure is adopted enabling robust calculations for incompressible flows, avoiding both the need of synchronization of the solution between different levels of refinement and usage of prolongation/restriction operators. The current solver implements a hybrid staggered/non-staggered grid layout, employing the implicit fractional step method to satisfy the continuity equation. The pressure-Poisson equation is discretized by using a novel second order fully implicit scheme for unstructured Cartesian grids and solved using an efficient Krylov subspace solver. The momentum equation is also discretized with second order accuracy and the high performance Newton-Krylov method is used for integrating them in time. Neumann and Dirichlet conditions are used to validate the Poisson solver against analytical functions and grid refinement results to a significant reduction of the solution error. The effectiveness of the fractional step method results in the stability of the overall algorithm and enables the performance of accurate multi-resolution real life simulations. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482.

Anisotropic Behaviour of Magnetic Power Spectra in Solar Wind Turbulence.

NASA Astrophysics Data System (ADS)

Banerjee, S.; Saur, J.; Gerick, F.; von Papen, M.

2017-12-01

Introduction:High altitude fast solar wind turbulence (SWT) shows different spectral properties as a function of the angle between the flow direction and the scale dependent mean magnetic field (Horbury et al., PRL, 2008). The average magnetic power contained in the near perpendicular direction (80º-90º) was found to be approximately 5 times larger than the average power in the parallel direction (0º- 10º). In addition, the parallel power spectra was found to give a steeper (-2) power law than the perpendicular power spectral density (PSD) which followed a near Kolmogorov slope (-5/3). Similar anisotropic behaviour has also been observed (Chen et al., MNRAS, 2011) for slow solar wind (SSW), but using a different method exploiting multi-spacecraft data of Cluster. Purpose:In the current study, using Ulysses data, we investigate (i) the anisotropic behaviour of near ecliptic slow solar wind using the same methodology (described below) as that of Horbury et al. (2008) and (ii) the dependence of the anisotropic behaviour of SWT as a function of the heliospheric latitude.Method:We apply the wavelet method to calculate the turbulent power spectra of the magnetic field fluctuations parallel and perpendicular to the local mean magnetic field (LMF). According to Horbury et al., LMF for a given scale (or size) is obtained using an envelope of the envelope of that size. Results:(i) SSW intervals always show near -5/3 perpendicular spectra. Unlike the fast solar wind (FSW) intervals, for SSW, we often find intervals where power parallel to the mean field is not observed. For a few intervals with sufficient power in parallel direction, slow wind turbulence also exhibit -2 parallel spectra similar to FSW.(ii) The behaviours of parallel and perpendicular power spectra are found to be independent of the heliospheric latitude. Conclusion:In the current study we do not find significant influence of the heliospheric latitude on the spectral slopes of parallel and perpendicular magnetic spectra. This indicates that the spectral anisotropy in parallel and perpendicular direction is governed by intrinsic properties of SWT.

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.

A Parallel Fast Sweeping Method for the Eikonal Equation

NASA Astrophysics Data System (ADS)

Baker, B.

2017-12-01

Recently, there has been an exciting emergence of probabilistic methods for travel time tomography. Unlike gradient-based optimization strategies, probabilistic tomographic methods are resistant to becoming trapped in a local minimum and provide a much better quantification of parameter resolution than, say, appealing to ray density or performing checkerboard reconstruction tests. The benefits associated with random sampling methods however are only realized by successive computation of predicted travel times in, potentially, strongly heterogeneous media. To this end this abstract is concerned with expediting the solution of the Eikonal equation. While many Eikonal solvers use a fast marching method, the proposed solver will use the iterative fast sweeping method because the eight fixed sweep orderings in each iteration are natural targets for parallelization. To reduce the number of iterations and grid points required the high-accuracy finite difference stencil of Nobel et al., 2014 is implemented. A directed acyclic graph (DAG) is created with a priori knowledge of the sweep ordering and finite different stencil. By performing a topological sort of the DAG sets of independent nodes are identified as candidates for concurrent updating. Additionally, the proposed solver will also address scalability during earthquake relocation, a necessary step in local and regional earthquake tomography and a barrier to extending probabilistic methods from active source to passive source applications, by introducing an asynchronous parallel forward solve phase for all receivers in the network. Synthetic examples using the SEG over-thrust model will be presented.

A semi-implicit augmented IIM for Navier–Stokes equations with open, traction, or free boundary conditions

PubMed Central

Li, Zhilin; Xiao, Li; Cai, Qin; Zhao, Hongkai; Luo, Ray

2016-01-01

In this paper, a new Navier–Stokes solver based on a finite difference approximation is proposed to solve incompressible flows on irregular domains with open, traction, and free boundary conditions, which can be applied to simulations of fluid structure interaction, implicit solvent model for biomolecular applications and other free boundary or interface problems. For some problems of this type, the projection method and the augmented immersed interface method (IIM) do not work well or does not work at all. The proposed new Navier–Stokes solver is based on the local pressure boundary method, and a semi-implicit augmented IIM. A fast Poisson solver can be used in our algorithm which gives us the potential for developing fast overall solvers in the future. The time discretization is based on a second order multi-step method. Numerical tests with exact solutions are presented to validate the accuracy of the method. Application to fluid structure interaction between an incompressible fluid and a compressible gas bubble is also presented. PMID:27087702

A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions.

PubMed

Li, Zhilin; Xiao, Li; Cai, Qin; Zhao, Hongkai; Luo, Ray

2015-08-15

In this paper, a new Navier-Stokes solver based on a finite difference approximation is proposed to solve incompressible flows on irregular domains with open, traction, and free boundary conditions, which can be applied to simulations of fluid structure interaction, implicit solvent model for biomolecular applications and other free boundary or interface problems. For some problems of this type, the projection method and the augmented immersed interface method (IIM) do not work well or does not work at all. The proposed new Navier-Stokes solver is based on the local pressure boundary method, and a semi-implicit augmented IIM. A fast Poisson solver can be used in our algorithm which gives us the potential for developing fast overall solvers in the future. The time discretization is based on a second order multi-step method. Numerical tests with exact solutions are presented to validate the accuracy of the method. Application to fluid structure interaction between an incompressible fluid and a compressible gas bubble is also presented.

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

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

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmermore » hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.« less

Biomechanical Comparison of Parallel and Crossed Suture Repair for Longitudinal Meniscus Tears.

PubMed

Milchteim, Charles; Branch, Eric A; Maughon, Ty; Hughey, Jay; Anz, Adam W

2016-04-01

Longitudinal meniscus tears are commonly encountered in clinical practice. Meniscus repair devices have been previously tested and presented; however, prior studies have not evaluated repair construct designs head to head. This study compared a new-generation meniscus repair device, SpeedCinch, with a similar established device, Fast-Fix 360, and a parallel repair construct to a crossed construct. Both devices utilize self-adjusting No. 2-0 ultra-high molecular weight polyethylene (UHMWPE) and 2 polyether ether ketone (PEEK) anchors. Crossed suture repair constructs have higher failure loads and stiffness compared with simple parallel constructs. The newer repair device would exhibit similar performance to an established device. Controlled laboratory study. Sutures were placed in an open fashion into the body and posterior horn regions of the medial and lateral menisci in 16 cadaveric knees. Evaluation of 2 repair devices and 2 repair constructs created 4 groups: 2 parallel vertical sutures created with the Fast-Fix 360 (2PFF), 2 crossed vertical sutures created with the Fast-Fix 360 (2XFF), 2 parallel vertical sutures created with the SpeedCinch (2PSC), and 2 crossed vertical sutures created with the SpeedCinch (2XSC). After open placement of the repair construct, each meniscus was explanted and tested to failure on a uniaxial material testing machine. All data were checked for normality of distribution, and 1-way analysis of variance by ranks was chosen to evaluate for statistical significance of maximum failure load and stiffness between groups. Statistical significance was defined as P < .05. The mean maximum failure loads ± 95% CI (range) were 89.6 ± 16.3 N (125.7-47.8 N) (2PFF), 72.1 ± 11.7 N (103.4-47.6 N) (2XFF), 71.9 ± 15.5 N (109.4-41.3 N) (2PSC), and 79.5 ± 25.4 N (119.1-30.9 N) (2XSC). Interconstruct comparison revealed no statistical difference between all 4 constructs regarding maximum failure loads (P = .49). Stiffness values were also similar, with no statistical difference on comparison (P = .28). Both devices in the current study had similar failure load and stiffness when 2 vertical or 2 crossed sutures were tested in cadaveric human menisci. Simple parallel vertical sutures perform similarly to crossed suture patterns at the time of implantation.

Simultaneous multigrid techniques for nonlinear eigenvalue problems: Solutions of the nonlinear Schrödinger-Poisson eigenvalue problem in two and three dimensions

NASA Astrophysics Data System (ADS)

Costiner, Sorin; Ta'asan, Shlomo

1995-07-01

Algorithms for nonlinear eigenvalue problems (EP's) often require solving self-consistently a large number of EP's. Convergence difficulties may occur if the solution is not sought in an appropriate region, if global constraints have to be satisfied, or if close or equal eigenvalues are present. Multigrid (MG) algorithms for nonlinear problems and for EP's obtained from discretizations of partial differential EP have often been shown to be more efficient than single level algorithms. This paper presents MG techniques and a MG algorithm for nonlinear Schrödinger Poisson EP's. The algorithm overcomes the above mentioned difficulties combining the following techniques: a MG simultaneous treatment of the eigenvectors and nonlinearity, and with the global constrains; MG stable subspace continuation techniques for the treatment of nonlinearity; and a MG projection coupled with backrotations for separation of solutions. These techniques keep the solutions in an appropriate region, where the algorithm converges fast, and reduce the large number of self-consistent iterations to only a few or one MG simultaneous iteration. The MG projection makes it possible to efficiently overcome difficulties related to clusters of close and equal eigenvalues. Computational examples for the nonlinear Schrödinger-Poisson EP in two and three dimensions, presenting special computational difficulties that are due to the nonlinearity and to the equal and closely clustered eigenvalues are demonstrated. For these cases, the algorithm requires O(qN) operations for the calculation of q eigenvectors of size N and for the corresponding eigenvalues. One MG simultaneous cycle per fine level was performed. The total computational cost is equivalent to only a few Gauss-Seidel relaxations per eigenvector. An asymptotic convergence rate of 0.15 per MG cycle is attained.

Simulation methods with extended stability for stiff biochemical Kinetics.

PubMed

Rué, Pau; Villà-Freixa, Jordi; Burrage, Kevin

2010-08-11

With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, tau, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where tau can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called tau-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as tau grows. In this paper we extend Poisson tau-leap methods to a general class of Runge-Kutta (RK) tau-leap methods. We show that with the proper selection of the coefficients, the variance of the extended tau-leap can be well-behaved, leading to significantly larger step sizes. The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original tau-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.

An embedded multi-core parallel model for real-time stereo imaging

NASA Astrophysics Data System (ADS)

He, Wenjing; Hu, Jian; Niu, Jingyu; Li, Chuanrong; Liu, Guangyu

2018-04-01

The real-time processing based on embedded system will enhance the application capability of stereo imaging for LiDAR and hyperspectral sensor. The task partitioning and scheduling strategies for embedded multiprocessor system starts relatively late, compared with that for PC computer. In this paper, aimed at embedded multi-core processing platform, a parallel model for stereo imaging is studied and verified. After analyzing the computing amount, throughout capacity and buffering requirements, a two-stage pipeline parallel model based on message transmission is established. This model can be applied to fast stereo imaging for airborne sensors with various characteristics. To demonstrate the feasibility and effectiveness of the parallel model, a parallel software was designed using test flight data, based on the 8-core DSP processor TMS320C6678. The results indicate that the design performed well in workload distribution and had a speed-up ratio up to 6.4.

Fractional Poisson Fields and Martingales

NASA Astrophysics Data System (ADS)

Aletti, Giacomo; Leonenko, Nikolai; Merzbach, Ely

2018-02-01

We present new properties for the Fractional Poisson process (FPP) and the Fractional Poisson field on the plane. A martingale characterization for FPPs is given. We extend this result to Fractional Poisson fields, obtaining some other characterizations. The fractional differential equations are studied. We consider a more general Mixed-Fractional Poisson process and show that this process is the stochastic solution of a system of fractional differential-difference equations. Finally, we give some simulations of the Fractional Poisson field on the plane.

On a Poisson homogeneous space of bilinear forms with a Poisson-Lie action

NASA Astrophysics Data System (ADS)

Chekhov, L. O.; Mazzocco, M.

2017-12-01

Let \\mathscr A be the space of bilinear forms on C^N with defining matrices A endowed with a quadratic Poisson structure of reflection equation type. The paper begins with a short description of previous studies of the structure, and then this structure is extended to systems of bilinear forms whose dynamics is governed by the natural action A\\mapsto B ABT} of the {GL}_N Poisson-Lie group on \\mathscr A. A classification is given of all possible quadratic brackets on (B, A)\\in {GL}_N× \\mathscr A preserving the Poisson property of the action, thus endowing \\mathscr A with the structure of a Poisson homogeneous space. Besides the product Poisson structure on {GL}_N× \\mathscr A, there are two other (mutually dual) structures, which (unlike the product Poisson structure) admit reductions by the Dirac procedure to a space of bilinear forms with block upper triangular defining matrices. Further generalisations of this construction are considered, to triples (B,C, A)\\in {GL}_N× {GL}_N× \\mathscr A with the Poisson action A\\mapsto B ACT}, and it is shown that \\mathscr A then acquires the structure of a Poisson symmetric space. Generalisations to chains of transformations and to the quantum and quantum affine algebras are investigated, as well as the relations between constructions of Poisson symmetric spaces and the Poisson groupoid. Bibliography: 30 titles.

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.

PubMed

Maruyama, Yutaka; Yoshida, Norio; Tadano, Hiroto; Takahashi, Daisuke; Sato, Mitsuhisa; Hirata, Fumio

2014-07-05

A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems. Copyright © 2014 Wiley Periodicals, Inc.

Plasma Physics Calculations on a Parallel Macintosh Cluster

NASA Astrophysics Data System (ADS)

Decyk, Viktor; Dauger, Dean; Kokelaar, Pieter

2000-03-01

We have constructed a parallel cluster consisting of 16 Apple Macintosh G3 computers running the MacOS, and achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. A subset of the MPI message-passing library was implemented in Fortran77 and C. This library enabled us to port code, without modification, from other parallel processors to the Macintosh cluster. For large problems where message packets are large and relatively few in number, performance of 50-150 MFlops/node is possible, depending on the problem. This is fast enough that 3D calculations can be routinely done. Unlike Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. Full details are available on our web site: http://exodus.physics.ucla.edu/appleseed/.

Plasma Physics Calculations on a Parallel Macintosh Cluster

NASA Astrophysics Data System (ADS)

Decyk, Viktor K.; Dauger, Dean E.; Kokelaar, Pieter R.

We have constructed a parallel cluster consisting of 16 Apple Macintosh G3 computers running the MacOS, and achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. A subset of the MPI message-passing library was implemented in Fortran77 and C. This library enabled us to port code, without modification, from other parallel processors to the Macintosh cluster. For large problems where message packets are large and relatively few in number, performance of 50-150 Mflops/node is possible, depending on the problem. This is fast enough that 3D calculations can be routinely done. Unlike Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. Full details are available on our web site: http://exodus.physics.ucla.edu/appleseed/.

On the Singularity of the Vlasov-Poisson System

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

and Hong Qin, Jian Zheng

2013-04-26

The Vlasov-Poisson system can be viewed as the collisionless limit of the corresponding Fokker- Planck-Poisson system. It is reasonable to expect that the result of Landau damping can also be obtained from the Fokker-Planck-Poisson system when the collision frequency v approaches zero. However, we show that the colllisionless Vlasov-Poisson system is a singular limit of the collisional Fokker-Planck-Poisson system, and Landau's result can be recovered only as the approaching zero from the positive side.

On the singularity of the Vlasov-Poisson system

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

Zheng, Jian; Qin, Hong; Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08550

2013-09-15

The Vlasov-Poisson system can be viewed as the collisionless limit of the corresponding Fokker-Planck-Poisson system. It is reasonable to expect that the result of Landau damping can also be obtained from the Fokker-Planck-Poisson system when the collision frequency ν approaches zero. However, we show that the collisionless Vlasov-Poisson system is a singular limit of the collisional Fokker-Planck-Poisson system, and Landau's result can be recovered only as the ν approaches zero from the positive side.

Fasting triglycerides as a predictor of incident diabetes, insulin resistance and β-cell function in a Canadian First Nation.

PubMed

Riediger, Natalie D; Clark, Kirsten; Lukianchuk, Virginia; Roulette, Joanne; Bruce, Sharon

2017-01-01

Diabetes prevalence is substantially higher among Canadian First Nations populations than the non-First Nation population. Fasting serum triglycerides have been found to be an important predictor of incident diabetes among non-indigenous populations. However, there is a great need to understand diabetes progression within specific ethnic groups, particularly First Nations populations. The purpose of this study was to test for an association between fasting serum triglycerides and incident diabetes, changes in insulin resistance and changes in β-cell function in a Manitoba First Nation cohort. Study data were from two diabetes screening studies in Sandy Bay First Nation in Manitoba, Canada, collected in 2002/2003 and 2011/2012. The cohort was composed of respondents to both screening studies (n=171). Fasting blood samples and anthropometric, health and demographic data were collected. A generalised linear model with Poisson distribution was used to test for an association between fasting triglycerides and incident diabetes. There were 35 incident cases of diabetes among 128 persons without diabetes at baseline. Participants who developed incident type 2 diabetes were significantly older and had significantly higher body mass index (BMI; p=0.012), total cholesterol (p=0.007), fasting triglycerides (p<0.001), and Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) (p<0.001). Fasting triglyceride level was found to be a statistically significant positive predictor of incident diabetes independent of age, sex and waist circumference at baseline. Participants with triglycerides in the highest tertile (≥2.11 mmol/l) had a 4.0-times higher risk of developing incident diabetes compared to those in the lowest tertile (p=0.03). Notably, neither waist circumference nor BMI were significant predictors of incident diabetes independent of age, sex and triglycerides. Fasting triglycerides may be useful as a clinical predictor of insulin resistance and diabetes development among First Nations populations. Unlike other ethnic groups, BMI and waist circumference may be less important factors in diabetes development.

Portion sizes and obesity: responses of fast-food companies.

PubMed

Young, Lisa R; Nestle, Marion

2007-07-01

Because the sizes of food portions, especially of fast food, have increased in parallel with rising rates of overweight, health authorities have called on fast-food chains to decrease the sizes of menu items. From 2002 to 2006, we examined responses of fast-food chains to such calls by determining the current sizes of sodas, French fries, and hamburgers at three leading chains and comparing them to sizes observed in 1998 and 2002. Although McDonald's recently phased out its largest offerings, current items are similar to 1998 sizes and greatly exceed those offered when the company opened in 1955. Burger King and Wendy's have increased portion sizes, even while health authorities are calling for portion size reductions. Fast-food portions in the United States are larger than in Europe. These observations suggest that voluntary efforts by fast-food companies to reduce portion sizes are unlikely to be effective, and that policy approaches are needed to reduce energy intake from fast food.

Fast word reading in pure alexia: "fast, yet serial".

PubMed

Bormann, Tobias; Wolfer, Sascha; Hachmann, Wibke; Neubauer, Claudia; Konieczny, Lars

2015-01-01

Pure alexia is a severe impairment of word reading in which individuals process letters serially with a pronounced length effect. Yet, there is considerable variation in the performance of alexic readers with generally very slow, but also occasionally fast responses, an observation addressed rarely in previous reports. It has been suggested that "fast" responses in pure alexia reflect residual parallel letter processing or that they may even be subserved by an independent reading system. Four experiments assessed fast and slow reading in a participant (DN) with pure alexia. Two behavioral experiments investigated frequency, neighborhood, and length effects in forced fast reading. Two further experiments measured eye movements when DN was forced to read quickly, or could respond faster because words were easier to process. Taken together, there was little support for the proposal that "qualitatively different" mechanisms or reading strategies underlie both types of responses in DN. Instead, fast responses are argued to be generated by the same serial-reading strategy.

Upper Mantle Responses to India-Eurasia Collision in Indochina, Malaysia, and the South China Sea

NASA Astrophysics Data System (ADS)

Hongsresawat, S.; Russo, R. M.

2016-12-01

We present new shear wave splitting and splitting intensity measurements from SK(K)S phases recorded at seismic stations of the Malaysian National Seismic Network. These results, in conjunction with results from Tibet and Yunnan provide a basis for testing the degree to which Indochina and South China Sea upper mantle fabrics are responses to India-Eurasia collision. Upper mantle fabrics derived from shear wave splitting measurements in Yunnan and eastern Tibet parallel geodetic surface motions north of 26°N, requiring transmission of tractions from upper mantle depths to surface, or consistent deformation boundary conditions throughout the upper 200 km of crust and mantle. Shear wave splitting fast trends and surface velocities diverge in eastern Yunnan and south of 26°N, indicating development of an asthenospheric layer that decouples crust and upper mantle, or corner flow above the subducted Indo-Burma slab. E-W fast shear wave splitting trends southwest of 26°N/104°E indicate strong gradients in any asthenospheric infiltration. Possible upper mantle flow regimes beneath Indochina include development of olivine b-axis anisotropic symmetry due to high strain and hydrous conditions in the syntaxis/Indo-Burma mantle wedge (i.e., southward flow), development of strong upper mantle corner flow in the Indo-Burma wedge with olivine a-axis anisotropic symmetry (i.e., westward flow), and simple asthenospheric flow due to eastward motion of Sundaland shearing underlying asthenosphere. Further south, shear-wave splitting delay times at Malaysian stations vary from 0.5 seconds on the Malay Peninsula to over 2 seconds at stations on Borneo. Splitting fast trends at Borneo stations and Singapore trend NE-SW, but in northern Peninsular Malaysia, the splitting fast polarization direction is NW-SE, parallel to the trend of the Peninsula. Thus, there is a sharp transition from low delay time and NW-SE fast polarization to high delay times and fast polarization directions that parallel the strike of the now-inoperative spreading center in the South China Sea. This transition appears to occur in the central portion of Peninsular Malaysia and may mark the boundary between Tethyan upper mantle extruded from the India-Asia collision zone and supra-subduction upper mantle of the Indonesian arc.

Influence of obliquely subducting slab on Pacific-North America shear motion inferred from seismic anisotropy along the Queen Charlotte margin

NASA Astrophysics Data System (ADS)

Cao, L.; Kao, H.; Wang, K.; Wang, Z.

2016-12-01

Haida Gwaii is located along the transpressive Queen Charlotte margin between the Pacific (PA) and North America (NA) plates. The highly oblique relative plate motion is partitioned, with the strike-slip component accommodated by the Queen Charlotte Fault (QCF) and the convergent component by a thrust fault offshore. To understand how the presence of a obliquely subducting slab influences shear deformation of the plate boundary, we investigate mantle anisotropy by analyzing shear-wave splitting of teleseismic SKS phases recorded at 17 seismic stations in and around Haida Gwaii. We used the MFAST program to determine the polarization direction of the fast wave (φ) and the delay time (δt) between the fast and slow phases. The fast directions derived from stations on Haida Gwaii and two stations to the north on the Alaska Panhandle are predominantly margin-parallel (NNW). However, away from the plate boundary, the fast direction transitions to WSW-trending, very oblique or perpendicular to the plate boundary. Because the average delay time of 0.6-2.45 s is much larger than values based on an associated local S phase splitting analysis in the same study area, it is reasonable to infer that most of the anisotropy from our SKS analysis originates from the upper mantle and is associated with lattice-preferred orientation of anisotropic minerals. The margin-parallel fast direction within about 100 km of the QCF (average φ = -40º and δt = 1.2 s) is likely induced by the PA-NA shear motion. The roughly margin-normal fast directions farther away, although more scatterd, are consistent with that previously observed in the NA continent and are attributed to the absolute motion of the NA plate. However, the transition between the two regimes based on our SKS analysis appears to be gradual, suggesting that the plate boundary shear influences a much broader region at mantle depths than would be inferred from the surface trace of the QCF. We think this is due to the presence of a subducted portion of the Pacific plate. Because the slab travels mostly in the strike direction, it is expected to induce margin-parallel shear deformation of the mantle material. This result has importance implications to the geodynamics of transpressive plate margins.

On the fractal characterization of Paretian Poisson processes

NASA Astrophysics Data System (ADS)

Eliazar, Iddo I.; Sokolov, Igor M.

2012-06-01

Paretian Poisson processes are Poisson processes which are defined on the positive half-line, have maximal points, and are quantified by power-law intensities. Paretian Poisson processes are elemental in statistical physics, and are the bedrock of a host of power-law statistics ranging from Pareto's law to anomalous diffusion. In this paper we establish evenness-based fractal characterizations of Paretian Poisson processes. Considering an array of socioeconomic evenness-based measures of statistical heterogeneity, we show that: amongst the realm of Poisson processes which are defined on the positive half-line, and have maximal points, Paretian Poisson processes are the unique class of 'fractal processes' exhibiting scale-invariance. The results established in this paper are diametric to previous results asserting that the scale-invariance of Poisson processes-with respect to physical randomness-based measures of statistical heterogeneity-is characterized by exponential Poissonian intensities.

High performance computing aspects of a dimension independent semi-Lagrangian discontinuous Galerkin code

NASA Astrophysics Data System (ADS)

Einkemmer, Lukas

2016-05-01

The recently developed semi-Lagrangian discontinuous Galerkin approach is used to discretize hyperbolic partial differential equations (usually first order equations). Since these methods are conservative, local in space, and able to limit numerical diffusion, they are considered a promising alternative to more traditional semi-Lagrangian schemes (which are usually based on polynomial or spline interpolation). In this paper, we consider a parallel implementation of a semi-Lagrangian discontinuous Galerkin method for distributed memory systems (so-called clusters). Both strong and weak scaling studies are performed on the Vienna Scientific Cluster 2 (VSC-2). In the case of weak scaling we observe a parallel efficiency above 0.8 for both two and four dimensional problems and up to 8192 cores. Strong scaling results show good scalability to at least 512 cores (we consider problems that can be run on a single processor in reasonable time). In addition, we study the scaling of a two dimensional Vlasov-Poisson solver that is implemented using the framework provided. All of the simulations are conducted in the context of worst case communication overhead; i.e., in a setting where the CFL (Courant-Friedrichs-Lewy) number increases linearly with the problem size. The framework introduced in this paper facilitates a dimension independent implementation of scientific codes (based on C++ templates) using both an MPI and a hybrid approach to parallelization. We describe the essential ingredients of our implementation.

The development of GPU-based parallel PRNG for Monte Carlo applications in CUDA Fortran

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

Kargaran, Hamed, E-mail: h-kargaran@sbu.ac.ir; Minuchehr, Abdolhamid; Zolfaghari, Ahmad

The implementation of Monte Carlo simulation on the CUDA Fortran requires a fast random number generation with good statistical properties on GPU. In this study, a GPU-based parallel pseudo random number generator (GPPRNG) have been proposed to use in high performance computing systems. According to the type of GPU memory usage, GPU scheme is divided into two work modes including GLOBAL-MODE and SHARED-MODE. To generate parallel random numbers based on the independent sequence method, the combination of middle-square method and chaotic map along with the Xorshift PRNG have been employed. Implementation of our developed PPRNG on a single GPU showedmore » a speedup of 150x and 470x (with respect to the speed of PRNG on a single CPU core) for GLOBAL-MODE and SHARED-MODE, respectively. To evaluate the accuracy of our developed GPPRNG, its performance was compared to that of some other commercially available PPRNGs such as MATLAB, FORTRAN and Miller-Park algorithm through employing the specific standard tests. The results of this comparison showed that the developed GPPRNG in this study can be used as a fast and accurate tool for computational science applications.« less

Implementation and audit of 'Fast-Track Surgery' in gynaecological oncology surgery.

PubMed

Sidhu, Verinder S; Lancaster, Letitia; Elliott, David; Brand, Alison H

2012-08-01

Fast-track surgery is a multidisciplinary approach to surgery that results in faster recovery from surgery and decreased length of stay (LOS). The aims of this study were as follows: (i) to report on the processes required for the introduction of fast-track surgery to a gynaecological oncology unit and (ii) to report the results of a clinical audit conducted after the protocol's implementation. A fast-track protocol, specific to our unit, was developed after a series of multidisciplinary meetings. The protocol, agreed upon by those involved in the care of women in our unit, was then introduced into clinical practice. An audit was conducted of all women undergoing laparotomy, with known or suspected malignancy. Information on LOS, complication and readmission rates was collected. Descriptive statistics and Poisson regression were used for statistical analysis. The developed protocol involved a multidisciplinary approach to pre-, intra- and postoperative care. The audit included 104 consecutive women over a 6-month period, who were followed for 6 weeks postoperatively. The median LOS was 4 days. The readmission rate was 7% and the complication rate was 19% (1% intraoperative, 4% major and 14% minor). Multivariate analysis revealed that increased duration of surgery and increasing age were predictors of longer LOS. The development of a fast-track protocol is achievable in a gynaecological oncology unit, with input from a multidisciplinary team. Effective implementation of the protocol can result in a short LOS, with acceptable complication and readmission rates when applied non-selectively to gynaecological oncology patients. © 2012 The Authors ANZJOG © 2012 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Algorithm for fast event parameters estimation on GEM acquired data

NASA Astrophysics Data System (ADS)

Linczuk, Paweł; Krawczyk, Rafał D.; Poźniak, Krzysztof T.; Kasprowicz, Grzegorz; Wojeński, Andrzej; Chernyshova, Maryna; Czarski, Tomasz

2016-09-01

We present study of a software-hardware environment for developing fast computation with high throughput and low latency methods, which can be used as back-end in High Energy Physics (HEP) and other High Performance Computing (HPC) systems, based on high amount of input from electronic sensor based front-end. There is a parallelization possibilities discussion and testing on Intel HPC solutions with consideration of applications with Gas Electron Multiplier (GEM) measurement systems presented in this paper.

Energetic ion, atom, and molecule reactions and excitation in low-current H2 discharges: H(alpha) Doppler profiles.

PubMed

Petrović, Z Lj; Phelps, A V

2009-12-01

Absolute spectral emissivities for Doppler broadened H(alpha) profiles are measured and compared with predictions of energetic hydrogen ion, atom, and molecule behavior in low-current electrical discharges in H2 at very high electric field E to gas density N ratios E/N and low values of Nd , where d is the parallel-plate electrode separation. These observations reflect the energy and angular distributions for the excited atoms and quantitatively test features of multiple-scattering kinetic models in weakly ionized hydrogen in the presence of an electric field that are not tested by the spatial distributions of H(alpha) emission. Absolute spectral intensities agree well with predictions. Asymmetries in Doppler profiles observed parallel to the electric field at 4

Nambu-Poisson gauge theory

NASA Astrophysics Data System (ADS)

Jurčo, Branislav; Schupp, Peter; Vysoký, Jan

2014-06-01

We generalize noncommutative gauge theory using Nambu-Poisson structures to obtain a new type of gauge theory with higher brackets and gauge fields. The approach is based on covariant coordinates and higher versions of the Seiberg-Witten map. We construct a covariant Nambu-Poisson gauge theory action, give its first order expansion in the Nambu-Poisson tensor and relate it to a Nambu-Poisson matrix model.

Hardware-efficient implementation of digital FIR filter using fast first-order moment algorithm

NASA Astrophysics Data System (ADS)

Cao, Li; Liu, Jianguo; Xiong, Jun; Zhang, Jing

2018-03-01

As the digital finite impulse response (FIR) filter can be transformed into the shift-add form of multiple small-sized firstorder moments, based on the existing fast first-order moment algorithm, this paper presents a novel multiplier-less structure to calculate any number of sequential filtering results in parallel. The theoretical analysis on its hardware and time-complexities reveals that by appropriately setting the degree of parallelism and the decomposition factor of a fixed word width, the proposed structure may achieve better area-time efficiency than the existing two-dimensional (2-D) memoryless-based filter. To evaluate the performance concretely, the proposed designs for different taps along with the existing 2-D memoryless-based filters, are synthesized by Synopsys Design Compiler with 0.18-μm SMIC library. The comparisons show that the proposed design has less area-time complexity and power consumption when the number of filter taps is larger than 48.

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.

Asynchronous multilevel adaptive methods for solving partial differential equations on multiprocessors - Performance results

NASA Technical Reports Server (NTRS)

Mccormick, S.; Quinlan, D.

1989-01-01

The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids (global and local) to provide adaptive resolution and fast solution of PDEs. Like all such methods, it offers parallelism by using possibly many disconnected patches per level, but is hindered by the need to handle these levels sequentially. The finest levels must therefore wait for processing to be essentially completed on all the coarser ones. A recently developed asynchronous version of FAC, called AFAC, completely eliminates this bottleneck to parallelism. This paper describes timing results for AFAC, coupled with a simple load balancing scheme, applied to the solution of elliptic PDEs on an Intel iPSC hypercube. These tests include performance of certain processes necessary in adaptive methods, including moving grids and changing refinement. A companion paper reports on numerical and analytical results for estimating convergence factors of AFAC applied to very large scale examples.

Parallel algorithms for placement and routing in VLSI design. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Brouwer, Randall Jay

1991-01-01

The computational requirements for high quality synthesis, analysis, and verification of very large scale integration (VLSI) designs have rapidly increased with the fast growing complexity of these designs. Research in the past has focused on the development of heuristic algorithms, special purpose hardware accelerators, or parallel algorithms for the numerous design tasks to decrease the time required for solution. Two new parallel algorithms are proposed for two VLSI synthesis tasks, standard cell placement and global routing. The first algorithm, a parallel algorithm for global routing, uses hierarchical techniques to decompose the routing problem into independent routing subproblems that are solved in parallel. Results are then presented which compare the routing quality to the results of other published global routers and which evaluate the speedups attained. The second algorithm, a parallel algorithm for cell placement and global routing, hierarchically integrates a quadrisection placement algorithm, a bisection placement algorithm, and the previous global routing algorithm. Unique partitioning techniques are used to decompose the various stages of the algorithm into independent tasks which can be evaluated in parallel. Finally, results are presented which evaluate the various algorithm alternatives and compare the algorithm performance to other placement programs. Measurements are presented on the parallel speedups available.

Research in Computational Aeroscience Applications Implemented on Advanced Parallel Computing Systems

NASA Technical Reports Server (NTRS)

Wigton, Larry

1996-01-01

Improving the numerical linear algebra routines for use in new Navier-Stokes codes, specifically Tim Barth's unstructured grid code, with spin-offs to TRANAIR is reported. A fast distance calculation routine for Navier-Stokes codes using the new one-equation turbulence models is written. The primary focus of this work was devoted to improving matrix-iterative methods. New algorithms have been developed which activate the full potential of classical Cray-class computers as well as distributed-memory parallel computers.

Fast realization of nonrecursive digital filters with limits on signal delay

NASA Astrophysics Data System (ADS)

Titov, M. A.; Bondarenko, N. N.

1983-07-01

Attention is given to the problem of achieving a fast realization of nonrecursive digital filters with the aim of reducing signal delay. It is shown that a realization wherein the impulse characteristic of the filter is divided into blocks satisfies the delay requirements and is almost as economical in terms of the number of multiplications as conventional fast convolution. In addition, the block method leads to a reduction in the needed size of the memory and in the number of additions; the short-convolution procedure is substantially simplified. Finally, the block method facilitates the paralleling of computations owing to the simple transfers between subfilters.

ON THE PARALLEL AND PERPENDICULAR PROPAGATING MOTIONS VISIBLE IN POLAR PLUMES: AN INCUBATOR FOR (FAST) SOLAR WIND ACCELERATION?

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

Liu, Jiajia; Wang, Yuming; McIntosh, Scott W.

We combine observations of the Coronal Multi-channel Polarimeter and the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory to study the characteristic properties of (propagating) Alfvénic motions and quasi-periodic intensity disturbances in polar plumes. This unique combination of instruments highlights the physical richness of the processes taking place at the base of the (fast) solar wind. The (parallel) intensity perturbations with intensity enhancements around 1% have an apparent speed of 120 km s{sup −1} (in both the 171 and 193 Å passbands) and a periodicity of 15 minutes, while the (perpendicular) Alfvénic wave motions have a velocity amplitude ofmore » 0.5 km s{sup −1}, a phase speed of 830 km s{sup −1}, and a shorter period of 5 minutes on the same structures. These observations illustrate a scenario where the excited Alfvénic motions are propagating along an inhomogeneously loaded magnetic field structure such that the combination could be a potential progenitor of the magnetohydrodynamic turbulence required to accelerate the fast solar wind.« less

A Three-dimensional Polymer Scaffolding Material Exhibiting a Zero Poisson's Ratio.

PubMed

Soman, Pranav; Fozdar, David Y; Lee, Jin Woo; Phadke, Ameya; Varghese, Shyni; Chen, Shaochen

2012-05-14

Poisson's ratio describes the degree to which a material contracts (expands) transversally when axially strained. A material with a zero Poisson's ratio does not transversally deform in response to an axial strain (stretching). In tissue engineering applications, scaffolding having a zero Poisson's ratio (ZPR) may be more suitable for emulating the behavior of native tissues and accommodating and transmitting forces to the host tissue site during wound healing (or tissue regrowth). For example, scaffolding with a zero Poisson's ratio may be beneficial in the engineering of cartilage, ligament, corneal, and brain tissues, which are known to possess Poisson's ratios of nearly zero. Here, we report a 3D biomaterial constructed from polyethylene glycol (PEG) exhibiting in-plane Poisson's ratios of zero for large values of axial strain. We use digital micro-mirror device projection printing (DMD-PP) to create single- and double-layer scaffolds composed of semi re-entrant pores whose arrangement and deformation mechanisms contribute the zero Poisson's ratio. Strain experiments prove the zero Poisson's behavior of the scaffolds and that the addition of layers does not change the Poisson's ratio. Human mesenchymal stem cells (hMSCs) cultured on biomaterials with zero Poisson's ratio demonstrate the feasibility of utilizing these novel materials for biological applications which require little to no transverse deformations resulting from axial strains. Techniques used in this work allow Poisson's ratio to be both scale-independent and independent of the choice of strut material for strains in the elastic regime, and therefore ZPR behavior can be imparted to a variety of photocurable biomaterial.

Seismic anisotropy of the lithosphere/asthenosphere system beneath the Rwenzori region of the Albertine Rift

NASA Astrophysics Data System (ADS)

Homuth, B.; Löbl, U.; Batte, A. G.; Link, K.; Kasereka, C. M.; Rümpker, G.

2016-09-01

Shear-wave splitting measurements from local and teleseismic earthquakes are used to investigate the seismic anisotropy in the upper mantle beneath the Rwenzori region of the East African Rift system. At most stations, shear-wave splitting parameters obtained from individual earthquakes exhibit only minor variations with backazimuth. We therefore employ a joint inversion of SKS waveforms to derive hypothetical one-layer parameters. The corresponding fast polarizations are generally rift parallel and the average delay time is about 1 s. Shear phases from local events within the crust are characterized by an average delay time of 0.04 s. Delay times from local mantle earthquakes are in the range of 0.2 s. This observation suggests that the dominant source region for seismic anisotropy beneath the rift is located within the mantle. We use finite-frequency waveform modeling to test different models of anisotropy within the lithosphere/asthenosphere system of the rift. The results show that the rift-parallel fast polarizations are consistent with horizontal transverse isotropy (HTI anisotropy) caused by rift-parallel magmatic intrusions or lenses located within the lithospheric mantle—as it would be expected during the early stages of continental rifting. Furthermore, the short-scale spatial variations in the fast polarizations observed in the southern part of the study area can be explained by effects due to sedimentary basins of low isotropic velocity in combination with a shift in the orientation of anisotropic fabrics in the upper mantle. A uniform anisotropic layer in relation to large-scale asthenospheric mantle flow is less consistent with the observed splitting parameters.

A parallel finite element simulator for ion transport through three-dimensional ion channel systems.

PubMed

Tu, Bin; Chen, Minxin; Xie, Yan; Zhang, Linbo; Eisenberg, Bob; Lu, Benzhuo

2013-09-15

A parallel finite element simulator, ichannel, is developed for ion transport through three-dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite element solver for a set of Poisson-Nernst-Planck (PNP) equations that describe the electrodiffusion process of ion transport, and a mesh generation tool chain for ion channel systems, which is an essential component for the finite element computations. The finite element method has advantages in modeling irregular geometries and complex boundary conditions. We have built a tool chain to get the surface and volume mesh for ion channel systems, which consists of a set of mesh generation tools. The adaptive finite element solver in our simulator is implemented using the parallel adaptive finite element package Parallel Hierarchical Grid (PHG) developed by one of the authors, which provides the capability of doing large scale parallel computations with high parallel efficiency and the flexibility of choosing high order elements to achieve high order accuracy. The simulator is applied to a real transmembrane protein, the gramicidin A (gA) channel protein, to calculate the electrostatic potential, ion concentrations and I - V curve, with which both primitive and transformed PNP equations are studied and their numerical performances are compared. To further validate the method, we also apply the simulator to two other ion channel systems, the voltage dependent anion channel (VDAC) and α-Hemolysin (α-HL). The simulation results agree well with Brownian dynamics (BD) simulation results and experimental results. Moreover, because ionic finite size effects can be included in PNP model now, we also perform simulations using a size-modified PNP (SMPNP) model on VDAC and α-HL. It is shown that the size effects in SMPNP can effectively lead to reduced current in the channel, and the results are closer to BD simulation results. Copyright © 2013 Wiley Periodicals, Inc.

An accurate, fast, and scalable solver for high-frequency wave propagation

NASA Astrophysics Data System (ADS)

Zepeda-Núñez, L.; Taus, M.; Hewett, R.; Demanet, L.

2017-12-01

In many science and engineering applications, solving time-harmonic high-frequency wave propagation problems quickly and accurately is of paramount importance. For example, in geophysics, particularly in oil exploration, such problems can be the forward problem in an iterative process for solving the inverse problem of subsurface inversion. It is important to solve these wave propagation problems accurately in order to efficiently obtain meaningful solutions of the inverse problems: low order forward modeling can hinder convergence. Additionally, due to the volume of data and the iterative nature of most optimization algorithms, the forward problem must be solved many times. Therefore, a fast solver is necessary to make solving the inverse problem feasible. For time-harmonic high-frequency wave propagation, obtaining both speed and accuracy is historically challenging. Recently, there have been many advances in the development of fast solvers for such problems, including methods which have linear complexity with respect to the number of degrees of freedom. While most methods scale optimally only in the context of low-order discretizations and smooth wave speed distributions, the method of polarized traces has been shown to retain optimal scaling for high-order discretizations, such as hybridizable discontinuous Galerkin methods and for highly heterogeneous (and even discontinuous) wave speeds. The resulting fast and accurate solver is consequently highly attractive for geophysical applications. To date, this method relies on a layered domain decomposition together with a preconditioner applied in a sweeping fashion, which has limited straight-forward parallelization. In this work, we introduce a new version of the method of polarized traces which reveals more parallel structure than previous versions while preserving all of its other advantages. We achieve this by further decomposing each layer and applying the preconditioner to these new components separately and in parallel. We demonstrate that this produces an even more effective and parallelizable preconditioner for a single right-hand side. As before, additional speed can be gained by pipelining several right-hand-sides.

From Loss of Memory to Poisson.

ERIC Educational Resources Information Center

Johnson, Bruce R.

1983-01-01

A way of presenting the Poisson process and deriving the Poisson distribution for upper-division courses in probability or mathematical statistics is presented. The main feature of the approach lies in the formulation of Poisson postulates with immediate intuitive appeal. (MNS)

A fast ultrasonic simulation tool based on massively parallel implementations

NASA Astrophysics Data System (ADS)

Lambert, Jason; Rougeron, Gilles; Lacassagne, Lionel; Chatillon, Sylvain

2014-02-01

This paper presents a CIVA optimized ultrasonic inspection simulation tool, which takes benefit of the power of massively parallel architectures: graphical processing units (GPU) and multi-core general purpose processors (GPP). This tool is based on the classical approach used in CIVA: the interaction model is based on Kirchoff, and the ultrasonic field around the defect is computed by the pencil method. The model has been adapted and parallelized for both architectures. At this stage, the configurations addressed by the tool are : multi and mono-element probes, planar specimens made of simple isotropic materials, planar rectangular defects or side drilled holes of small diameter. Validations on the model accuracy and performances measurements are presented.

Ordered fast Fourier transforms on a massively parallel hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Tong, Charles; Swarztrauber, Paul N.

1991-01-01

The present evaluation of alternative, massively parallel hypercube processor-applicable designs for ordered radix-2 decimation-in-frequency FFT algorithms gives attention to the reduction of computation time-dominating communication. A combination of the order and computational phases of the FFT is accordingly employed, in conjunction with sequence-to-processor maps which reduce communication. Two orderings, 'standard' and 'cyclic', in which the order of the transform is the same as that of the input sequence, can be implemented with ease on the Connection Machine (where orderings are determined by geometries and priorities. A parallel method for trigonometric coefficient computation is presented which does not employ trigonometric functions or interprocessor communication.

An implicit boundary integral method for computing electric potential of macromolecules in solvent

NASA Astrophysics Data System (ADS)

Zhong, Yimin; Ren, Kui; Tsai, Richard

2018-04-01

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

SGR-like behaviour of the repeating FRB 121102

NASA Astrophysics Data System (ADS)

Wang, F. Y.; Yu, H.

2017-03-01

Fast radio bursts (FRBs) are millisecond-duration radio signals occurring at cosmological distances. However the physical model of FRBs is mystery, many models have been proposed. Here we study the frequency distributions of peak flux, fluence, duration and waiting time for the repeating FRB 121102. The cumulative distributions of peak flux, fluence and duration show power-law forms. The waiting time distribution also shows power-law distribution, and is consistent with a non-stationary Poisson process. These distributions are similar as those of soft gamma repeaters (SGRs). We also use the statistical results to test the proposed models for FRBs. These distributions are consistent with the predictions from avalanche models of slowly driven nonlinear dissipative systems.

Fast parallel molecular algorithms for DNA-based computation: factoring integers.

PubMed

Chang, Weng-Long; Guo, Minyi; Ho, Michael Shan-Hui

2005-06-01

The RSA public-key cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA public-key cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNA-based algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.

Fast forward kinematics algorithm for real-time and high-precision control of the 3-RPS parallel mechanism

NASA Astrophysics Data System (ADS)

Wang, Yue; Yu, Jingjun; Pei, Xu

2018-06-01

A new forward kinematics algorithm for the mechanism of 3-RPS (R: Revolute; P: Prismatic; S: Spherical) parallel manipulators is proposed in this study. This algorithm is primarily based on the special geometric conditions of the 3-RPS parallel mechanism, and it eliminates the errors produced by parasitic motions to improve and ensure accuracy. Specifically, the errors can be less than 10-6. In this method, only the group of solutions that is consistent with the actual situation of the platform is obtained rapidly. This algorithm substantially improves calculation efficiency because the selected initial values are reasonable, and all the formulas in the calculation are analytical. This novel forward kinematics algorithm is well suited for real-time and high-precision control of the 3-RPS parallel mechanism.

A nonlinear equation for ionic diffusion in a strong binary electrolyte

PubMed Central

Ghosal, Sandip; Chen, Zhen

2010-01-01

The problem of the one-dimensional electro-diffusion of ions in a strong binary electrolyte is considered. The mathematical description, known as the Poisson–Nernst–Planck (PNP) system, consists of a diffusion equation for each species augmented by transport owing to a self-consistent electrostatic field determined by the Poisson equation. This description is also relevant to other important problems in physics, such as electron and hole diffusion across semiconductor junctions and the diffusion of ions in plasmas. If concentrations do not vary appreciably over distances of the order of the Debye length, the Poisson equation can be replaced by the condition of local charge neutrality first introduced by Planck. It can then be shown that both species diffuse at the same rate with a common diffusivity that is intermediate between that of the slow and fast species (ambipolar diffusion). Here, we derive a more general theory by exploiting the ratio of the Debye length to a characteristic length scale as a small asymptotic parameter. It is shown that the concentration of either species may be described by a nonlinear partial differential equation that provides a better approximation than the classical linear equation for ambipolar diffusion, but reduces to it in the appropriate limit. PMID:21818176

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

PubMed

Forouzesh, Negin; Izadi, Saeed; Onufriev, Alexey V

2017-10-23

Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG pol ) and binding free energies (ΔΔG pol ). The model tolerates a relatively coarse grid size h = 0.5 Å, where the grid artifact error in computing ΔΔG pol remains in the range of k B T ∼ 0.6 kcal/mol. The estimated ΔΔG pol s are well correlated (r 2 = 0.97) with the numerical Poisson-Boltzmann reference, while showing virtually no systematic bias and RMSE = 1.43 kcal/mol. The grid-based GBNSR6 model is available in Amber (AmberTools) package of molecular simulation programs.

Nonlocal Poisson-Fermi model for ionic solvent.

PubMed

Xie, Dexuan; Liu, Jinn-Liang; Eisenberg, Bob

2016-07-01

We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.

Nonlinear Poisson Equation for Heterogeneous Media

PubMed Central

Hu, Langhua; Wei, Guo-Wei

2012-01-01

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. PMID:22947937

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

PubMed Central

Vestergaard, Christian L.; Génois, Mathieu

2015-01-01

Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling. PMID:26517860

Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.

PubMed

Vestergaard, Christian L; Génois, Mathieu

2015-10-01

Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.

Computational electromagnetics: the physics of smooth versus oscillatory fields.

PubMed

Chew, W C

2004-03-15

This paper starts by discussing the difference in the physics between solutions to Laplace's equation (static) and Maxwell's equations for dynamic problems (Helmholtz equation). Their differing physical characters are illustrated by how the two fields convey information away from their source point. The paper elucidates the fact that their differing physical characters affect the use of Laplacian field and Helmholtz field in imaging. They also affect the design of fast computational algorithms for electromagnetic scattering problems. Specifically, a comparison is made between fast algorithms developed using wavelets, the simple fast multipole method, and the multi-level fast multipole algorithm for electrodynamics. The impact of the physical characters of the dynamic field on the parallelization of the multi-level fast multipole algorithm is also discussed. The relationship of diagonalization of translators to group theory is presented. Finally, future areas of research for computational electromagnetics are described.

Fast Mapping Across Time: Memory Processes Support Children's Retention of Learned Words.

PubMed

Vlach, Haley A; Sandhofer, Catherine M

2012-01-01

Children's remarkable ability to map linguistic labels to referents in the world is commonly called fast mapping. The current study examined children's (N = 216) and adults' (N = 54) retention of fast-mapped words over time (immediately, after a 1-week delay, and after a 1-month delay). The fast mapping literature often characterizes children's retention of words as consistently high across timescales. However, the current study demonstrates that learners forget word mappings at a rapid rate. Moreover, these patterns of forgetting parallel forgetting functions of domain-general memory processes. Memory processes are critical to children's word learning and the role of one such process, forgetting, is discussed in detail - forgetting supports extended mapping by promoting the memory and generalization of words and categories.

BRAIN initiative: fast and parallel solver for real-time monitoring of the eddy current in the brain for TMS applications.

PubMed

Sabouni, Abas; Pouliot, Philippe; Shmuel, Amir; Lesage, Frederic

2014-01-01

This paper introduce a fast and efficient solver for simulating the induced (eddy) current distribution in the brain during transcranial magnetic stimulation procedure. This solver has been integrated with MRI and neuronavigation software to accurately model the electromagnetic field and show eddy current in the head almost in real-time. To examine the performance of the proposed technique, we used a 3D anatomically accurate MRI model of the 25 year old female subject.

Rapid enhancement of low energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

DOE PAGES

Yue, Chao; Li, Wen; Reeves, Geoffrey D.; ...

2016-07-01

Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H +, He +, and O +, were enhanced dramatically in both the parallel and perpendicular directions.more » During the 2 October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. Furthermore, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.« less

Rapid enhancement of low energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

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

Yue, Chao; Li, Wen; Reeves, Geoffrey D.

Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H +, He +, and O +, were enhanced dramatically in both the parallel and perpendicular directions.more » During the 2 October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. Furthermore, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.« less

Saint-Venant end effects for materials with negative Poisson's ratios

NASA Technical Reports Server (NTRS)

Lakes, R. S.

1992-01-01

Results are presented from an analysis of Saint-Venant end effects for materials with negative Poisson's ratio. Examples are presented showing that slow decay of end stress occurs in circular cylinders of negative Poisson's ratio, whereas a sandwich panel containing rigid face sheets and a compliant core exhibits no anomalous effects for negative Poisson's ratio (but exhibits slow stress decay for core Poisson's ratios approaching 0.5). In sand panels with stiff but not perfectly rigid face sheets, a negative Poisson's ratio results in end stress decay, which is faster than it would be otherwise. It is suggested that the slow decay previously predicted for sandwich strips in plane deformation as a result of the geometry can be mitigated by the use of a negative Poisson's ratio material for the core.

Poisson's ratio of fiber-reinforced composites

NASA Astrophysics Data System (ADS)

Christiansson, Henrik; Helsing, Johan

1996-05-01

Poisson's ratio flow diagrams, that is, the Poisson's ratio versus the fiber fraction, are obtained numerically for hexagonal arrays of elastic circular fibers in an elastic matrix. High numerical accuracy is achieved through the use of an interface integral equation method. Questions concerning fixed point theorems and the validity of existing asymptotic relations are investigated and partially resolved. Our findings for the transverse effective Poisson's ratio, together with earlier results for random systems by other authors, make it possible to formulate a general statement for Poisson's ratio flow diagrams: For composites with circular fibers and where the phase Poisson's ratios are equal to 1/3, the system with the lowest stiffness ratio has the highest Poisson's ratio. For other choices of the elastic moduli for the phases, no simple statement can be made.

Consumption of fast food, sugar-sweetened beverages, artificially-sweetened beverages and allostatic load among young adults.

PubMed

van Draanen, Jenna; Prelip, Michael; Upchurch, Dawn M

2018-06-01

This study investigates the associations between recent consumption of fast foods, sugar-sweetened beverages, and artificially-sweetened beverages on level of allostatic load, a measure of cumulative biological risk, in young adults in the US. Data from Wave IV of the National Longitudinal Study of Adolescent to Adult Health were analyzed. Negative binomial regression models were used to estimate the associations between consumption of fast foods, sugar-sweetened, and artificially-sweetened beverages and allostatic load. Poisson and logistic regression models were used to estimate the associations between these diet parameters and combined biomarkers of physiological subsystems that comprise our measure of allostatic load. All analyses were weighted and findings are representative of young adults in the US, ages 24-34 in 2008 (n = 11,562). Consumption of fast foods, sugar-sweetened, and artificially-sweetened beverages were associated with higher allostatic load at a bivariate level. Accounting for demographics and medication use, only artificially-sweetened beverages remained significantly associated with allostatic load. When all three dietary components were simultaneously included in a model, both sugar- and artificially-sweetened beverage consumption were associated with higher allostatic load. Differences in allostatic load emerge early in the life course and young adults consuming sugar- or artificially-sweetened beverages have higher allostatic load, net of demographics and medication use. Public health messages to young adults may need to include cautions about both sugar- and artificially-sweetened beverages.

Characterization of Nonhomogeneous Poisson Processes Via Moment Conditions.

DTIC Science & Technology

1986-08-01

Poisson processes play an important role in many fields. The Poisson process is one of the simplest counting processes and is a building block for...place of independent increments. This provides a somewhat different viewpoint for examining Poisson processes . In addition, new characterizations for

Poisson Mixture Regression Models for Heart Disease Prediction.

PubMed

Mufudza, Chipo; Erol, Hamza

2016-01-01

Early heart disease control can be achieved by high disease prediction and diagnosis efficiency. This paper focuses on the use of model based clustering techniques to predict and diagnose heart disease via Poisson mixture regression models. Analysis and application of Poisson mixture regression models is here addressed under two different classes: standard and concomitant variable mixture regression models. Results show that a two-component concomitant variable Poisson mixture regression model predicts heart disease better than both the standard Poisson mixture regression model and the ordinary general linear Poisson regression model due to its low Bayesian Information Criteria value. Furthermore, a Zero Inflated Poisson Mixture Regression model turned out to be the best model for heart prediction over all models as it both clusters individuals into high or low risk category and predicts rate to heart disease componentwise given clusters available. It is deduced that heart disease prediction can be effectively done by identifying the major risks componentwise using Poisson mixture regression model.

Constructions and classifications of projective Poisson varieties.

PubMed

Pym, Brent

2018-01-01

This paper is intended both as an introduction to the algebraic geometry of holomorphic Poisson brackets, and as a survey of results on the classification of projective Poisson manifolds that have been obtained in the past 20 years. It is based on the lecture series delivered by the author at the Poisson 2016 Summer School in Geneva. The paper begins with a detailed treatment of Poisson surfaces, including adjunction, ruled surfaces and blowups, and leading to a statement of the full birational classification. We then describe several constructions of Poisson threefolds, outlining the classification in the regular case, and the case of rank-one Fano threefolds (such as projective space). Following a brief introduction to the notion of Poisson subspaces, we discuss Bondal's conjecture on the dimensions of degeneracy loci on Poisson Fano manifolds. We close with a discussion of log symplectic manifolds with simple normal crossings degeneracy divisor, including a new proof of the classification in the case of rank-one Fano manifolds.

Poisson Mixture Regression Models for Heart Disease Prediction

PubMed Central

Erol, Hamza

2016-01-01

Early heart disease control can be achieved by high disease prediction and diagnosis efficiency. This paper focuses on the use of model based clustering techniques to predict and diagnose heart disease via Poisson mixture regression models. Analysis and application of Poisson mixture regression models is here addressed under two different classes: standard and concomitant variable mixture regression models. Results show that a two-component concomitant variable Poisson mixture regression model predicts heart disease better than both the standard Poisson mixture regression model and the ordinary general linear Poisson regression model due to its low Bayesian Information Criteria value. Furthermore, a Zero Inflated Poisson Mixture Regression model turned out to be the best model for heart prediction over all models as it both clusters individuals into high or low risk category and predicts rate to heart disease componentwise given clusters available. It is deduced that heart disease prediction can be effectively done by identifying the major risks componentwise using Poisson mixture regression model. PMID:27999611

Constructions and classifications of projective Poisson varieties

NASA Astrophysics Data System (ADS)

Pym, Brent

2018-03-01

This paper is intended both as an introduction to the algebraic geometry of holomorphic Poisson brackets, and as a survey of results on the classification of projective Poisson manifolds that have been obtained in the past 20 years. It is based on the lecture series delivered by the author at the Poisson 2016 Summer School in Geneva. The paper begins with a detailed treatment of Poisson surfaces, including adjunction, ruled surfaces and blowups, and leading to a statement of the full birational classification. We then describe several constructions of Poisson threefolds, outlining the classification in the regular case, and the case of rank-one Fano threefolds (such as projective space). Following a brief introduction to the notion of Poisson subspaces, we discuss Bondal's conjecture on the dimensions of degeneracy loci on Poisson Fano manifolds. We close with a discussion of log symplectic manifolds with simple normal crossings degeneracy divisor, including a new proof of the classification in the case of rank-one Fano manifolds.

Application of an Elongated Kelvin Model to Space Shuttle Foams

NASA Technical Reports Server (NTRS)

Sullivan, Roy M.; Ghosn, Louis J.; Lerch, Bradley A.

2008-01-01

Spray-on foam insulation is applied to the exterior of the Space Shuttle s External Tank to limit propellant boil-off and to prevent ice formation. The Space Shuttle foams are rigid closed-cell polyurethane foams. The two foams used most extensively on the Space Shuttle External Tank are BX-265 and NCFI24-124. Since the catastrophic loss of the Space Shuttle Columbia, numerous studies have been conducted to mitigate the likelihood and the severity of foam shedding during the Shuttle s ascent to space. Due to the foaming and rising process, the foam microstructures are elongated in the rise direction. As a result, these two foams exhibit a non-isotropic mechanical behavior. In this paper, a detailed microstructural characterization of the two foams is presented. The key features of the foam cells are summarized and the average cell dimensions in the two foams are compared. Experimental studies to measure the room temperature mechanical response of the two foams in the two principal material directions (parallel to the rise and perpendicular to the rise) are also reported. The measured elastic modulus, proportional limit stress, ultimate tensile stress and the Poisson s ratios for the two foams are compared. The generalized elongated Kelvin foam model previously developed by the authors is reviewed and the equations which result from this model are presented. The resulting equations show that the ratio of the elastic modulus in the rise direction to that in the perpendicular-to-rise direction as well as the ratio of the strengths in the two material directions is only a function of the microstructural dimensions. Using the measured microstructural dimensions and the measured stiffness ratio, the foam tensile strength ratio and Poisson s ratios are predicted for both foams. The predicted tensile strength ratio is in close agreement with the measured strength ratios for both BX-265 and NCFI24-124. The comparison between the predicted Poisson s ratios and the measured values is not as favorable.

Lateral terahertz hot-electron bolometer based on an array of Sn nanothreads in GaAs

NASA Astrophysics Data System (ADS)

Ponomarev, D. S.; Lavrukhin, D. V.; Yachmenev, A. E.; Khabibullin, R. A.; Semenikhin, I. E.; Vyurkov, V. V.; Ryzhii, M.; Otsuji, T.; Ryzhii, V.

2018-04-01

We report on the proposal and the theoretical and experimental studies of the terahertz hot-electron bolometer (THz HEB) based on a gated GaAs structure like the field-effect transistor with the array of parallel Sn nanothreads (Sn-NTs). The operation of the HEB is associated with an increase in the density of the delocalized electrons due to their heating by the incoming THz radiation. The quantum and the classical device models were developed, the quantum one was based on the self-consistent solution of the Poisson and Schrödinger equations, the classical model involved the Poisson equation and density of states omitting quantization. We calculated the electron energy distributions in the channels formed around the Sn-NTs for different gate voltages and found the fraction of the delocalized electrons propagating across the energy barriers between the NTs. Since the fraction of the delocalized electrons strongly depends on the average electron energy (effective temperature), the proposed THz HEB can exhibit an elevated responsivity compared with the HEBs based on more standard heterostructures. Due to a substantial anisotropy of the device structure, the THz HEB may demonstrate a noticeable polarization selectivity of the response to the in-plane polarized THz radiation. The features of the THz HEB might be useful in their practical applications in biology, medicine and material science.

Monitoring Poisson observations using combined applications of Shewhart and EWMA charts

NASA Astrophysics Data System (ADS)

Abujiya, Mu'azu Ramat

2017-11-01

The Shewhart and exponentially weighted moving average (EWMA) charts for nonconformities are the most widely used procedures of choice for monitoring Poisson observations in modern industries. Individually, the Shewhart EWMA charts are only sensitive to large and small shifts, respectively. To enhance the detection abilities of the two schemes in monitoring all kinds of shifts in Poisson count data, this study examines the performance of combined applications of the Shewhart, and EWMA Poisson control charts. Furthermore, the study proposes modifications based on well-structured statistical data collection technique, ranked set sampling (RSS), to detect shifts in the mean of a Poisson process more quickly. The relative performance of the proposed Shewhart-EWMA Poisson location charts is evaluated in terms of the average run length (ARL), standard deviation of the run length (SDRL), median run length (MRL), average ratio ARL (ARARL), average extra quadratic loss (AEQL) and performance comparison index (PCI). Consequently, all the new Poisson control charts based on RSS method are generally more superior than most of the existing schemes for monitoring Poisson processes. The use of these combined Shewhart-EWMA Poisson charts is illustrated with an example to demonstrate the practical implementation of the design procedure.

Comment on: 'A Poisson resampling method for simulating reduced counts in nuclear medicine images'.

PubMed

de Nijs, Robin

2015-07-21

In order to be able to calculate half-count images from already acquired data, White and Lawson published their method based on Poisson resampling. They verified their method experimentally by measurements with a Co-57 flood source. In this comment their results are reproduced and confirmed by a direct numerical simulation in Matlab. Not only Poisson resampling, but also two direct redrawing methods were investigated. Redrawing methods were based on a Poisson and a Gaussian distribution. Mean, standard deviation, skewness and excess kurtosis half-count/full-count ratios were determined for all methods, and compared to the theoretical values for a Poisson distribution. Statistical parameters showed the same behavior as in the original note and showed the superiority of the Poisson resampling method. Rounding off before saving of the half count image had a severe impact on counting statistics for counts below 100. Only Poisson resampling was not affected by this, while Gaussian redrawing was less affected by it than Poisson redrawing. Poisson resampling is the method of choice, when simulating half-count (or less) images from full-count images. It simulates correctly the statistical properties, also in the case of rounding off of the images.

A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

1997-01-01

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.

Parallel VLSI architecture emulation and the organization of APSA/MPP

NASA Technical Reports Server (NTRS)

Odonnell, John T.

1987-01-01

The Applicative Programming System Architecture (APSA) combines an applicative language interpreter with a novel parallel computer architecture that is well suited for Very Large Scale Integration (VLSI) implementation. The Massively Parallel Processor (MPP) can simulate VLSI circuits by allocating one processing element in its square array to an area on a square VLSI chip. As long as there are not too many long data paths, the MPP can simulate a VLSI clock cycle very rapidly. The APSA circuit contains a binary tree with a few long paths and many short ones. A skewed H-tree layout allows every processing element to simulate a leaf cell and up to four tree nodes, with no loss in parallelism. Emulation of a key APSA algorithm on the MPP resulted in performance 16,000 times faster than a Vax. This speed will make it possible for the APSA language interpreter to run fast enough to support research in parallel list processing algorithms.

Deformation, crystal preferred orientations, and seismic anisotropy in the Earth's D″ layer

NASA Astrophysics Data System (ADS)

Tommasi, Andréa; Goryaeva, Alexandra; Carrez, Philippe; Cordier, Patrick; Mainprice, David

2018-06-01

We use a forward multiscale model that couples atomistic modeling of intracrystalline plasticity mechanisms (dislocation glide ± twinning) in MgSiO3 post-perovskite (PPv) and periclase (MgO) at lower mantle pressures and temperatures to polycrystal plasticity simulations to predict crystal preferred orientations (CPO) development and seismic anisotropy in D″. We model the CPO evolution in aggregates of 70% PPv and 30% MgO submitted to simple shear, axial shortening, and along corner-flow streamlines, which simulate changes in flow orientation similar to those expected at the transition between a downwelling and flow parallel to the core-mantle boundary (CMB) within D″ or between CMB-parallel flow and upwelling at the borders of the large low shear wave velocity provinces (LLSVP) in the lowermost mantle. Axial shortening results in alignment of PPv [010] axes with the shortening direction. Simple shear produces PPv CPO with a monoclinic symmetry that rapidly rotates towards parallelism between the dominant [100](010) slip system and the macroscopic shear. These predictions differ from MgSiO3 post-perovskite textures formed in diamond-anvil cell experiments, but agree with those obtained in simple shear and compression experiments using CaIrO3 post-perovskite. Development of CPO in PPv and MgO results in seismic anisotropy in D″. For shear parallel to the CMB, at low strain, the inclination of ScS, Sdiff, and SKKS fast polarizations and delay times vary depending on the propagation direction. At moderate and high shear strains, all S-waves are polarized nearly horizontally. Downwelling flow produces Sdiff, ScS, and SKKS fast polarization directions and birefringence that vary gradually as a function of the back-azimuth from nearly parallel to inclined by up to 70° to CMB and from null to ∼5%. Change in the flow to shear parallel to the CMB results in dispersion of the CPO, weakening of the anisotropy, and strong azimuthal variation of the S-wave splitting up to 250 km from the corner. Transition from horizontal shear to upwelling also produces weakening of the CPO and complex seismic anisotropy patterns, with dominantly inclined fast ScS and SKKS polarizations, over most of the upwelling path. Models that take into account twinning in PPv explain most observations of seismic anisotropy in D″, but heterogeneity of the flow at scales <1000 km is needed to comply with the seismological evidence for low apparent birefringence in D″.

Systematic design of 3D auxetic lattice materials with programmable Poisson's ratio for finite strains

NASA Astrophysics Data System (ADS)

Wang, Fengwen

2018-05-01

This paper presents a systematic approach for designing 3D auxetic lattice materials, which exhibit constant negative Poisson's ratios over large strain intervals. A unit cell model mimicking tensile tests is established and based on the proposed model, the secant Poisson's ratio is defined as the negative ratio between the lateral and the longitudinal engineering strains. The optimization problem for designing a material unit cell with a target Poisson's ratio is formulated to minimize the average lateral engineering stresses under the prescribed deformations. Numerical results demonstrate that 3D auxetic lattice materials with constant Poisson's ratios can be achieved by the proposed optimization formulation and that two sets of material architectures are obtained by imposing different symmetry on the unit cell. Moreover, inspired by the topology-optimized material architecture, a subsequent shape optimization is proposed by parametrizing material architectures using super-ellipsoids. By designing two geometrical parameters, simple optimized material microstructures with different target Poisson's ratios are obtained. By interpolating these two parameters as polynomial functions of Poisson's ratios, material architectures for any Poisson's ratio in the interval of ν ∈ [ - 0.78 , 0.00 ] are explicitly presented. Numerical evaluations show that interpolated auxetic lattice materials exhibit constant Poisson's ratios in the target strain interval of [0.00, 0.20] and that 3D auxetic lattice material architectures with programmable Poisson's ratio are achievable.

Nonlinear Poisson equation for heterogeneous media.

PubMed

Hu, Langhua; Wei, Guo-Wei

2012-08-22

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Revisiting Parallel Cyclic Reduction and Parallel Prefix-Based Algorithms for Block Tridiagonal System of Equations

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

Seal, Sudip K; Perumalla, Kalyan S; Hirshman, Steven Paul

2013-01-01

Simulations that require solutions of block tridiagonal systems of equations rely on fast parallel solvers for runtime efficiency. Leading parallel solvers that are highly effective for general systems of equations, dense or sparse, are limited in scalability when applied to block tridiagonal systems. This paper presents scalability results as well as detailed analyses of two parallel solvers that exploit the special structure of block tridiagonal matrices to deliver superior performance, often by orders of magnitude. A rigorous analysis of their relative parallel runtimes is shown to reveal the existence of a critical block size that separates the parameter space spannedmore » by the number of block rows, the block size and the processor count, into distinct regions that favor one or the other of the two solvers. Dependence of this critical block size on the above parameters as well as on machine-specific constants is established. These formal insights are supported by empirical results on up to 2,048 cores of a Cray XT4 system. To the best of our knowledge, this is the highest reported scalability for parallel block tridiagonal solvers to date.« less

Decomposition method for fast computation of gigapixel-sized Fresnel holograms on a graphics processing unit cluster.

PubMed

Jackin, Boaz Jessie; Watanabe, Shinpei; Ootsu, Kanemitsu; Ohkawa, Takeshi; Yokota, Takashi; Hayasaki, Yoshio; Yatagai, Toyohiko; Baba, Takanobu

2018-04-20

A parallel computation method for large-size Fresnel computer-generated hologram (CGH) is reported. The method was introduced by us in an earlier report as a technique for calculating Fourier CGH from 2D object data. In this paper we extend the method to compute Fresnel CGH from 3D object data. The scale of the computation problem is also expanded to 2 gigapixels, making it closer to real application requirements. The significant feature of the reported method is its ability to avoid communication overhead and thereby fully utilize the computing power of parallel devices. The method exhibits three layers of parallelism that favor small to large scale parallel computing machines. Simulation and optical experiments were conducted to demonstrate the workability and to evaluate the efficiency of the proposed technique. A two-times improvement in computation speed has been achieved compared to the conventional method, on a 16-node cluster (one GPU per node) utilizing only one layer of parallelism. A 20-times improvement in computation speed has been estimated utilizing two layers of parallelism on a very large-scale parallel machine with 16 nodes, where each node has 16 GPUs.

Unimodularity criteria for Poisson structures on foliated manifolds

NASA Astrophysics Data System (ADS)

Pedroza, Andrés; Velasco-Barreras, Eduardo; Vorobiev, Yury

2018-03-01

We study the behavior of the modular class of an orientable Poisson manifold and formulate some unimodularity criteria in the semilocal context, around a (singular) symplectic leaf. Our results generalize some known unimodularity criteria for regular Poisson manifolds related to the notion of the Reeb class. In particular, we show that the unimodularity of the transverse Poisson structure of the leaf is a necessary condition for the semilocal unimodular property. Our main tool is an explicit formula for a bigraded decomposition of modular vector fields of a coupling Poisson structure on a foliated manifold. Moreover, we also exploit the notion of the modular class of a Poisson foliation and its relationship with the Reeb class.

Parallel equilibrium current effect on existence of reversed shear Alfvén eigenmodes

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

Xie, Hua-sheng, E-mail: huashengxie@gmail.com; Xiao, Yong, E-mail: yxiao@zju.edu.cn

2015-02-15

A new fast global eigenvalue code, where the terms are segregated according to their physics contents, is developed to study Alfvén modes in tokamak plasmas, particularly, the reversed shear Alfvén eigenmode (RSAE). Numerical calculations show that the parallel equilibrium current corresponding to the kink term is strongly unfavorable for the existence of the RSAE. An improved criterion for the RSAE existence is given for with and without the parallel equilibrium current. In the limits of ideal magnetohydrodynamics (MHD) and zero-pressure, the toroidicity effect is the main possible favorable factor for the existence of the RSAE, which is however usually small.more » This suggests that it is necessary to include additional physics such as kinetic term in the MHD model to overcome the strong unfavorable effect of the parallel current in order to enable the existence of RSAE.« less

Mantle flow through a tear in the Nazca slab inferred from shear wave splitting

NASA Astrophysics Data System (ADS)

Lynner, Colton; Anderson, Megan L.; Portner, Daniel E.; Beck, Susan L.; Gilbert, Hersh

2017-07-01

A tear in the subducting Nazca slab is located between the end of the Pampean flat slab and normally subducting oceanic lithosphere. Tomographic studies suggest mantle material flows through this opening. The best way to probe this hypothesis is through observations of seismic anisotropy, such as shear wave splitting. We examine patterns of shear wave splitting using data from two seismic deployments in Argentina that lay updip of the slab tear. We observe a simple pattern of plate-motion-parallel fast splitting directions, indicative of plate-motion-parallel mantle flow, beneath the majority of the stations. Our observed splitting contrasts previous observations to the north and south of the flat slab region. Since plate-motion-parallel splitting occurs only coincidentally with the slab tear, we propose mantle material flows through the opening resulting in Nazca plate-motion-parallel flow in both the subslab mantle and mantle wedge.

Symplectic molecular dynamics simulations on specially designed parallel computers.

PubMed

Borstnik, Urban; Janezic, Dusanka

2005-01-01

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Fast parallel 3D profilometer with DMD technology

NASA Astrophysics Data System (ADS)

Hou, Wenmei; Zhang, Yunbo

2011-12-01

Confocal microscope has been a powerful tool for three-dimensional profile analysis. Single mode confocal microscope is limited by scanning speed. This paper presents a 3D profilometer prototype of parallel confocal microscope based on DMD (Digital Micromirror Device). In this system the DMD takes the place of Nipkow Disk which is a classical parallel scanning scheme to realize parallel lateral scanning technique. Operated with certain pattern, the DMD generates a virtual pinholes array which separates the light into multi-beams. The key parameters that affect the measurement (pinhole size and the lateral scanning distance) can be configured conveniently by different patterns sent to DMD chip. To avoid disturbance between two virtual pinholes working at the same time, a scanning strategy is adopted. Depth response curve both axial and abaxial were extract. Measurement experiments have been carried out on silicon structured sample, and axial resolution of 55nm is achieved.

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

PubMed Central

Farreras, Montse

2014-01-01

Abstract The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes. PMID:24597675

Parallelization and automatic data distribution for nuclear reactor simulations

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

Liebrock, L.M.

1997-07-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directlymore » affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.« less

A Massively Parallel Code for Polarization Calculations

NASA Astrophysics Data System (ADS)

Akiyama, Shizuka; Höflich, Peter

2001-03-01

We present an implementation of our Monte-Carlo radiation transport method for rapidly expanding, NLTE atmospheres for massively parallel computers which utilizes both the distributed and shared memory models. This allows us to take full advantage of the fast communication and low latency inherent to nodes with multiple CPUs, and to stretch the limits of scalability with the number of nodes compared to a version which is based on the shared memory model. Test calculations on a local 20-node Beowulf cluster with dual CPUs showed an improved scalability by about 40%.

One-step trinary signed-digit arithmetic using an efficient encoding scheme

NASA Astrophysics Data System (ADS)

Salim, W. Y.; Fyath, R. S.; Ali, S. A.; Alam, Mohammad S.

2000-11-01

The trinary signed-digit (TSD) number system is of interest for ultra fast optoelectronic computing systems since it permits parallel carry-free addition and borrow-free subtraction of two arbitrary length numbers in constant time. In this paper, a simple coding scheme is proposed to encode the decimal number directly into the TSD form. The coding scheme enables one to perform parallel one-step TSD arithmetic operation. The proposed coding scheme uses only a 5-combination coding table instead of the 625-combination table reported recently for recoded TSD arithmetic technique.

Simulation of 2D Kinetic Effects in Plasmas using the Grid Based Continuum Code LOKI

NASA Astrophysics Data System (ADS)

Banks, Jeffrey; Berger, Richard; Chapman, Tom; Brunner, Stephan

2016-10-01

Kinetic simulation of multi-dimensional plasma waves through direct discretization of the Vlasov equation is a useful tool to study many physical interactions and is particularly attractive for situations where minimal fluctuation levels are desired, for instance, when measuring growth rates of plasma wave instabilities. However, direct discretization of phase space can be computationally expensive, and as a result there are few examples of published results using Vlasov codes in more than a single configuration space dimension. In an effort to fill this gap we have developed the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The code is designed to reduce the cost of phase-space computation by using fully 4th order accurate conservative finite differencing, while retaining excellent parallel scalability that efficiently uses large scale computing resources. In this poster I will discuss the algorithms used in the code as well as some aspects of their parallel implementation using MPI. I will also overview simulation results of basic plasma wave instabilities relevant to laser plasma interaction, which have been obtained using the code.

Stationary and non-stationary occurrences of miniature end plate potentials are well described as stationary and non-stationary Poisson processes in the mollusc Navanax inermis.

PubMed

Cappell, M S; Spray, D C; Bennett, M V

1988-06-28

Protractor muscles in the gastropod mollusc Navanax inermis exhibit typical spontaneous miniature end plate potentials with mean amplitude 1.71 +/- 1.19 (standard deviation) mV. The evoked end plate potential is quantized, with a quantum equal to the miniature end plate potential amplitude. When their rate is stationary, occurrence of miniature end plate potentials is a random, Poisson process. When non-stationary, spontaneous miniature end plate potential occurrence is a non-stationary Poisson process, a Poisson process with the mean frequency changing with time. This extends the random Poisson model for miniature end plate potentials to the frequently observed non-stationary occurrence. Reported deviations from a Poisson process can sometimes be accounted for by the non-stationary Poisson process and more complex models, such as clustered release, are not always needed.

A test of inflated zeros for Poisson regression models.

PubMed

He, Hua; Zhang, Hui; Ye, Peng; Tang, Wan

2017-01-01

Excessive zeros are common in practice and may cause overdispersion and invalidate inference when fitting Poisson regression models. There is a large body of literature on zero-inflated Poisson models. However, methods for testing whether there are excessive zeros are less well developed. The Vuong test comparing a Poisson and a zero-inflated Poisson model is commonly applied in practice. However, the type I error of the test often deviates seriously from the nominal level, rendering serious doubts on the validity of the test in such applications. In this paper, we develop a new approach for testing inflated zeros under the Poisson model. Unlike the Vuong test for inflated zeros, our method does not require a zero-inflated Poisson model to perform the test. Simulation studies show that when compared with the Vuong test our approach not only better at controlling type I error rate, but also yield more power.

Neighbourhood food and physical activity environments in England, UK: does ethnic density matter?

PubMed Central

2012-01-01

Background In England, obesity is more common in some ethnic minority groups than in Whites. This study examines the relationship between ethnic concentration and access to fast food outlets, supermarkets and physical activity facilities. Methods Data on ethnic concentration, fast food outlets, supermarkets and physical activity facilities were obtained at the lower super output area (LSOA) (population average of 1500). Poisson multilevel modelling was used to examine the association between own ethnic concentration and facilities, adjusted for area deprivation, urbanicity, population size and clustering of LSOAs within local authority areas. Results There was a higher proportion of ethnic minorities residing in areas classified as most deprived. Fast food outlets and supermarkets were more common and outdoor physical activity facilities were less common in most than least deprived areas. A gradient was not observed for the relationship between indoor physical activity facilities and area deprivation quintiles. In contrast to White British, increasing ethnic minority concentration was associated with increasing rates of fast food outlets. Rate ratios comparing rates of fast food outlets in high with those in low level of ethnic concentration ranged between 1.28, 95% confidence interval 1.06-1.55 (Bangladeshi) and 2.62, 1.46-4.70 (Chinese). Similar to White British, however, increasing ethnic minority concentration was associated with increasing rate of supermarkets and indoor physical activity facilities. Outdoor physical activity facilities were less likely to be in high than low ethnic concentration areas for some minority groups. Conclusions Overall, ethnic minority concentration was associated with a mixture of both advantages and disadvantages in the provision of food outlets and physical activity facilities. These issues might contribute to ethnic differences in food choices and engagement in physical activity. PMID:22709527

Neighbourhood food and physical activity environments in England, UK: does ethnic density matter?

PubMed

Molaodi, Oarabile R; Leyland, Alastair H; Ellaway, Anne; Kearns, Ade; Harding, Seeromanie

2012-06-18

In England, obesity is more common in some ethnic minority groups than in Whites. This study examines the relationship between ethnic concentration and access to fast food outlets, supermarkets and physical activity facilities. Data on ethnic concentration, fast food outlets, supermarkets and physical activity facilities were obtained at the lower super output area (LSOA) (population average of 1500). Poisson multilevel modelling was used to examine the association between own ethnic concentration and facilities, adjusted for area deprivation, urbanicity, population size and clustering of LSOAs within local authority areas. There was a higher proportion of ethnic minorities residing in areas classified as most deprived. Fast food outlets and supermarkets were more common and outdoor physical activity facilities were less common in most than least deprived areas. A gradient was not observed for the relationship between indoor physical activity facilities and area deprivation quintiles. In contrast to White British, increasing ethnic minority concentration was associated with increasing rates of fast food outlets. Rate ratios comparing rates of fast food outlets in high with those in low level of ethnic concentration ranged between 1.28, 95% confidence interval 1.06-1.55 (Bangladeshi) and 2.62, 1.46-4.70 (Chinese). Similar to White British, however, increasing ethnic minority concentration was associated with increasing rate of supermarkets and indoor physical activity facilities. Outdoor physical activity facilities were less likely to be in high than low ethnic concentration areas for some minority groups. Overall, ethnic minority concentration was associated with a mixture of both advantages and disadvantages in the provision of food outlets and physical activity facilities. These issues might contribute to ethnic differences in food choices and engagement in physical activity.

Calculation of the Poisson cumulative distribution function

NASA Technical Reports Server (NTRS)

Bowerman, Paul N.; Nolty, Robert G.; Scheuer, Ernest M.

1990-01-01

A method for calculating the Poisson cdf (cumulative distribution function) is presented. The method avoids computer underflow and overflow during the process. The computer program uses this technique to calculate the Poisson cdf for arbitrary inputs. An algorithm that determines the Poisson parameter required to yield a specified value of the cdf is presented.

Poisson's Ratio of a Hyperelastic Foam Under Quasi-static and Dynamic Loading

DOE PAGES

Sanborn, Brett; Song, Bo

2018-06-03

Poisson's ratio is a material constant representing compressibility of material volume. However, when soft, hyperelastic materials such as silicone foam are subjected to large deformation into densification, the Poisson's ratio may rather significantly change, which warrants careful consideration in modeling and simulation of impact/shock mitigation scenarios where foams are used as isolators. The evolution of Poisson's ratio of silicone foam materials has not yet been characterized, particularly under dynamic loading. In this study, radial and axial measurements of specimen strain are conducted simultaneously during quasi-static and dynamic compression tests to determine the Poisson's ratio of silicone foam. The Poisson's ratiomore » of silicone foam exhibited a transition from compressible to nearly incompressible at a threshold strain that coincided with the onset of densification in the material. Poisson's ratio as a function of engineering strain was different at quasi-static and dynamic rates. Here, the Poisson's ratio behavior is presented and can be used to improve constitutive modeling of silicone foams subjected to a broad range of mechanical loading.« less

Poisson's Ratio of a Hyperelastic Foam Under Quasi-static and Dynamic Loading

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

Sanborn, Brett; Song, Bo

Poisson's ratio is a material constant representing compressibility of material volume. However, when soft, hyperelastic materials such as silicone foam are subjected to large deformation into densification, the Poisson's ratio may rather significantly change, which warrants careful consideration in modeling and simulation of impact/shock mitigation scenarios where foams are used as isolators. The evolution of Poisson's ratio of silicone foam materials has not yet been characterized, particularly under dynamic loading. In this study, radial and axial measurements of specimen strain are conducted simultaneously during quasi-static and dynamic compression tests to determine the Poisson's ratio of silicone foam. The Poisson's ratiomore » of silicone foam exhibited a transition from compressible to nearly incompressible at a threshold strain that coincided with the onset of densification in the material. Poisson's ratio as a function of engineering strain was different at quasi-static and dynamic rates. Here, the Poisson's ratio behavior is presented and can be used to improve constitutive modeling of silicone foams subjected to a broad range of mechanical loading.« less

A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Kinetic-scale fluctuations resolved with the Fast Plasma Investigation on NASA's Magnetospheric Multiscale mission.

NASA Astrophysics Data System (ADS)

Gershman, D. J.; Figueroa-Vinas, A.; Dorelli, J.; Goldstein, M. L.; Shuster, J. R.; Avanov, L. A.; Boardsen, S. A.; Stawarz, J. E.; Schwartz, S. J.; Schiff, C.; Lavraud, B.; Saito, Y.; Paterson, W. R.; Giles, B. L.; Pollock, C. J.; Strangeway, R. J.; Russell, C. T.; Torbert, R. B.; Moore, T. E.; Burch, J. L.

2017-12-01

Measurements from the Fast Plasma Investigation (FPI) on NASA's Magnetospheric Multiscale (MMS) mission have enabled unprecedented analyses of kinetic-scale plasma physics. FPI regularly provides estimates of current density and pressure gradients of sufficient accuracy to evaluate the relative contribution of terms in plasma equations of motion. In addition, high-resolution three-dimensional velocity distribution functions of both ions and electrons provide new insights into kinetic-scale processes. As an example, for a monochromatic kinetic Alfven wave (KAW) we find non-zero, but out-of-phase parallel current density and electric field fluctuations, providing direct confirmation of the conservative energy exchange between the wave field and particles. In addition, we use fluctuations in current density and magnetic field to calculate the perpendicular and parallel wavelengths of the KAW. Furthermore, examination of the electron velocity distribution inside the KAW reveals a population of electrons non-linearly trapped in the kinetic-scale magnetic mirror formed between successive wave peaks. These electrons not only contribute to the wave's parallel electric field but also account for over half of the density fluctuations within the wave, supplying an unexpected mechanism for maintaining quasi-neutrality in a KAW. Finally, we demonstrate that the employed wave vector determination technique is also applicable to broadband fluctuations found in Earth's turbulent magnetosheath.

Comparison of temporal and spectral scattering methods using acoustically large breast models derived from magnetic resonance images.

PubMed

Hesford, Andrew J; Tillett, Jason C; Astheimer, Jeffrey P; Waag, Robert C

2014-08-01

Accurate and efficient modeling of ultrasound propagation through realistic tissue models is important to many aspects of clinical ultrasound imaging. Simplified problems with known solutions are often used to study and validate numerical methods. Greater confidence in a time-domain k-space method and a frequency-domain fast multipole method is established in this paper by analyzing results for realistic models of the human breast. Models of breast tissue were produced by segmenting magnetic resonance images of ex vivo specimens into seven distinct tissue types. After confirming with histologic analysis by pathologists that the model structures mimicked in vivo breast, the tissue types were mapped to variations in sound speed and acoustic absorption. Calculations of acoustic scattering by the resulting model were performed on massively parallel supercomputer clusters using parallel implementations of the k-space method and the fast multipole method. The efficient use of these resources was confirmed by parallel efficiency and scalability studies using large-scale, realistic tissue models. Comparisons between the temporal and spectral results were performed in representative planes by Fourier transforming the temporal results. An RMS field error less than 3% throughout the model volume confirms the accuracy of the methods for modeling ultrasound propagation through human breast.

Improved preconditioned conjugate gradient algorithm and application in 3D inversion of gravity-gradiometry data

NASA Astrophysics Data System (ADS)

Wang, Tai-Han; Huang, Da-Nian; Ma, Guo-Qing; Meng, Zhao-Hai; Li, Ye

2017-06-01

With the continuous development of full tensor gradiometer (FTG) measurement techniques, three-dimensional (3D) inversion of FTG data is becoming increasingly used in oil and gas exploration. In the fast processing and interpretation of large-scale high-precision data, the use of the graphics processing unit process unit (GPU) and preconditioning methods are very important in the data inversion. In this paper, an improved preconditioned conjugate gradient algorithm is proposed by combining the symmetric successive over-relaxation (SSOR) technique and the incomplete Choleksy decomposition conjugate gradient algorithm (ICCG). Since preparing the preconditioner requires extra time, a parallel implement based on GPU is proposed. The improved method is then applied in the inversion of noisecontaminated synthetic data to prove its adaptability in the inversion of 3D FTG data. Results show that the parallel SSOR-ICCG algorithm based on NVIDIA Tesla C2050 GPU achieves a speedup of approximately 25 times that of a serial program using a 2.0 GHz Central Processing Unit (CPU). Real airborne gravity-gradiometry data from Vinton salt dome (southwest Louisiana, USA) are also considered. Good results are obtained, which verifies the efficiency and feasibility of the proposed parallel method in fast inversion of 3D FTG data.

Modeling electrokinetics in ionic liquids: General

DOE PAGES

Wang, Chao; Bao, Jie; Pan, Wenxiao; ...

2017-04-01

Using direct numerical simulations, we provide a thorough study regarding the electrokinetics of ionic liquids. In particular, modified Poisson–Nernst–Planck equations are solved to capture the crowding and overscreening effects characteristic of an ionic liquid. For modeling electrokinetic flows in an ionic liquid, the modified Poisson-Nernst-Planck equations are coupled with Navier–Stokes equations to study the coupling of ion transport, hydrodynamics, and electrostatic forces. Specifically, we consider the ion transport between two parallel charged surfaces, charging dynamics in a nanopore, capacitance of electric double-layer capacitors, electroosmotic flow in a nanochannel, electroconvective instability on a plane ion-selective surface, and electroconvective flow on amore » curved ionselective surface. Lastly, we also discuss how crowding and overscreening and their interplay affect the electrokinetic behaviors of ionic liquids in these application problems.« less

Imfit: A Fast, Flexible Program for Astronomical Image Fitting

NASA Astrophysics Data System (ADS)

Erwin, Peter

2014-08-01

Imift is an open-source astronomical image-fitting program specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. Its object-oriented design allows new types of image components (2D surface-brightness functions) to be easily written and added to the program. Image functions provided with Imfit include Sersic, exponential, and Gaussian galaxy decompositions along with Core-Sersic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through 3D luminosity-density models of disks and rings seen at arbitrary inclinations. Available minimization algorithms include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard chi^2 statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or the Cash statistic; the latter is particularly appropriate for cases of Poisson data in the low-count regime. The C++ source code for Imfit is available under the GNU Public License.

MMPP Traffic Generator for the Testing of the SCAR 2 Fast Packet Switch

NASA Technical Reports Server (NTRS)

Chren, William A., Jr.

1995-01-01

A prototype MWP Traffic Generator (TG) has been designed for testing of the COMSAT-supplied SCAR II Fast Packet Switch. By generating packets distributed according to a Markov-Modulated Poisson Process (MMPP) model. it allows the assessment of the switch performance under traffic conditions that are more realistic than could be generated using the COMSAT-supplied Traffic Generator Module. The MMPP model is widely believed to model accurately real-world superimposed voice and data communications traffic. The TG was designed to be as much as possible of a "drop-in" replacement for the COMSAT Traffic Generator Module. The latter fit on two Altera EPM7256EGC 192-pin CPLDs and produced traffic for one switch input port. No board changes are necessary because it has been partitioned to use the existing board traces. The TG, consisting of parts "TGDATPROC" and "TGRAMCTL" must merely be reprogrammed into the Altera devices of the same name. However, the 040 controller software must be modified to provide TG initialization data. This data will be given in Section II.

Mechanism of formation of subnanosecond current front in high-voltage pulse open discharge

NASA Astrophysics Data System (ADS)

Schweigert, I. V.; Alexandrov, A. L.; Zakrevsky, Dm. E.; Bokhan, P. A.

2014-11-01

The mechanism of subnanosecond current front rise observed previously in the experiment in high-voltage pulse open discharge in helium is studied in kinetic particle-in-cell simulations. The Boltzmann equations for electrons, ions, and fast atoms are solved self-consistently with the Poisson equations for the electrical potential. The partial contributions to the secondary electron emission from the ions, fast atoms, photons, and electrons, bombarding the electrode, are calculated. In simulations, as in the experiment, the discharge glows between two symmetrical cathodes and the anode grid in the midplane at P =6 Torr and the applied voltage of 20 kV. The electron avalanche development is considered for two experimental situations during the last stage of breakdown: (i) with constant voltage and (ii) with decreasing voltage. For case (i), the subnanosecond current front rise is set by photons from the collisional excitation transfer reactions. For the case (ii), the energetic electrons swamp the cathode during voltage drop and provide the secondary electron emission for the subnanosecond current rise, observed in the experiment.

Two-dimensional hybrid Monte Carlo–fluid modelling of dc glow discharges: Comparison with fluid models, reliability, and accuracy

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

Eylenceoğlu, E.; Rafatov, I., E-mail: rafatov@metu.edu.tr; Kudryavtsev, A. A.

2015-01-15

Two-dimensional hybrid Monte Carlo–fluid numerical code is developed and applied to model the dc glow discharge. The model is based on the separation of electrons into two parts: the low energetic (slow) and high energetic (fast) electron groups. Ions and slow electrons are described within the fluid model using the drift-diffusion approximation for particle fluxes. Fast electrons, represented by suitable number of super particles emitted from the cathode, are responsible for ionization processes in the discharge volume, which are simulated by the Monte Carlo collision method. Electrostatic field is obtained from the solution of Poisson equation. The test calculations weremore » carried out for an argon plasma. Main properties of the glow discharge are considered. Current-voltage curves, electric field reversal phenomenon, and the vortex current formation are developed and discussed. The results are compared to those obtained from the simple and extended fluid models. Contrary to reports in the literature, the analysis does not reveal significant advantages of existing hybrid methods over the extended fluid model.« less

Application of the Hyper-Poisson Generalized Linear Model for Analyzing Motor Vehicle Crashes.

PubMed

Khazraee, S Hadi; Sáez-Castillo, Antonio Jose; Geedipally, Srinivas Reddy; Lord, Dominique

2015-05-01

The hyper-Poisson distribution can handle both over- and underdispersion, and its generalized linear model formulation allows the dispersion of the distribution to be observation-specific and dependent on model covariates. This study's objective is to examine the potential applicability of a newly proposed generalized linear model framework for the hyper-Poisson distribution in analyzing motor vehicle crash count data. The hyper-Poisson generalized linear model was first fitted to intersection crash data from Toronto, characterized by overdispersion, and then to crash data from railway-highway crossings in Korea, characterized by underdispersion. The results of this study are promising. When fitted to the Toronto data set, the goodness-of-fit measures indicated that the hyper-Poisson model with a variable dispersion parameter provided a statistical fit as good as the traditional negative binomial model. The hyper-Poisson model was also successful in handling the underdispersed data from Korea; the model performed as well as the gamma probability model and the Conway-Maxwell-Poisson model previously developed for the same data set. The advantages of the hyper-Poisson model studied in this article are noteworthy. Unlike the negative binomial model, which has difficulties in handling underdispersed data, the hyper-Poisson model can handle both over- and underdispersed crash data. Although not a major issue for the Conway-Maxwell-Poisson model, the effect of each variable on the expected mean of crashes is easily interpretable in the case of this new model. © 2014 Society for Risk Analysis.

Catastrophic onset of fast magnetic reconnection with a guide field

NASA Astrophysics Data System (ADS)

Cassak, P. A.; Drake, J. F.; Shay, M. A.

2007-05-01

It was recently shown that the slow (collisional) Sweet-Parker and the fast (collisionless) Hall magnetic reconnection solutions simultaneously exist for a wide range of resistivities; reconnection is bistable [Cassak, Shay, and Drake, Phys. Rev. Lett., 95, 235002 (2005)]. When the thickness of the dissipation region becomes smaller than a critical value, the Sweet-Parker solution disappears and fast reconnection ensues, potentially explaining how large amounts of magnetic free energy can accrue without significant release before the onset of fast reconnection. Two-fluid numerical simulations extending the previous results for anti-parallel reconnection (where the critical thickness is the ion skin depth) to component reconnection with a large guide field (where the critical thickness is the thermal ion Larmor radius) are presented. Applications to laboratory experiments of magnetic reconnection and the sawtooth crash are discussed.

GRAPE- TWO-DIMENSIONAL GRIDS ABOUT AIRFOILS AND OTHER SHAPES BY THE USE OF POISSON'S EQUATION

NASA Technical Reports Server (NTRS)

Sorenson, R. L.

1994-01-01

The ability to treat arbitrary boundary shapes is one of the most desirable characteristics of a method for generating grids, including those about airfoils. In a grid used for computing aerodynamic flow over an airfoil, or any other body shape, the surface of the body is usually treated as an inner boundary and often cannot be easily represented as an analytic function. The GRAPE computer program was developed to incorporate a method for generating two-dimensional finite-difference grids about airfoils and other shapes by the use of the Poisson differential equation. GRAPE can be used with any boundary shape, even one specified by tabulated points and including a limited number of sharp corners. The GRAPE program has been developed to be numerically stable and computationally fast. GRAPE can provide the aerodynamic analyst with an efficient and consistent means of grid generation. The GRAPE procedure generates a grid between an inner and an outer boundary by utilizing an iterative procedure to solve the Poisson differential equation subject to geometrical restraints. In this method, the inhomogeneous terms of the equation are automatically chosen such that two important effects are imposed on the grid. The first effect is control of the spacing between mesh points along mesh lines intersecting the boundaries. The second effect is control of the angles with which mesh lines intersect the boundaries. Along with the iterative solution to Poisson's equation, a technique of coarse-fine sequencing is employed to accelerate numerical convergence. GRAPE program control cards and input data are entered via the NAMELIST feature. Each variable has a default value such that user supplied data is kept to a minimum. Basic input data consists of the boundary specification, mesh point spacings on the boundaries, and mesh line angles at the boundaries. Output consists of a dataset containing the grid data and, if requested, a plot of the generated mesh. The GRAPE program is written in FORTRAN IV for batch execution and has been implemented on a CDC 6000 series computer with a central memory requirement of approximately 135K (octal) of 60 bit words. For plotted output the commercially available DISSPLA graphics software package is required. The GRAPE program was developed in 1980.

A Martingale Characterization of Mixed Poisson Processes.

DTIC Science & Technology

1985-10-01

03LA A 11. TITLE (Inciuae Security Clanafication, ",A martingale characterization of mixed Poisson processes " ________________ 12. PERSONAL AUTHOR... POISSON PROCESSES Jostification .......... . ... . . Di.;t ib,,jtion by Availability Codes Dietmar Pfeifer* Technical University Aachen Dist Special and...Mixed Poisson processes play an important role in many branches of applied probability, for instance in insurance mathematics and physics (see Albrecht

Generation of Non-Homogeneous Poisson Processes by Thinning: Programming Considerations and Comparision with Competing Algorithms.

DTIC Science & Technology

1978-12-01

Poisson processes . The method is valid for Poisson processes with any given intensity function. The basic thinning algorithm is modified to exploit several refinements which reduce computer execution time by approximately one-third. The basic and modified thinning programs are compared with the Poisson decomposition and gap-statistics algorithm, which is easily implemented for Poisson processes with intensity functions of the form exp(a sub 0 + a sub 1t + a sub 2 t-squared. The thinning programs are competitive in both execution

Deformation mechanisms in negative Poisson's ratio materials - Structural aspects

NASA Technical Reports Server (NTRS)

Lakes, R.

1991-01-01

Poisson's ratio in materials is governed by the following aspects of the microstructure: the presence of rotational degrees of freedom, non-affine deformation kinematics, or anisotropic structure. Several structural models are examined. The non-affine kinematics are seen to be essential for the production of negative Poisson's ratios for isotropic materials containing central force linkages of positive stiffness. Non-central forces combined with pre-load can also give rise to a negative Poisson's ratio in isotropic materials. A chiral microstructure with non-central force interaction or non-affine deformation can also exhibit a negative Poisson's ratio. Toughness and damage resistance in these materials may be affected by the Poisson's ratio itself, as well as by generalized continuum aspects associated with the microstructure.

Exact solution for the Poisson field in a semi-infinite strip.

PubMed

Cohen, Yossi; Rothman, Daniel H

2017-04-01

The Poisson equation is associated with many physical processes. Yet exact analytic solutions for the two-dimensional Poisson field are scarce. Here we derive an analytic solution for the Poisson equation with constant forcing in a semi-infinite strip. We provide a method that can be used to solve the field in other intricate geometries. We show that the Poisson flux reveals an inverse square-root singularity at a tip of a slit, and identify a characteristic length scale in which a small perturbation, in a form of a new slit, is screened by the field. We suggest that this length scale expresses itself as a characteristic spacing between tips in real Poisson networks that grow in response to fluxes at tips.

GPU-based ultra-fast dose calculation using a finite size pencil beam model.

PubMed

Gu, Xuejun; Choi, Dongju; Men, Chunhua; Pan, Hubert; Majumdar, Amitava; Jiang, Steve B

2009-10-21

Online adaptive radiation therapy (ART) is an attractive concept that promises the ability to deliver an optimal treatment in response to the inter-fraction variability in patient anatomy. However, it has yet to be realized due to technical limitations. Fast dose deposit coefficient calculation is a critical component of the online planning process that is required for plan optimization of intensity-modulated radiation therapy (IMRT). Computer graphics processing units (GPUs) are well suited to provide the requisite fast performance for the data-parallel nature of dose calculation. In this work, we develop a dose calculation engine based on a finite-size pencil beam (FSPB) algorithm and a GPU parallel computing framework. The developed framework can accommodate any FSPB model. We test our implementation in the case of a water phantom and the case of a prostate cancer patient with varying beamlet and voxel sizes. All testing scenarios achieved speedup ranging from 200 to 400 times when using a NVIDIA Tesla C1060 card in comparison with a 2.27 GHz Intel Xeon CPU. The computational time for calculating dose deposition coefficients for a nine-field prostate IMRT plan with this new framework is less than 1 s. This indicates that the GPU-based FSPB algorithm is well suited for online re-planning for adaptive radiotherapy.

Mild hypercholesterolemia, normal plasma triglycerides, and normal glucose levels across dementia staging in Alzheimer's disease: a clinical setting-based retrospective study.

PubMed

Ramdane, Said; Daoudi-Gueddah, Doria

2011-08-01

We examined retrospectively the concurrent relationships between fasting plasma total cholesterol, triglycerides, and glucose levels, and Alzheimer's disease (AD), in a clinical setting-based study. Total cholesterol level was higher in patients with AD compared to elderly controls; triglycerides or glucose levels did not significantly differ between the 2 groups. Respective plotted trajectories of change in cholesterol level across age were fairly parallel. No significant difference in total cholesterol levels was recorded between patients with AD classified by the Clinical Dementia Rating (CDR) score subgroups. These results suggest that patients with AD have relative mild total hypercholesterolemia, normal triglyceridemia, and normal fasting plasma glucose level. Mild total hypercholesterolemia seems to be permanent across age, and across dementia severity staging, and fairly parallels the trajectory of age-related change in total cholesterolemia of healthy controls. We speculate that these biochemical parameters pattern may be present long before-a decade at least-the symptomatic onset of the disease.

Spectral Anisotropy of Magnetic Field Fluctuations around Ion Scales in the Fast Solar Wind

NASA Astrophysics Data System (ADS)

Wang, X.; Tu, C.; He, J.; Marsch, E.; Wang, L.

2016-12-01

The power spectra of magnetic field at ion scales are significantly influenced by waves and structures. In this work, we study the ΘRB angle dependence of the contribution of waves on the spectral index of the magnetic field. Wavelet technique is applied to the high time-resolution magnetic field data from WIND spacecraft measurements in the fast solar wind. It is found that around ion scales, the parallel spectrum has a slope of -4.6±0.1 originally. When we remove the waves, which correspond to the data points with relatively larger value of magnetic helicity, the parallel spectrum gets shallower gradually to -3.2±0.2. However, the perpendicular spectrum does not change significantly during the wave-removal process, and its slope remains -3.1±0.1. It means that when the waves are removed from the original data, the spectral anisotropy gets weaker. This result may help us understand the physical nature of the spectral anisotropy around the ion scales.

Seismic anisotropy and large-scale deformation of the Eastern Alps

NASA Astrophysics Data System (ADS)

Bokelmann, Götz; Qorbani, Ehsan; Bianchi, Irene

2013-12-01

Mountain chains at the Earth's surface result from deformation processes within the Earth. Such deformation processes can be observed by seismic anisotropy, via the preferred alignment of elastically anisotropic minerals. The Alps show complex deformation at the Earth's surface. In contrast, we show here that observations of seismic anisotropy suggest a relatively simple pattern of internal deformation. Together with earlier observations from the Western Alps, the SKS shear-wave splitting observations presented here show one of the clearest examples yet of mountain chain-parallel fast orientations worldwide, with a simple pattern nearly parallel to the trend of the mountain chain. In the Eastern Alps, the fast orientations do not connect with neighboring mountain chains, neither the present-day Carpathians, nor the present-day Dinarides. In that region, the lithosphere is thin and the observed anisotropy thus resides within the asthenosphere. The deformation is consistent with the eastward extrusion toward the Pannonian basin that was previously suggested based on seismicity and surface geology.

SGR-like behaviour of the repeating FRB 121102

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

Wang, F.Y.; Yu, H., E-mail: fayinwang@nju.edu.cn, E-mail: yuhai@smail.nju.edu.cn

2017-03-01

Fast radio bursts (FRBs) are millisecond-duration radio signals occurring at cosmological distances. However the physical model of FRBs is mystery, many models have been proposed. Here we study the frequency distributions of peak flux, fluence, duration and waiting time for the repeating FRB 121102. The cumulative distributions of peak flux, fluence and duration show power-law forms. The waiting time distribution also shows power-law distribution, and is consistent with a non-stationary Poisson process. These distributions are similar as those of soft gamma repeaters (SGRs). We also use the statistical results to test the proposed models for FRBs. These distributions are consistentmore » with the predictions from avalanche models of slowly driven nonlinear dissipative systems.« less

High-resolution brain SPECT imaging by combination of parallel and tilted detector heads.

PubMed

Suzuki, Atsuro; Takeuchi, Wataru; Ishitsu, Takafumi; Morimoto, Yuichi; Kobashi, Keiji; Ueno, Yuichiro

2015-10-01

To improve the spatial resolution of brain single-photon emission computed tomography (SPECT), we propose a new brain SPECT system in which the detector heads are tilted towards the rotation axis so that they are closer to the brain. In addition, parallel detector heads are used to obtain the complete projection data set. We evaluated this parallel and tilted detector head system (PT-SPECT) in simulations. In the simulation study, the tilt angle of the detector heads relative to the axis was 45°. The distance from the collimator surface of the parallel detector heads to the axis was 130 mm. The distance from the collimator surface of the tilted detector heads to the origin on the axis was 110 mm. A CdTe semiconductor panel with a 1.4 mm detector pitch and a parallel-hole collimator were employed in both types of detector head. A line source phantom, cold-rod brain-shaped phantom, and cerebral blood flow phantom were evaluated. The projection data were generated by forward-projection of the phantom images using physics models, and Poisson noise at clinical levels was applied to the projection data. The ordered-subsets expectation maximization algorithm with physics models was used. We also evaluated conventional SPECT using four parallel detector heads for the sake of comparison. The evaluation of the line source phantom showed that the transaxial FWHM in the central slice for conventional SPECT ranged from 6.1 to 8.5 mm, while that for PT-SPECT ranged from 5.3 to 6.9 mm. The cold-rod brain-shaped phantom image showed that conventional SPECT could visualize up to 8-mm-diameter rods. By contrast, PT-SPECT could visualize up to 6-mm-diameter rods in upper slices of a cerebrum. The cerebral blood flow phantom image showed that the PT-SPECT system provided higher resolution at the thalamus and caudate nucleus as well as at the longitudinal fissure of the cerebrum compared with conventional SPECT. PT-SPECT provides improved image resolution at not only upper but also at central slices of the cerebrum.

A fast algorithm for computer aided collimation gamma camera (CACAO)

NASA Astrophysics Data System (ADS)

Jeanguillaume, C.; Begot, S.; Quartuccio, M.; Douiri, A.; Franck, D.; Pihet, P.; Ballongue, P.

2000-08-01

The computer aided collimation gamma camera is aimed at breaking down the resolution sensitivity trade-off of the conventional parallel hole collimator. It uses larger and longer holes, having an added linear movement at the acquisition sequence. A dedicated algorithm including shift and sum, deconvolution, parabolic filtering and rotation is described. Examples of reconstruction are given. This work shows that a simple and fast algorithm, based on a diagonal dominant approximation of the problem can be derived. Its gives a practical solution to the CACAO reconstruction problem.

Large-Constraint-Length, Fast Viterbi Decoder

NASA Technical Reports Server (NTRS)

Collins, O.; Dolinar, S.; Hsu, In-Shek; Pollara, F.; Olson, E.; Statman, J.; Zimmerman, G.

1990-01-01

Scheme for efficient interconnection makes VLSI design feasible. Concept for fast Viterbi decoder provides for processing of convolutional codes of constraint length K up to 15 and rates of 1/2 to 1/6. Fully parallel (but bit-serial) architecture developed for decoder of K = 7 implemented in single dedicated VLSI circuit chip. Contains six major functional blocks. VLSI circuits perform branch metric computations, add-compare-select operations, and then store decisions in traceback memory. Traceback processor reads appropriate memory locations and puts out decoded bits. Used as building block for decoders of larger K.

HONEI: A collection of libraries for numerical computations targeting multiple processor architectures

NASA Astrophysics Data System (ADS)

van Dyk, Danny; Geveler, Markus; Mallach, Sven; Ribbrock, Dirk; Göddeke, Dominik; Gutwenger, Carsten

2009-12-01

We present HONEI, an open-source collection of libraries offering a hardware oriented approach to numerical calculations. HONEI abstracts the hardware, and applications written on top of HONEI can be executed on a wide range of computer architectures such as CPUs, GPUs and the Cell processor. We demonstrate the flexibility and performance of our approach with two test applications, a Finite Element multigrid solver for the Poisson problem and a robust and fast simulation of shallow water waves. By linking against HONEI's libraries, we achieve a two-fold speedup over straight forward C++ code using HONEI's SSE backend, and additional 3-4 and 4-16 times faster execution on the Cell and a GPU. A second important aspect of our approach is that the full performance capabilities of the hardware under consideration can be exploited by adding optimised application-specific operations to the HONEI libraries. HONEI provides all necessary infrastructure for development and evaluation of such kernels, significantly simplifying their development. Program summaryProgram title: HONEI Catalogue identifier: AEDW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 No. of lines in distributed program, including test data, etc.: 216 180 No. of bytes in distributed program, including test data, etc.: 1 270 140 Distribution format: tar.gz Programming language: C++ Computer: x86, x86_64, NVIDIA CUDA GPUs, Cell blades and PlayStation 3 Operating system: Linux RAM: at least 500 MB free Classification: 4.8, 4.3, 6.1 External routines: SSE: none; [1] for GPU, [2] for Cell backend Nature of problem: Computational science in general and numerical simulation in particular have reached a turning point. The revolution developers are facing is not primarily driven by a change in (problem-specific) methodology, but rather by the fundamental paradigm shift of the underlying hardware towards heterogeneity and parallelism. This is particularly relevant for data-intensive problems stemming from discretisations with local support, such as finite differences, volumes and elements. Solution method: To address these issues, we present a hardware aware collection of libraries combining the advantages of modern software techniques and hardware oriented programming. Applications built on top of these libraries can be configured trivially to execute on CPUs, GPUs or the Cell processor. In order to evaluate the performance and accuracy of our approach, we provide two domain specific applications; a multigrid solver for the Poisson problem and a fully explicit solver for 2D shallow water equations. Restrictions: HONEI is actively being developed, and its feature list is continuously expanded. Not all combinations of operations and architectures might be supported in earlier versions of the code. Obtaining snapshots from http://www.honei.org is recommended. Unusual features: The considered applications as well as all library operations can be run on NVIDIA GPUs and the Cell BE. Running time: Depending on the application, and the input sizes. The Poisson solver executes in few seconds, while the SWE solver requires up to 5 minutes for large spatial discretisations or small timesteps. References:http://www.nvidia.com/cuda. http://www.ibm.com/developerworks/power/cell.

Direct numerical simulation of droplet-laden isotropic turbulence

NASA Astrophysics Data System (ADS)

Dodd, Michael S.

Interaction of liquid droplets with turbulence is important in numerous applications ranging from rain formation to oil spills to spray combustion. The physical mechanisms of droplet-turbulence interaction are largely unknown, especially when compared to that of solid particles. Compared to solid particles, droplets can deform, break up, coalesce and have internal fluid circulation. The main goal of this work is to investigate using direct numerical simulation (DNS) the physical mechanisms of droplet-turbulence interaction, both for non-evaporating and evaporating droplets. To achieve this objective, we develop and couple a new pressure-correction method with the volume-of-fluid (VoF) method for simulating incompressible two-fluid flows. The method's main advantage is that the variable coefficient Poisson equation that arises in solving the incompressible Navier-Stokes equations for two-fluid flows is reduced to a constant coefficient equation. This equation can then be solved directly using, e.g., the FFT-based parallel Poisson solver. For a 10243 mesh, our new pressure-correction method using a fast Poisson solver is ten to forty times faster than the standard pressure-correction method using multigrid. Using the coupled pressure-correction and VoF method, we perform direct numerical simulations (DNS) of 3130 finite-size, non-evaporating droplets of diameter approximately equal to the Taylor lengthscale and with 5% droplet volume fraction in decaying isotropic turbulence at initial Taylor-scale Reynolds number Relambda = 83. In the droplet-laden cases, we vary one of the following three parameters: the droplet Weber number based on the r.m.s. velocity of turbulence (0.1 ≤ Werms ≤ 5), the droplet- to carrier-fluid density ratio (1 ≤ rhod/rho c ≤ 100) or the droplet- to carrier-fluid viscosity ratio (1 ≤ mud/muc ≤ 100). We derive the turbulence kinetic energy (TKE) equations for the two-fluid, carrier-fluid and droplet-fluid flow. These equations allow us to explain the pathways for TKE exchange between the carrier turbulent flow and the flow inside the droplet. We also explain the role of the interfacial surface energy in the two-fluid TKE equation through work performed by surface tension. Furthermore, we derive the relationship between the power of surface tension and the rate of change of total droplet surface area. This link allows us to explain how droplet deformation, breakup and coalescence play roles in the temporal evolution of TKE. We then extend the code for non-evaporating droplets and develop a combined VoF method and low-Mach-number approach to simulate evaporating and condensing droplets. The two main novelties of the method are: (i) the VOF algorithm captures the motion of the liquid gas interface in the presence of mass transfer due to evaporation and condensation without requiring a projection step for the liquid velocity, and (ii) the low-Mach-number approach allows for local volume changes caused by phase change while the total volume of the liquid-gas system is constant. The method is verified against an analytical solution for a Stefan flow problem, and the D2 law is verified for a single droplet in quiescent gas. Finally, we perform DNS of an evaporating liquid droplet in forced isotropic turbulence. We show that the method accurately captures the temperature and vapor fields in the turbulent regime, and that the local evaporation rate can vary along the droplet surface depending on the structure of the surrounding vapor cloud. We also report the time evolution of the mean Sherwood number, which indicates that turbulence enhances the vaporization rate of liquid droplets.

Fasting triglycerides as a predictor of incident diabetes, insulin resistance and β-cell function in a Canadian First Nation

PubMed Central

Riediger, Natalie D.; Clark, Kirsten; Lukianchuk, Virginia; Roulette, Joanne; Bruce, Sharon

2017-01-01

ABSTRACT Background: Diabetes prevalence is substantially higher among Canadian First Nations populations than the non-First Nation population. Fasting serum triglycerides have been found to be an important predictor of incident diabetes among non-indigenous populations. However, there is a great need to understand diabetes progression within specific ethnic groups, particularly First Nations populations. Objective: The purpose of this study was to test for an association between fasting serum triglycerides and incident diabetes, changes in insulin resistance and changes in β-cell function in a Manitoba First Nation cohort. Methods: Study data were from two diabetes screening studies in Sandy Bay First Nation in Manitoba, Canada, collected in 2002/2003 and 2011/2012. The cohort was composed of respondents to both screening studies (n=171). Fasting blood samples and anthropometric, health and demographic data were collected. A generalised linear model with Poisson distribution was used to test for an association between fasting triglycerides and incident diabetes. Results: There were 35 incident cases of diabetes among 128 persons without diabetes at baseline. Participants who developed incident type 2 diabetes were significantly older and had significantly higher body mass index (BMI; p=0.012), total cholesterol (p=0.007), fasting triglycerides (p<0.001), and Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) (p<0.001). Fasting triglyceride level was found to be a statistically significant positive predictor of incident diabetes independent of age, sex and waist circumference at baseline. Participants with triglycerides in the highest tertile (≥2.11 mmol/l) had a 4.0-times higher risk of developing incident diabetes compared to those in the lowest tertile (p=0.03). Notably, neither waist circumference nor BMI were significant predictors of incident diabetes independent of age, sex and triglycerides. Conclusion: Fasting triglycerides may be useful as a clinical predictor of insulin resistance and diabetes development among First Nations populations. Unlike other ethnic groups, BMI and waist circumference may be less important factors in diabetes development. PMID:28406758

ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer.

PubMed

Wang, Zihao; Chen, Yu; Zhang, Jingrong; Li, Lun; Wan, Xiaohua; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2018-03-01

Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset. However, the huge computational demand has become a bottleneck for the application of ICON. In this work, we implemented a parallel acceleration technology ICON-many integrated core (MIC) on Xeon Phi cards to address the huge computational demand of ICON. During this step, we parallelize the element-wise matrix operations and use the efficient summation of a matrix to reduce the cost of matrix computation. We also developed parallel versions of NUFFT on MIC to achieve a high acceleration of ICON by using more efficient fast Fourier transform (FFT) calculation. We then proposed a hybrid task allocation strategy (two-level load balancing) to improve the overall performance of ICON-MIC by making full use of the idle resources on Tianhe-2 supercomputer. Experimental results using two different datasets show that ICON-MIC has high accuracy in biological specimens under different noise levels and a significant acceleration, up to 13.3 × , compared with the CPU version. Further, ICON-MIC has good scalability efficiency and overall performance on Tianhe-2 supercomputer.

Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency.

PubMed

Kepper, Nick; Ettig, Ramona; Dickmann, Frank; Stehr, Rene; Grosveld, Frank G; Wedemann, Gero; Knoch, Tobias A

2010-01-01

Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we-can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency.

An implementation of a tree code on a SIMD, parallel computer

NASA Technical Reports Server (NTRS)

Olson, Kevin M.; Dorband, John E.

1994-01-01

We describe a fast tree algorithm for gravitational N-body simulation on SIMD parallel computers. The tree construction uses fast, parallel sorts. The sorted lists are recursively divided along their x, y and z coordinates. This data structure is a completely balanced tree (i.e., each particle is paired with exactly one other particle) and maintains good spatial locality. An implementation of this tree-building algorithm on a 16k processor Maspar MP-1 performs well and constitutes only a small fraction (approximately 15%) of the entire cycle of finding the accelerations. Each node in the tree is treated as a monopole. The tree search and the summation of accelerations also perform well. During the tree search, node data that is needed from another processor is simply fetched. Roughly 55% of the tree search time is spent in communications between processors. We apply the code to two problems of astrophysical interest. The first is a simulation of the close passage of two gravitationally, interacting, disk galaxies using 65,636 particles. We also simulate the formation of structure in an expanding, model universe using 1,048,576 particles. Our code attains speeds comparable to one head of a Cray Y-MP, so single instruction, multiple data (SIMD) type computers can be used for these simulations. The cost/performance ratio for SIMD machines like the Maspar MP-1 make them an extremely attractive alternative to either vector processors or large multiple instruction, multiple data (MIMD) type parallel computers. With further optimizations (e.g., more careful load balancing), speeds in excess of today's vector processing computers should be possible.

Performance of the modified Poisson regression approach for estimating relative risks from clustered prospective data.

PubMed

Yelland, Lisa N; Salter, Amy B; Ryan, Philip

2011-10-15

Modified Poisson regression, which combines a log Poisson regression model with robust variance estimation, is a useful alternative to log binomial regression for estimating relative risks. Previous studies have shown both analytically and by simulation that modified Poisson regression is appropriate for independent prospective data. This method is often applied to clustered prospective data, despite a lack of evidence to support its use in this setting. The purpose of this article is to evaluate the performance of the modified Poisson regression approach for estimating relative risks from clustered prospective data, by using generalized estimating equations to account for clustering. A simulation study is conducted to compare log binomial regression and modified Poisson regression for analyzing clustered data from intervention and observational studies. Both methods generally perform well in terms of bias, type I error, and coverage. Unlike log binomial regression, modified Poisson regression is not prone to convergence problems. The methods are contrasted by using example data sets from 2 large studies. The results presented in this article support the use of modified Poisson regression as an alternative to log binomial regression for analyzing clustered prospective data when clustering is taken into account by using generalized estimating equations.

A Review of Multivariate Distributions for Count Data Derived from the Poisson Distribution.

PubMed

Inouye, David; Yang, Eunho; Allen, Genevera; Ravikumar, Pradeep

2017-01-01

The Poisson distribution has been widely studied and used for modeling univariate count-valued data. Multivariate generalizations of the Poisson distribution that permit dependencies, however, have been far less popular. Yet, real-world high-dimensional count-valued data found in word counts, genomics, and crime statistics, for example, exhibit rich dependencies, and motivate the need for multivariate distributions that can appropriately model this data. We review multivariate distributions derived from the univariate Poisson, categorizing these models into three main classes: 1) where the marginal distributions are Poisson, 2) where the joint distribution is a mixture of independent multivariate Poisson distributions, and 3) where the node-conditional distributions are derived from the Poisson. We discuss the development of multiple instances of these classes and compare the models in terms of interpretability and theory. Then, we empirically compare multiple models from each class on three real-world datasets that have varying data characteristics from different domains, namely traffic accident data, biological next generation sequencing data, and text data. These empirical experiments develop intuition about the comparative advantages and disadvantages of each class of multivariate distribution that was derived from the Poisson. Finally, we suggest new research directions as explored in the subsequent discussion section.

Application of zero-inflated poisson mixed models in prognostic factors of hepatitis C.

PubMed

Akbarzadeh Baghban, Alireza; Pourhoseingholi, Asma; Zayeri, Farid; Jafari, Ali Akbar; Alavian, Seyed Moayed

2013-01-01

In recent years, hepatitis C virus (HCV) infection represents a major public health problem. Evaluation of risk factors is one of the solutions which help protect people from the infection. This study aims to employ zero-inflated Poisson mixed models to evaluate prognostic factors of hepatitis C. The data was collected from a longitudinal study during 2005-2010. First, mixed Poisson regression (PR) model was fitted to the data. Then, a mixed zero-inflated Poisson model was fitted with compound Poisson random effects. For evaluating the performance of the proposed mixed model, standard errors of estimators were compared. The results obtained from mixed PR showed that genotype 3 and treatment protocol were statistically significant. Results of zero-inflated Poisson mixed model showed that age, sex, genotypes 2 and 3, the treatment protocol, and having risk factors had significant effects on viral load of HCV patients. Of these two models, the estimators of zero-inflated Poisson mixed model had the minimum standard errors. The results showed that a mixed zero-inflated Poisson model was the almost best fit. The proposed model can capture serial dependence, additional overdispersion, and excess zeros in the longitudinal count data.

Generalized master equation via aging continuous-time random walks.

PubMed

Allegrini, Paolo; Aquino, Gerardo; Grigolini, Paolo; Palatella, Luigi; Rosa, Angelo

2003-11-01

We discuss the problem of the equivalence between continuous-time random walk (CTRW) and generalized master equation (GME). The walker, making instantaneous jumps from one site of the lattice to another, resides in each site for extended times. The sojourn times have a distribution density psi(t) that is assumed to be an inverse power law with the power index micro. We assume that the Onsager principle is fulfilled, and we use this assumption to establish a complete equivalence between GME and the Montroll-Weiss CTRW. We prove that this equivalence is confined to the case where psi(t) is an exponential. We argue that is so because the Montroll-Weiss CTRW, as recently proved by Barkai [E. Barkai, Phys. Rev. Lett. 90, 104101 (2003)], is nonstationary, thereby implying aging, while the Onsager principle is valid only in the case of fully aged systems. The case of a Poisson distribution of sojourn times is the only one with no aging associated to it, and consequently with no need to establish special initial conditions to fulfill the Onsager principle. We consider the case of a dichotomous fluctuation, and we prove that the Onsager principle is fulfilled for any form of regression to equilibrium provided that the stationary condition holds true. We set the stationary condition on both the CTRW and the GME, thereby creating a condition of total equivalence, regardless of the nature of the waiting-time distribution. As a consequence of this procedure we create a GME that is a bona fide master equation, in spite of being non-Markov. We note that the memory kernel of the GME affords information on the interaction between system of interest and its bath. The Poisson case yields a bath with infinitely fast fluctuations. We argue that departing from the Poisson form has the effect of creating a condition of infinite memory and that these results might be useful to shed light on the problem of how to unravel non-Markov quantum master equations.

Evaluation and application of a fast module in a PLC based interlock and control system

NASA Astrophysics Data System (ADS)

Zaera-Sanz, M.

2009-08-01

The LHC Beam Interlock system requires a controller performing a simple matrix function to collect the different beam dump requests. To satisfy the expected safety level of the Interlock, the system should be robust and reliable. The PLC is a promising candidate to fulfil both aspects but too slow to meet the expected response time which is of the order of μseconds. Siemens has introduced a ``so called'' fast module (FM352-5 Boolean Processor). It provides independent and extremely fast control of a process within a larger control system using an onboard processor, a Field Programmable Gate Array (FPGA), to execute code in parallel which results in extremely fast scan times. It is interesting to investigate its features and to evaluate it as a possible candidate for the beam interlock system. This paper publishes the results of this study. As well, this paper could be useful for other applications requiring fast processing using a PLC.

Current drive with combined electron cyclotron wave and high harmonic fast wave in tokamak plasmas

NASA Astrophysics Data System (ADS)

Li, J. C.; Gong, X. Y.; Dong, J. Q.; Wang, J.; Zhang, N.; Zheng, P. W.; Yin, C. Y.

2016-12-01

The current driven by combined electron cyclotron wave (ECW) and high harmonic fast wave is investigated using the GENRAY/CQL3D package. It is shown that no significant synergetic current is found in a range of cases with a combined ECW and fast wave (FW). This result is consistent with a previous study [Harvey et al., in Proceedings of IAEA TCM on Fast Wave Current Drive in Reactor Scale Tokamaks (Synergy and Complimentarily with LHCD and ECRH), Arles, France, IAEA, Vienna, 1991]. However, a positive synergy effect does appear with the FW in the lower hybrid range of frequencies. This positive synergy effect can be explained using a picture of the electron distribution function induced by the ECW and a very high harmonic fast wave (helicon). The dependence of the synergy effect on the radial position of the power deposition, the wave power, the wave frequency, and the parallel refractive index is also analyzed, both numerically and physically.

Fasting Activation of AgRP Neurons Requires NMDA Receptors and Involves Spinogenesis and Increased Excitatory Tone

PubMed Central

Liu, Tiemin; Kong, Dong; Shah, Bhavik P.; Ye, Chianping; Koda, Shuichi; Saunders, Arpiar; Ding, Jun B.; Yang, Zongfang; Sabatini, Bernardo L.; Lowell, Bradford B.

2012-01-01

SUMMARY AgRP neuron activity drives feeding and weight gain while that of nearby POMC neurons does the opposite. However, the role of excitatory glutamatergic input in controlling these neurons is unknown. To address this question, we generated mice lacking NMDA receptors (NMDARs) on either AgRP or POMC neurons. Deletion of NMDARs from AgRP neurons markedly reduced weight, body fat and food intake whereas deletion from POMC neurons had no effect. Activation of AgRP neurons by fasting, as assessed by c-Fos, Agrp and Npy mRNA expression, AMPA receptor-mediated EPSCs, depolarization and firing rates, required NMDARs. Furthermore, AgRP but not POMC neurons have dendritic spines and increased glutamatergic input onto AgRP neurons caused by fasting was paralleled by an increase in spines, suggesting fasting induced synaptogenesis and spinogenesis. Thus glutamatergic synaptic transmission and its modulation by NMDARs play key roles in controlling AgRP neurons and determining the cellular and behavioral response to fasting. PMID:22325203

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

NASA Astrophysics Data System (ADS)

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

2018-04-01

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λDe, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρe and λDe, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τs, versus fast-ion charge are in agreement with unmagnetized slowing-down theory; with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. The implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.

Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

NASA Astrophysics Data System (ADS)

Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

2016-12-01

The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB.

Impedance matching for repetitive high voltage all-solid-state Marx generator and excimer DBD UV sources

NASA Astrophysics Data System (ADS)

Wang, Yonggang; Tong, Liqing; Liu, Kefu

2017-06-01

The purpose of impedance matching for a Marx generator and DBD lamp is to limit the output current of the Marx generator, provide a large discharge current at ignition, and obtain fast voltage rising/falling edges and large overshoot. In this paper, different impedance matching circuits (series inductor, parallel capacitor, and series inductor combined with parallel capacitor) are analyzed. It demonstrates that a series inductor could limit the Marx current. However, the discharge current is also limited. A parallel capacitor could provide a large discharge current, but the Marx current is also enlarged. A series inductor combined with a parallel capacitor takes full advantage of the inductor and capacitor, and avoids their shortcomings. Therefore, it is a good solution. Experimental results match the theoretical analysis well and show that both the series inductor and parallel capacitor improve the performance of the system. However, the series inductor combined with the parallel capacitor has the best performance. Compared with driving the DBD lamp with a Marx generator directly, an increase of 97.3% in radiant power and an increase of 59.3% in system efficiency are achieved using this matching circuit.

Method and apparatus for offloading compute resources to a flash co-processing appliance

DOEpatents

Tzelnic, Percy; Faibish, Sorin; Gupta, Uday K.; Bent, John; Grider, Gary Alan; Chen, Hsing -bung

2015-10-13

Solid-State Drive (SSD) burst buffer nodes are interposed into a parallel supercomputing cluster to enable fast burst checkpoint of cluster memory to or from nearby interconnected solid-state storage with asynchronous migration between the burst buffer nodes and slower more distant disk storage. The SSD nodes also perform tasks offloaded from the compute nodes or associated with the checkpoint data. For example, the data for the next job is preloaded in the SSD node and very fast uploaded to the respective compute node just before the next job starts. During a job, the SSD nodes perform fast visualization and statistical analysis upon the checkpoint data. The SSD nodes can also perform data reduction and encryption of the checkpoint data.

Fast iterative censoring CFAR algorithm for ship detection from SAR images

NASA Astrophysics Data System (ADS)

Gu, Dandan; Yue, Hui; Zhang, Yuan; Gao, Pengcheng

2017-11-01

Ship detection is one of the essential techniques for ship recognition from synthetic aperture radar (SAR) images. This paper presents a fast iterative detection procedure to eliminate the influence of target returns on the estimation of local sea clutter distributions for constant false alarm rate (CFAR) detectors. A fast block detector is first employed to extract potential target sub-images; and then, an iterative censoring CFAR algorithm is used to detect ship candidates from each target blocks adaptively and efficiently, where parallel detection is available, and statistical parameters of G0 distribution fitting local sea clutter well can be quickly estimated based on an integral image operator. Experimental results of TerraSAR-X images demonstrate the effectiveness of the proposed technique.

Fedosov’s formal symplectic groupoids and contravariant connections

NASA Astrophysics Data System (ADS)

Karabegov, Alexander V.

2006-10-01

Using Fedosov's approach we give a geometric construction of a formal symplectic groupoid over any Poisson manifold endowed with a torsion-free Poisson contravariant connection. In the case of Kähler-Poisson manifolds this construction provides, in particular, the formal symplectic groupoids with separation of variables. We show that the dual of a semisimple Lie algebra does not admit torsion-free Poisson contravariant connections.

Complete synchronization of the global coupled dynamical network induced by Poisson noises.

PubMed

Guo, Qing; Wan, Fangyi

2017-01-01

The different Poisson noise-induced complete synchronization of the global coupled dynamical network is investigated. Based on the stability theory of stochastic differential equations driven by Poisson process, we can prove that Poisson noises can induce synchronization and sufficient conditions are established to achieve complete synchronization with probability 1. Furthermore, numerical examples are provided to show the agreement between theoretical and numerical analysis.

Weight gain in the first two years of life, asthma and atopy: the SCAALA cohort study.

PubMed

Matos, Sheila M A; Jesus, Sandra R; Saldiva, Silvia R D M; Prado, Matildes S; D'Innocenzo, Silvana; Assis, Ana M O; Rodrigues, Laura C; Alcantara-Neves, Neuza M; Cruz, Alvaro A; Simões, Silvia de Magalhães; Fiaccone, Rosemeire L; Barreto, Maurício L

2014-11-01

To evaluate the association between weight gain in the first two years of life and the occurrence of wheezing, asthma, serum IgE, skin reactivity and pulmonary function. Cohort study. The metropolitan region of Salvador, Bahia, Brazil. The association was studied between 1997 and 2005 in 669 children up to 11 years of age. Data were collected on asthma and risk factors, both current factors and those present in the first years of life. Weight gain was considered fast when the Z-score was >0·67. Poisson regression was used in the multivariate statistical analysis. Wheezing was reported in 25·6 % of the children. Weight gain was considered fast (Z-score >0·67) in 29·6 % of the children and slow (Z-score <-0·67) in 13·9 %. Children in the slow weight gain group had 36 % fewer symptoms of asthma (prevalence ratio = 0·65; 95 % CI 0·42, 0·99). Slower weight gain in the early years of life may constitute a protective factor against symptoms of asthma. The relevance of this finding for public health is not yet certain, since it is known that children with slow and fast weight gain may be more likely to develop adverse health consequences related to both these situations.

Two-dimensional extended fluid model for a dc glow discharge with nonlocal ionization source term

NASA Astrophysics Data System (ADS)

Rafatov, Ismail; Bogdanov, Eugeny; Kudryavtsev, Anatoliy

2013-09-01

Numerical techniques applied to the gas discharge plasma modelling are generally grouped into fluid and kinetic (particle) methods, and their combinations which lead to the hybrid models. Hybrid models usually employ Monte Carlo method to simulate fast electron dynamics, while slow plasma species are described as fluids. However, since fast electrons contribution to these models is limited to deriving the ionization rate distribution, their effect can be expressed by the analytical approximation of the ionization source function, and then integrating it into the fluid model. In the context of this approach, we incorporated effect of fast electrons into the ``extended fluid model'' of glow discharge, using two spatial dimensions. Slow electrons, ions and excited neutral species are described by the fluid plasma equations. Slow electron transport (diffusion and mobility) coefficients as well as electron induced reaction rates are determined from the solutions of the electron Boltzmann equation. The self-consistent electric field is calculated using the Poisson equation. We carried out test calculations for the discharge in argon gas. Comparison with the experimental data as well as with the hybrid model results exhibits good applicability of the proposed model. The work was supported by the joint research grant from the Scientific and Technical Research Council of Turkey (TUBITAK) 212T164 and Russian Foundation for Basic Research (RFBR).

Probability and shape of the spectral line of a single bulk characteristic energy loss of a fast electron in a medium with electron absorption and strong spatial dispersion

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

Libenson, B. N., E-mail: libenson-b@yandex.ru

2011-10-15

The probability of single characteristic energy loss of a fast electron in a reflection experiment has been calculated. Unlike many works concerning this subject, the bremsstrahlung of bulk plasmons in the non- Cherenkov ranges of frequencies and wavevectors of a plasmon has been taken into account. The contributions to the probability of single loss and to the shape of the spectral line from a quantum correction that is due to the interference of elastic and inelastic electron scattering events have been determined. The probability has been calculated in the kinetic approximation for the relative permittivity, where the short-wavelength range ofmore » the plasmon spectrum is correctly taken into account. In view of these circumstances, the expression for the mean free path of the electron with respect to the emission of a bulk plasmon that was obtained by Pines [D. Pines, Elementary Excitations in Solids (Benjamin, New York, 1963)] has been refined. The coherence length of the fast electron in the medium-energy range under consideration has been estimated. The shape of the spectral line of energy losses in the non-Cherenkov frequency range has been determined. It has been shown that the probability of the single emission of the bulk plasmon incompletely corresponds to the Poisson statistics.« less

Numerical study of the existence criterion for the reversed shear Alfven eigenmode in the presence of a parallel equilibrium current

NASA Astrophysics Data System (ADS)

Shahzad, M.; Rizvi, H.; Panwar, A.; Ryu, C. M.

2017-06-01

We have re-visited the existence criterion of the reverse shear Alfven eigenmodes (RSAEs) in the presence of the parallel equilibrium current by numerically solving the eigenvalue equation using a fast eigenvalue solver code KAES. The parallel equilibrium current can bring in the kink effect and is known to be strongly unfavorable for the RSAE. We have numerically estimated the critical value of the toroidicity factor Qtor in a circular tokamak plasma, above which RSAEs can exist, and compared it to the analytical one. The difference between the numerical and analytical critical values is small for low frequency RSAEs, but it increases as the frequency of the mode increases, becoming greater for higher poloidal harmonic modes.

Parallel processing approach to transform-based image coding

NASA Astrophysics Data System (ADS)

Normile, James O.; Wright, Dan; Chu, Ken; Yeh, Chia L.

1991-06-01

This paper describes a flexible parallel processing architecture designed for use in real time video processing. The system consists of floating point DSP processors connected to each other via fast serial links, each processor has access to a globally shared memory. A multiple bus architecture in combination with a dual ported memory allows communication with a host control processor. The system has been applied to prototyping of video compression and decompression algorithms. The decomposition of transform based algorithms for decompression into a form suitable for parallel processing is described. A technique for automatic load balancing among the processors is developed and discussed, results ar presented with image statistics and data rates. Finally techniques for accelerating the system throughput are analyzed and results from the application of one such modification described.

A convenient and accurate parallel Input/Output USB device for E-Prime.

PubMed

Canto, Rosario; Bufalari, Ilaria; D'Ausilio, Alessandro

2011-03-01

Psychological and neurophysiological experiments require the accurate control of timing and synchrony for Input/Output signals. For instance, a typical Event-Related Potential (ERP) study requires an extremely accurate synchronization of stimulus delivery with recordings. This is typically done via computer software such as E-Prime, and fast communications are typically assured by the Parallel Port (PP). However, the PP is an old and disappearing technology that, for example, is no longer available on portable computers. Here we propose a convenient USB device enabling parallel I/O capabilities. We tested this device against the PP on both a desktop and a laptop machine in different stress tests. Our data demonstrate the accuracy of our system, which suggests that it may be a good substitute for the PP with E-Prime.

Merlin - Massively parallel heterogeneous computing

NASA Technical Reports Server (NTRS)

Wittie, Larry; Maples, Creve

1989-01-01

Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.

A transient-enhanced NMOS low dropout voltage regulator with parallel feedback compensation

NASA Astrophysics Data System (ADS)

Han, Wang; Lin, Tan

2016-02-01

This paper presents a transient-enhanced NMOS low-dropout regulator (LDO) for portable applications with parallel feedback compensation. The parallel feedback structure adds a dynamic zero to get an adequate phase margin with a load current variation from 0 to 1 A. A class-AB error amplifier and a fast charging/discharging unit are adopted to enhance the transient performance. The proposed LDO has been implemented in a 0.35 μm BCD process. From experimental results, the regulator can operate with a minimum dropout voltage of 150 mV at a maximum 1 A load and IQ of 165 μA. Under the full range load current step, the voltage undershoot and overshoot of the proposed LDO are reduced to 38 mV and 27 mV respectively.

2D-RBUC for efficient parallel compression of residuals

NASA Astrophysics Data System (ADS)

Đurđević, Đorđe M.; Tartalja, Igor I.

2018-02-01

In this paper, we present a method for lossless compression of residuals with an efficient SIMD parallel decompression. The residuals originate from lossy or near lossless compression of height fields, which are commonly used to represent models of terrains. The algorithm is founded on the existing RBUC method for compression of non-uniform data sources. We have adapted the method to capture 2D spatial locality of height fields, and developed the data decompression algorithm for modern GPU architectures already present even in home computers. In combination with the point-level SIMD-parallel lossless/lossy high field compression method HFPaC, characterized by fast progressive decompression and seamlessly reconstructed surface, the newly proposed method trades off small efficiency degradation for a non negligible compression ratio (measured up to 91%) benefit.

Wideband aperture array using RF channelizers and massively parallel digital 2D IIR filterbank

NASA Astrophysics Data System (ADS)

Sengupta, Arindam; Madanayake, Arjuna; Gómez-García, Roberto; Engeberg, Erik D.

2014-05-01

Wideband receive-mode beamforming applications in wireless location, electronically-scanned antennas for radar, RF sensing, microwave imaging and wireless communications require digital aperture arrays that offer a relatively constant far-field beam over several octaves of bandwidth. Several beamforming schemes including the well-known true time-delay and the phased array beamformers have been realized using either finite impulse response (FIR) or fast Fourier transform (FFT) digital filter-sum based techniques. These beamforming algorithms offer the desired selectivity at the cost of a high computational complexity and frequency-dependant far-field array patterns. A novel approach to receiver beamforming is the use of massively parallel 2-D infinite impulse response (IIR) fan filterbanks for the synthesis of relatively frequency independent RF beams at an order of magnitude lower multiplier complexity compared to FFT or FIR filter based conventional algorithms. The 2-D IIR filterbanks demand fast digital processing that can support several octaves of RF bandwidth, fast analog-to-digital converters (ADCs) for RF-to-bits type direct conversion of wideband antenna element signals. Fast digital implementation platforms that can realize high-precision recursive filter structures necessary for real-time beamforming, at RF radio bandwidths, are also desired. We propose a novel technique that combines a passive RF channelizer, multichannel ADC technology, and single-phase massively parallel 2-D IIR digital fan filterbanks, realized at low complexity using FPGA and/or ASIC technology. There exists native support for a larger bandwidth than the maximum clock frequency of the digital implementation technology. We also strive to achieve More-than-Moore throughput by processing a wideband RF signal having content with N-fold (B = N Fclk/2) bandwidth compared to the maximum clock frequency Fclk Hz of the digital VLSI platform under consideration. Such increase in bandwidth is achieved without use of polyphase signal processing or time-interleaved ADC methods. That is, all digital processors operate at the same Fclk clock frequency without phasing, while wideband operation is achieved by sub-sampling of narrower sub-bands at the the RF channelizer outputs.

Application of the Conway-Maxwell-Poisson generalized linear model for analyzing motor vehicle crashes.

PubMed

Lord, Dominique; Guikema, Seth D; Geedipally, Srinivas Reddy

2008-05-01

This paper documents the application of the Conway-Maxwell-Poisson (COM-Poisson) generalized linear model (GLM) for modeling motor vehicle crashes. The COM-Poisson distribution, originally developed in 1962, has recently been re-introduced by statisticians for analyzing count data subjected to over- and under-dispersion. This innovative distribution is an extension of the Poisson distribution. The objectives of this study were to evaluate the application of the COM-Poisson GLM for analyzing motor vehicle crashes and compare the results with the traditional negative binomial (NB) model. The comparison analysis was carried out using the most common functional forms employed by transportation safety analysts, which link crashes to the entering flows at intersections or on segments. To accomplish the objectives of the study, several NB and COM-Poisson GLMs were developed and compared using two datasets. The first dataset contained crash data collected at signalized four-legged intersections in Toronto, Ont. The second dataset included data collected for rural four-lane divided and undivided highways in Texas. Several methods were used to assess the statistical fit and predictive performance of the models. The results of this study show that COM-Poisson GLMs perform as well as NB models in terms of GOF statistics and predictive performance. Given the fact the COM-Poisson distribution can also handle under-dispersed data (while the NB distribution cannot or has difficulties converging), which have sometimes been observed in crash databases, the COM-Poisson GLM offers a better alternative over the NB model for modeling motor vehicle crashes, especially given the important limitations recently documented in the safety literature about the latter type of model.

Conditional Poisson models: a flexible alternative to conditional logistic case cross-over analysis.

PubMed

Armstrong, Ben G; Gasparrini, Antonio; Tobias, Aurelio

2014-11-24

The time stratified case cross-over approach is a popular alternative to conventional time series regression for analysing associations between time series of environmental exposures (air pollution, weather) and counts of health outcomes. These are almost always analyzed using conditional logistic regression on data expanded to case-control (case crossover) format, but this has some limitations. In particular adjusting for overdispersion and auto-correlation in the counts is not possible. It has been established that a Poisson model for counts with stratum indicators gives identical estimates to those from conditional logistic regression and does not have these limitations, but it is little used, probably because of the overheads in estimating many stratum parameters. The conditional Poisson model avoids estimating stratum parameters by conditioning on the total event count in each stratum, thus simplifying the computing and increasing the number of strata for which fitting is feasible compared with the standard unconditional Poisson model. Unlike the conditional logistic model, the conditional Poisson model does not require expanding the data, and can adjust for overdispersion and auto-correlation. It is available in Stata, R, and other packages. By applying to some real data and using simulations, we demonstrate that conditional Poisson models were simpler to code and shorter to run than are conditional logistic analyses and can be fitted to larger data sets than possible with standard Poisson models. Allowing for overdispersion or autocorrelation was possible with the conditional Poisson model but when not required this model gave identical estimates to those from conditional logistic regression. Conditional Poisson regression models provide an alternative to case crossover analysis of stratified time series data with some advantages. The conditional Poisson model can also be used in other contexts in which primary control for confounding is by fine stratification.

Do bacterial cell numbers follow a theoretical Poisson distribution? Comparison of experimentally obtained numbers of single cells with random number generation via computer simulation.

PubMed

Koyama, Kento; Hokunan, Hidekazu; Hasegawa, Mayumi; Kawamura, Shuso; Koseki, Shigenobu

2016-12-01

We investigated a bacterial sample preparation procedure for single-cell studies. In the present study, we examined whether single bacterial cells obtained via 10-fold dilution followed a theoretical Poisson distribution. Four serotypes of Salmonella enterica, three serotypes of enterohaemorrhagic Escherichia coli and one serotype of Listeria monocytogenes were used as sample bacteria. An inoculum of each serotype was prepared via a 10-fold dilution series to obtain bacterial cell counts with mean values of one or two. To determine whether the experimentally obtained bacterial cell counts follow a theoretical Poisson distribution, a likelihood ratio test between the experimentally obtained cell counts and Poisson distribution which parameter estimated by maximum likelihood estimation (MLE) was conducted. The bacterial cell counts of each serotype sufficiently followed a Poisson distribution. Furthermore, to examine the validity of the parameters of Poisson distribution from experimentally obtained bacterial cell counts, we compared these with the parameters of a Poisson distribution that were estimated using random number generation via computer simulation. The Poisson distribution parameters experimentally obtained from bacterial cell counts were within the range of the parameters estimated using a computer simulation. These results demonstrate that the bacterial cell counts of each serotype obtained via 10-fold dilution followed a Poisson distribution. The fact that the frequency of bacterial cell counts follows a Poisson distribution at low number would be applied to some single-cell studies with a few bacterial cells. In particular, the procedure presented in this study enables us to develop an inactivation model at the single-cell level that can estimate the variability of survival bacterial numbers during the bacterial death process. Copyright © 2016 Elsevier Ltd. All rights reserved.

MMS Observations of Parallel Electric Fields During a Quasi-Perpendicular Bow Shock Crossing

NASA Astrophysics Data System (ADS)

Goodrich, K.; Schwartz, S. J.; Ergun, R.; Wilder, F. D.; Holmes, J.; Burch, J. L.; Gershman, D. J.; Giles, B. L.; Khotyaintsev, Y. V.; Le Contel, O.; Lindqvist, P. A.; Strangeway, R. J.; Russell, C.; Torbert, R. B.

2016-12-01

Previous observations of the terrestrial bow shock have frequently shown large-amplitude fluctuations in the parallel electric field. These parallel electric fields are seen as both nonlinear solitary structures, such as double layers and electron phase-space holes, and short-wavelength waves, which can reach amplitudes greater than 100 mV/m. The Magnetospheric Multi-Scale (MMS) Mission has crossed the Earth's bow shock more than 200 times. The parallel electric field signatures observed in these crossings are seen in very discrete packets and evolve over time scales of less than a second, indicating the presence of a wealth of kinetic-scale activity. The high time resolution of the Fast Particle Instrument (FPI) available on MMS offers greater detail of the kinetic-scale physics that occur at bow shocks than ever before, allowing greater insight into the overall effect of these observed electric fields. We present a characterization of these parallel electric fields found in a single bow shock event and how it reflects the kinetic-scale activity that can occur at the terrestrial bow shock.

Neoclassical parallel flow calculation in the presence of external parallel momentum sources in Heliotron J

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

Nishioka, K.; Nakamura, Y.; Nishimura, S.

A moment approach to calculate neoclassical transport in non-axisymmetric torus plasmas composed of multiple ion species is extended to include the external parallel momentum sources due to unbalanced tangential neutral beam injections (NBIs). The momentum sources that are included in the parallel momentum balance are calculated from the collision operators of background particles with fast ions. This method is applied for the clarification of the physical mechanism of the neoclassical parallel ion flows and the multi-ion species effect on them in Heliotron J NBI plasmas. It is found that parallel ion flow can be determined by the balance between themore » parallel viscosity and the external momentum source in the region where the external source is much larger than the thermodynamic force driven source in the collisional plasmas. This is because the friction between C{sup 6+} and D{sup +} prevents a large difference between C{sup 6+} and D{sup +} flow velocities in such plasmas. The C{sup 6+} flow velocities, which are measured by the charge exchange recombination spectroscopy system, are numerically evaluated with this method. It is shown that the experimentally measured C{sup 6+} impurity flow velocities do not contradict clearly with the neoclassical estimations, and the dependence of parallel flow velocities on the magnetic field ripples is consistent in both results.« less

Characterizing the performance of the Conway-Maxwell Poisson generalized linear model.

PubMed

Francis, Royce A; Geedipally, Srinivas Reddy; Guikema, Seth D; Dhavala, Soma Sekhar; Lord, Dominique; LaRocca, Sarah

2012-01-01

Count data are pervasive in many areas of risk analysis; deaths, adverse health outcomes, infrastructure system failures, and traffic accidents are all recorded as count events, for example. Risk analysts often wish to estimate the probability distribution for the number of discrete events as part of doing a risk assessment. Traditional count data regression models of the type often used in risk assessment for this problem suffer from limitations due to the assumed variance structure. A more flexible model based on the Conway-Maxwell Poisson (COM-Poisson) distribution was recently proposed, a model that has the potential to overcome the limitations of the traditional model. However, the statistical performance of this new model has not yet been fully characterized. This article assesses the performance of a maximum likelihood estimation method for fitting the COM-Poisson generalized linear model (GLM). The objectives of this article are to (1) characterize the parameter estimation accuracy of the MLE implementation of the COM-Poisson GLM, and (2) estimate the prediction accuracy of the COM-Poisson GLM using simulated data sets. The results of the study indicate that the COM-Poisson GLM is flexible enough to model under-, equi-, and overdispersed data sets with different sample mean values. The results also show that the COM-Poisson GLM yields accurate parameter estimates. The COM-Poisson GLM provides a promising and flexible approach for performing count data regression. © 2011 Society for Risk Analysis.

Plasma FGF21 concentrations, adipose fibroblast growth factor receptor-1 and β-klotho expression decrease with fasting in northern elephant seals.

PubMed

Suzuki, Miwa; Lee, Andrew Y; Vázquez-Medina, José Pablo; Viscarra, Jose A; Crocker, Daniel E; Ortiz, Rudy M

2015-05-15

Fibroblast growth factor (FGF)-21 is secreted from the liver, pancreas, and adipose in response to prolonged fasting/starvation to facilitate lipid and glucose metabolism. Northern elephant seals naturally fast for several months, maintaining a relatively elevated metabolic rate to satisfy their energetic requirements. Thus, to better understand the impact of prolonged food deprivation on FGF21-associated changes, we analyzed the expression of FGF21, FGF receptor-1 (FGFR1), β-klotho (KLB; a co-activator of FGFR) in adipose, and plasma FGF21, glucose and 3-hydroxybutyrate in fasted elephant seal pups. Expression of FGFR1 and KLB mRNA decreased 98% and 43%, respectively, with fasting duration. While the 80% decrease in mean adipose FGF21 mRNA expression with fasting did not reach statistical significance, it paralleled the 39% decrease in plasma FGF21 concentrations suggesting that FGF21 is suppressed with fasting in elephant seals. Data demonstrate an atypical response of FGF21 to prolonged fasting in a mammal suggesting that FGF21-mediated mechanisms have evolved differentially in elephant seals. Furthermore, the typical fasting-induced, FGF21-mediated actions such as the inhibition of lipolysis in adipose may not be required in elephant seals as part of a naturally adapted mechanism to support their unique metabolic demands during prolonged fasting. Copyright © 2015 Elsevier Inc. All rights reserved.

Plasma FGF21 Concentrations, Adipose Fibroblast Growth Factor Receptor-1 and β-Klotho Expression Decrease with Fasting in Northern Elephant Seals

PubMed Central

Suzuki, Miwa; Lee, Andrew; Vázquez-Medina, Jose Pablo; Viscarra, Jose A.; Crocker, Daniel E.; Ortiz, Rudy M.

2015-01-01

Fibroblast growth factor (FGF)-21 is secreted from the liver, pancreas, and adipose in response to prolonged fasting/starvation to facilitate lipid and glucose metabolism. Northern elephant seals naturally fast for several months, maintaining a relatively elevated metabolic rate to satisfy their energetic requirements. Thus, to better understand the impact of prolonged food deprivation on FGF21-associated changes, we analyzed the expression of FGF21, FGF receptor-1 (FGFR1), β-klotho (KLB; a co-activator of FGFR) in adipose, and plasma FGF21, glucose and 3-hydroxybutyrate in fasted elephant seal pups. Expression of FGFR1 and KLB mRNA decreased 98% and 43%, respectively, with fasting duration. While the 80% decrease in mean adipose FGF21 mRNA expression with fasting did not reach statistical significance, it paralleled the 39% decrease in plasma FGF21 concentrations suggesting that FGF21 is suppressed with fasting in elephant seals. Data demonstrate an atypical response of FGF21 to prolonged fasting in a mammal suggesting that FGF21-mediated mechanisms have evolved differentially in elephant seals. Furthermore, the typical fasting-induced, FGF21-mediated actions such as the inhibition of lipolysis in adipose may not be required in elephant seals as part of a naturally adapted mechanism to support their unique metabolic demands during prolonged fasting. PMID:25857751

A fast pulse design for parallel excitation with gridding conjugate gradient.

PubMed

Feng, Shuo; Ji, Jim

2013-01-01

Parallel excitation (pTx) is recognized as a crucial technique in high field MRI to address the transmit field inhomogeneity problem. However, it can be time consuming to design pTx pulses which is not desirable. In this work, we propose a pulse design with gridding conjugate gradient (CG) based on the small-tip-angle approximation. The two major time consuming matrix-vector multiplications are substituted by two operators which involves with FFT and gridding only. Simulation results have shown that the proposed method is 3 times faster than conventional method and the memory cost is reduced by 1000 times.

MCBooster: a library for fast Monte Carlo generation of phase-space decays on massively parallel platforms.

NASA Astrophysics Data System (ADS)

Alves Júnior, A. A.; Sokoloff, M. D.

2017-10-01

MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. This contribution summarizes the main features of MCBooster. A basic description of the user interface and some examples of applications are provided, along with measurements of performance in a variety of environments

ADDER CIRCUIT

DOEpatents

Jacobsohn, D.H.; Merrill, L.C.

1959-01-20

An improved parallel addition unit is described which is especially adapted for use in electronic digital computers and characterized by propagation of the carry signal through each of a plurality of denominationally ordered stages within a minimum time interval. In its broadest aspects, the invention incorporates a fast multistage parallel digital adder including a plurality of adder circuits, carry-propagation circuit means in all but the most significant digit stage, means for conditioning each carry-propagation circuit during the time period in which information is placed into the adder circuits, and means coupling carry-generation portions of thc adder circuit to the carry propagating means.

Perceptual learning in visual search: fast, enduring, but non-specific.

PubMed

Sireteanu, R; Rettenbach, R

1995-07-01

Visual search has been suggested as a tool for isolating visual primitives. Elementary "features" were proposed to involve parallel search, while serial search is necessary for items without a "feature" status, or, in some cases, for conjunctions of "features". In this study, we investigated the role of practice in visual search tasks. We found that, under some circumstances, initially serial tasks can become parallel after a few hundred trials. Learning in visual search is far less specific than learning of visual discriminations and hyperacuity, suggesting that it takes place at another level in the central visual pathway, involving different neural circuits.

A Fast parallel tridiagonal algorithm for a class of CFD applications

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Sun, Xian-He

1996-01-01

The parallel diagonal dominant (PDD) algorithm is an efficient tridiagonal solver. This paper presents for study a variation of the PDD algorithm, the reduced PDD algorithm. The new algorithm maintains the minimum communication provided by the PDD algorithm, but has a reduced operation count. The PDD algorithm also has a smaller operation count than the conventional sequential algorithm for many applications. Accuracy analysis is provided for the reduced PDD algorithm for symmetric Toeplitz tridiagonal (STT) systems. Implementation results on Langley's Intel Paragon and IBM SP2 show that both the PDD and reduced PDD algorithms are efficient and scalable.

A Method of Poisson's Ration Imaging Within a Material Part

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1994-01-01

The present invention is directed to a method of displaying the Poisson's ratio image of a material part. In the present invention, longitudinal data is produced using a longitudinal wave transducer and shear wave data is produced using a shear wave transducer. The respective data is then used to calculate the Poisson's ratio for the entire material part. The Poisson's ratio approximations are then used to display the data.

Method of Poisson's ratio imaging within a material part

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1996-01-01

The present invention is directed to a method of displaying the Poisson's ratio image of a material part. In the present invention longitudinal data is produced using a longitudinal wave transducer and shear wave data is produced using a shear wave transducer. The respective data is then used to calculate the Poisson's ratio for the entire material part. The Poisson's ratio approximations are then used to displayed the image.

Effect of Poisson's loss factor of rubbery material on underwater sound absorption of anechoic coatings

NASA Astrophysics Data System (ADS)

Zhong, Jie; Zhao, Honggang; Yang, Haibin; Yin, Jianfei; Wen, Jihong

2018-06-01

Rubbery coatings embedded with air cavities are commonly used on underwater structures to reduce reflection of incoming sound waves. In this paper, the relationships between Poisson's and modulus loss factors of rubbery materials are theoretically derived, the different effects of the tiny Poisson's loss factor on characterizing the loss factors of shear and longitudinal moduli are revealed. Given complex Young's modulus and dynamic Poisson's ratio, it is found that the shear loss factor has almost invisible variation with the Poisson's loss factor and is very close to the loss factor of Young's modulus, while the longitudinal loss factor almost linearly decreases with the increase of Poisson's loss factor. Then, a finite element (FE) model is used to investigate the effect of the tiny Poisson's loss factor, which is generally neglected in some FE models, on the underwater sound absorption of rubbery coatings. Results show that the tiny Poisson's loss factor has a significant effect on the sound absorption of homogeneous coatings within the concerned frequency range, while it has both frequency- and structure-dependent influence on the sound absorption of inhomogeneous coatings with embedded air cavities. Given the material parameters and cavity dimensions, more obvious effect can be observed for the rubbery coating with a larger lattice constant and/or a thicker cover layer.

A Review of Multivariate Distributions for Count Data Derived from the Poisson Distribution

PubMed Central

Inouye, David; Yang, Eunho; Allen, Genevera; Ravikumar, Pradeep

2017-01-01

The Poisson distribution has been widely studied and used for modeling univariate count-valued data. Multivariate generalizations of the Poisson distribution that permit dependencies, however, have been far less popular. Yet, real-world high-dimensional count-valued data found in word counts, genomics, and crime statistics, for example, exhibit rich dependencies, and motivate the need for multivariate distributions that can appropriately model this data. We review multivariate distributions derived from the univariate Poisson, categorizing these models into three main classes: 1) where the marginal distributions are Poisson, 2) where the joint distribution is a mixture of independent multivariate Poisson distributions, and 3) where the node-conditional distributions are derived from the Poisson. We discuss the development of multiple instances of these classes and compare the models in terms of interpretability and theory. Then, we empirically compare multiple models from each class on three real-world datasets that have varying data characteristics from different domains, namely traffic accident data, biological next generation sequencing data, and text data. These empirical experiments develop intuition about the comparative advantages and disadvantages of each class of multivariate distribution that was derived from the Poisson. Finally, we suggest new research directions as explored in the subsequent discussion section. PMID:28983398

Non-linear properties of metallic cellular materials with a negative Poisson's ratio

NASA Technical Reports Server (NTRS)

Choi, J. B.; Lakes, R. S.

1992-01-01

Negative Poisson's ratio copper foam was prepared and characterized experimentally. The transformation into re-entrant foam was accomplished by applying sequential permanent compressions above the yield point to achieve a triaxial compression. The Poisson's ratio of the re-entrant foam depended on strain and attained a relative minimum at strains near zero. Poisson's ratio as small as -0.8 was achieved. The strain dependence of properties occurred over a narrower range of strain than in the polymer foams studied earlier. Annealing of the foam resulted in a slightly greater magnitude of negative Poisson's ratio and greater toughness at the expense of a decrease in the Young's modulus.

Nonlinear and Anisotropic Tensile Properties of Graft Materials used in Soft Tissue Applications

PubMed Central

Yoder, Jonathon H; Elliott, Dawn M

2010-01-01

Background The mechanical properties of extracellular matrix grafts that are intended to augment or replace soft tissues should be comparable to the native tissue. Such grafts are often used in fiber-reinforced tissue applications that undergo multi-axial loading and therefore knowledge of the anisotropic and nonlinear properties are needed, including the moduli and Poisson's ratio in two orthogonal directions within the plane of the graft. The objective of this study was to measure the tensile mechanical properties of several marketed grafts: Alloderm, Restore, CuffPatch, and OrthADAPT. Methods The degree of anisotropy and nonlinearity within each graft was evaluated from uniaxial tensile tests and compared to their native tissue. Results The Alloderm graft was anisotropic in both the toe and linear-region of the stress-strain response, was highly nonlinear, and generally had low properties. The Restore and CuffPatch grafts had similar stress-strain responses, were largely isotropic, had a linear-region modulus of 18 MPa, and were nonlinear. OrthADAPT was anisotropic in the linear region (131 vs 47 MPa) and was highly nonlinear. The Poisson ratio for all grafts was between 0.4 and 0.7, except for the parallel orientation of Restore which was greater than 1.0. Interpretation Having an informed understanding of how the available grafts perform mechanically will allow for better assessment by the physician for which graft to apply depending upon its application. PMID:20129728

Nonlinear and anisotropic tensile properties of graft materials used in soft tissue applications.

PubMed

Yoder, Jonathon H; Elliott, Dawn M

2010-05-01

The mechanical properties of extracellular matrix grafts that are intended to augment or replace soft tissues should be comparable to the native tissue. Such grafts are often used in fiber-reinforced tissue applications that undergo multi-axial loading and therefore knowledge of the anisotropic and nonlinear properties are needed, including the moduli and Poisson's ratio in two orthogonal directions within the plane of the graft. The objective of this study was to measure the tensile mechanical properties of several marketed grafts: Alloderm, Restore, CuffPatch, and OrthADAPT. The degree of anisotropy and non-linearity within each graft was evaluated from uniaxial tensile tests and compared to their native tissue. The Alloderm graft was anisotropic in both the toe- and linear-region of the stress-strain response, was highly nonlinear, and generally had low properties. The Restore and CuffPatch grafts had similar stress-strain responses, were largely isotropic, had a linear-region modulus of 18MPa, and were nonlinear. OrthADAPT was anisotropic in the linear-region (131 MPA vs 47MPa in the toe-region) and was highly nonlinear. The Poisson ratio for all grafts was between 0.4 and 0.7, except for the parallel orientation of Restore which was greater than 1.0. Having an informed understanding of how the available grafts perform mechanically will allow for better assessment by the physician for which graft to apply depending upon its application. Copyright 2010 Elsevier Ltd. All rights reserved.

rfpipe: Radio interferometric transient search pipeline

NASA Astrophysics Data System (ADS)

Law, Casey J.

2017-10-01

rfpipe supports Python-based analysis of radio interferometric data (especially from the Very Large Array) and searches for fast radio transients. This extends on the rtpipe library (ascl:1706.002) with new approaches to parallelization, acceleration, and more portable data products. rfpipe can run in standalone mode or be in a cluster environment.

Fast comprehensive analysis of vitamin D and triacylglycerols in dietary supplements using multiple parallel mass spectrometers

USDA-ARS?s Scientific Manuscript database

New, faster methods have been developed for analysis of vitamin D and triacylglycerols that eliminate hours of wet chemistry and preparative chromatography, while providing more information than classical methods for analysis. Unprecedented detail is provided by combining liquid chromatography with ...

Compositions, Random Sums and Continued Random Fractions of Poisson and Fractional Poisson Processes

NASA Astrophysics Data System (ADS)

Orsingher, Enzo; Polito, Federico

2012-08-01

In this paper we consider the relation between random sums and compositions of different processes. In particular, for independent Poisson processes N α ( t), N β ( t), t>0, we have that N_{α}(N_{β}(t)) stackrel{d}{=} sum_{j=1}^{N_{β}(t)} Xj, where the X j s are Poisson random variables. We present a series of similar cases, where the outer process is Poisson with different inner processes. We highlight generalisations of these results where the external process is infinitely divisible. A section of the paper concerns compositions of the form N_{α}(tauk^{ν}), ν∈(0,1], where tauk^{ν} is the inverse of the fractional Poisson process, and we show how these compositions can be represented as random sums. Furthermore we study compositions of the form Θ( N( t)), t>0, which can be represented as random products. The last section is devoted to studying continued fractions of Cauchy random variables with a Poisson number of levels. We evaluate the exact distribution and derive the scale parameter in terms of ratios of Fibonacci numbers.

Modeling electrokinetics in ionic liquids: General

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

Wang, Chao; Bao, Jie; Pan, Wenxiao

2017-04-07

Using direct numerical simulations we provide a thorough study on the electrokinetics of ionic liquids. In particular, the modfied Poisson-Nernst-Planck (MPNP) equations are solved to capture the crowding and overscreening effects that are the characteristics of an ionic liquid. For modeling electrokinetic flows in an ionic liquid, the MPNP equations are coupled with the Navier-Stokes equations to study the coupling of ion transport, hydrodynamics, and electrostatic forces. Specifically, we consider the ion transport between two parallel plates, charging dynamics in a 2D straight-walled pore, electro-osmotic ow in a nano-channel, electroconvective instability on a plane ion-selective surface, and electroconvective ow onmore » a curved ion-selective surface. We discuss how the crowding and overscreening effects and their interplay affect the electrokinetic behaviors of ionic liquids in these application problems.« less

Seismic anisotropy in the Hellenic subduction zone: Effects of slab segmentation and subslab mantle flow

NASA Astrophysics Data System (ADS)

Evangelidis, C. P.

2017-12-01

The segmentation and differentiation of subducting slabs have considerable effects on mantle convection and tectonics. The Hellenic subduction zone is a complex convergent margin with strong curvature and fast slab rollback. The upper mantle seismic anisotropy in the region is studied focusing at its western and eastern edges in order to explore the effects of possible slab segmentation on mantle flow and fabrics. Complementary to new SKS shear-wave splitting measurements in regions not adequately sampled so far, the source-side splitting technique is applied to constrain the depth of anisotropy and to densify measurements. In the western Hellenic arc, a trench-normal subslab anisotropy is observed near the trench. In the forearc domain, source-side and SKS measurements reveal a trench-parallel pattern. This indicates subslab trench-parallel mantle flow, associated with return flow due to the fast slab rollback. The passage from continental to oceanic subduction in the western Hellenic zone is illustrated by a forearc transitional anisotropy pattern. This indicates subslab mantle flow parallel to a NE-SW smooth ramp that possibly connects the two subducted slabs. A young tear fault initiated at the Kefalonia Transform Fault is likely not entirely developed, as this trench-parallel anisotropy pattern is observed along the entire western Hellenic subduction system, even following this horizontal offset between the two slabs. At the eastern side of the Hellenic subduction zone, subslab source-side anisotropy measurements show a general trench-normal pattern. These are associated with mantle flow through a possible ongoing tearing of the oceanic lithosphere in the area. Although the exact geometry of this slab tear is relatively unknown, SKS trench-parallel measurements imply that the tear has not reached the surface yet. Further exploration of the Hellenic subduction system is necessary; denser seismic networks should be deployed at both its edges in order to achieve a more definite image of the structure and geodynamics of this area.

An O(N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles

NASA Astrophysics Data System (ADS)

Jiang, Xikai; Li, Jiyuan; Zhao, Xujun; Qin, Jian; Karpeev, Dmitry; Hernandez-Ortiz, Juan; de Pablo, Juan J.; Heinonen, Olle

2016-08-01

Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct computational evaluation requires O(N2) operations, where N is the number of unknowns. Such a scaling, which arises from the many-body nature of the relevant Green's function, has precluded wide-spread adoption of integral methods for solution of large-scale scientific and engineering problems. In this work, a parallel computational approach is presented that relies on using scalable open source libraries and utilizes a kernel-independent Fast Multipole Method (FMM) to evaluate the integrals in O(N) operations, with O(N) memory cost, thereby substantially improving the scalability and efficiency of computational integral methods. We demonstrate the accuracy, efficiency, and scalability of our approach in the context of two examples. In the first, we solve a boundary value problem for a ferroelectric/ferromagnetic volume in free space. In the second, we solve an electrostatic problem involving polarizable dielectric bodies in an unbounded dielectric medium. The results from these test cases show that our proposed parallel approach, which is built on a kernel-independent FMM, can enable highly efficient and accurate simulations and allow for considerable flexibility in a broad range of applications.

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

PubMed

Vollmar, S; Michel, C; Treffert, J T; Newport, D F; Casey, M; Knöss, C; Wienhard, K; Liu, X; Defrise, M; Heiss, W D

2002-08-07

Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

Adropin induction of lipoprotein lipase expression in tilapia hepatocytes.

PubMed

Lian, Anji; Wu, Keqiang; Liu, Tianqiang; Jiang, Nan; Jiang, Quan

2016-01-01

The peptide hormone adropin plays a role in energy homeostasis. However, biological actions of adropin in non-mammalian species are still lacking. Using tilapia as a model, we examined the role of adropin in lipoprotein lipase (LPL) regulation in hepatocytes. To this end, the structural identity of tilapia adropin was established by 5'/3'-rapid amplification of cDNA ends (RACE). The transcripts of tilapia adropin were ubiquitously expressed in various tissues with the highest levels in the liver and hypothalamus. The prolonged fasting could elevate tilapia hepatic adropin gene expression, whereas no effect of fasting was observed on hypothalamic adropin gene levels. In primary cultures of tilapia hepatocytes, synthetic adropin was effective in stimulating LPL release, cellular LPL content, and total LPL production. The increase in LPL production also occurred with parallel rises in LPL gene levels. In parallel experiments, adropin could elevate cAMP production and up-regulate protein kinase A (PKA) and PKC activities. Using a pharmacological approach, cAMP/PKA and PLC/inositol trisphosphate (IP3)/PKC cascades were shown to be involved in adropin-stimulated LPL gene expression. Parallel inhibition of p38MAPK and Erk1/2, however, were not effective in these regards. Our findings provide, for the first time, evidence that adropin could stimulate LPL gene expression via direct actions in tilapia hepatocytes through the activation of multiple signaling mechanisms. © 2016 Society for Endocrinology.

An O( N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles

DOE PAGES

Jiang, Xikai; Li, Jiyuan; Zhao, Xujun; ...

2016-08-10

Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct computational evaluation requires O( N 2) operations, where N is the number of unknowns. Such a scaling, which arises from the many-body nature of the relevant Green's function, has precluded wide-spread adoption of integral methods for solution of large-scale scientific and engineering problems. In this work, a parallel computational approach is presented that relies on using scalable open source libraries and utilizes a kernel-independent Fast Multipole Methodmore » (FMM) to evaluate the integrals in O( N) operations, with O( N) memory cost, thereby substantially improving the scalability and efficiency of computational integral methods. We demonstrate the accuracy, efficiency, and scalability of our approach in the context of two examples. In the first, we solve a boundary value problem for a ferroelectric/ferromagnetic volume in free space. In the second, we solve an electrostatic problem involving polarizable dielectric bodies in an unbounded dielectric medium. Lastly, the results from these test cases show that our proposed parallel approach, which is built on a kernel-independent FMM, can enable highly efficient and accurate simulations and allow for considerable flexibility in a broad range of applications.« less

Non-Poisson Processes: Regression to Equilibrium Versus Equilibrium Correlation Functions

DTIC Science & Technology

2004-07-07

ARTICLE IN PRESSPhysica A 347 (2005) 268–2880378-4371/$ - doi:10.1016/j Correspo E-mail adwww.elsevier.com/locate/physaNon- Poisson processes : regression...05.40.a; 89.75.k; 02.50.Ey Keywords: Stochastic processes; Non- Poisson processes ; Liouville and Liouville-like equations; Correlation function...which is not legitimate with renewal non- Poisson processes , is a correct property if the deviation from the exponential relaxation is obtained by time

Probabilistic Estimation of Rare Random Collisions in 3 Space

DTIC Science & Technology

2009-03-01

extended Poisson process as a feature of probability theory. With the bulk of research in extended Poisson processes going into parame- ter estimation, the...application of extended Poisson processes to spatial processes is largely untouched. Faddy performed a short study of spatial data, but overtly...the theory of extended Poisson processes . To date, the processes are limited in that the rates only depend on the number of arrivals at some time

Block-Parallel Data Analysis with DIY2

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

Morozov, Dmitriy; Peterka, Tom

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial,more » parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.« less

Poisson-type inequalities for growth properties of positive superharmonic functions.

PubMed

Luan, Kuan; Vieira, John

2017-01-01

In this paper, we present new Poisson-type inequalities for Poisson integrals with continuous data on the boundary. The obtained inequalities are used to obtain growth properties at infinity of positive superharmonic functions in a smooth cone.

Information transmission using non-poisson regular firing.

PubMed

Koyama, Shinsuke; Omi, Takahiro; Kass, Robert E; Shinomoto, Shigeru

2013-04-01

In many cortical areas, neural spike trains do not follow a Poisson process. In this study, we investigate a possible benefit of non-Poisson spiking for information transmission by studying the minimal rate fluctuation that can be detected by a Bayesian estimator. The idea is that an inhomogeneous Poisson process may make it difficult for downstream decoders to resolve subtle changes in rate fluctuation, but by using a more regular non-Poisson process, the nervous system can make rate fluctuations easier to detect. We evaluate the degree to which regular firing reduces the rate fluctuation detection threshold. We find that the threshold for detection is reduced in proportion to the coefficient of variation of interspike intervals.

Fast cat-eye effect target recognition based on saliency extraction

NASA Astrophysics Data System (ADS)

Li, Li; Ren, Jianlin; Wang, Xingbin

2015-09-01

Background complexity is a main reason that results in false detection in cat-eye target recognition. Human vision has selective attention property which can help search the salient target from complex unknown scenes quickly and precisely. In the paper, we propose a novel cat-eye effect target recognition method named Multi-channel Saliency Processing before Fusion (MSPF). This method combines traditional cat-eye target recognition with the selective characters of visual attention. Furthermore, parallel processing enables it to achieve fast recognition. Experimental results show that the proposed method performs better in accuracy, robustness and speed compared to other methods.

A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

2003-01-01

In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

Graphic Simulations of the Poisson Process.

DTIC Science & Technology

1982-10-01

RANDOM NUMBERS AND TRANSFORMATIONS..o......... 11 Go THE RANDOM NUMBERGENERATOR....... .oo..... 15 III. POISSON PROCESSES USER GUIDE....oo.ooo ......... o...again. In the superimposed mode, two Poisson processes are active, each with a different rate parameter, (call them Type I and Type II with respective...occur. The value ’p’ is generated by the following equation where ’Li’ and ’L2’ are the rates of the two Poisson processes ; p = Li / (Li + L2) The value

Soft network materials with isotropic negative Poisson's ratios over large strains.

PubMed

Liu, Jianxing; Zhang, Yihui

2018-01-31

Auxetic materials with negative Poisson's ratios have important applications across a broad range of engineering areas, such as biomedical devices, aerospace engineering and automotive engineering. A variety of design strategies have been developed to achieve artificial auxetic materials with controllable responses in the Poisson's ratio. The development of designs that can offer isotropic negative Poisson's ratios over large strains can open up new opportunities in emerging biomedical applications, which, however, remains a challenge. Here, we introduce deterministic routes to soft architected materials that can be tailored precisely to yield the values of Poisson's ratio in the range from -1 to 1, in an isotropic manner, with a tunable strain range from 0% to ∼90%. The designs rely on a network construction in a periodic lattice topology, which incorporates zigzag microstructures as building blocks to connect lattice nodes. Combined experimental and theoretical studies on broad classes of network topologies illustrate the wide-ranging utility of these concepts. Quantitative mechanics modeling under both infinitesimal and finite deformations allows the development of a rigorous design algorithm that determines the necessary network geometries to yield target Poisson ratios over desired strain ranges. Demonstrative examples in artificial skin with both the negative Poisson's ratio and the nonlinear stress-strain curve precisely matching those of the cat's skin and in unusual cylindrical structures with engineered Poisson effect and shape memory effect suggest potential applications of these network materials.

Universal Poisson Statistics of mRNAs with Complex Decay Pathways.

PubMed

Thattai, Mukund

2016-01-19

Messenger RNA (mRNA) dynamics in single cells are often modeled as a memoryless birth-death process with a constant probability per unit time that an mRNA molecule is synthesized or degraded. This predicts a Poisson steady-state distribution of mRNA number, in close agreement with experiments. This is surprising, since mRNA decay is known to be a complex process. The paradox is resolved by realizing that the Poisson steady state generalizes to arbitrary mRNA lifetime distributions. A mapping between mRNA dynamics and queueing theory highlights an identifiability problem: a measured Poisson steady state is consistent with a large variety of microscopic models. Here, I provide a rigorous and intuitive explanation for the universality of the Poisson steady state. I show that the mRNA birth-death process and its complex decay variants all take the form of the familiar Poisson law of rare events, under a nonlinear rescaling of time. As a corollary, not only steady-states but also transients are Poisson distributed. Deviations from the Poisson form occur only under two conditions, promoter fluctuations leading to transcriptional bursts or nonindependent degradation of mRNA molecules. These results place severe limits on the power of single-cell experiments to probe microscopic mechanisms, and they highlight the need for single-molecule measurements. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Modularized Parallel Neutron Instrument Simulation on the TeraGrid

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

Chen, Meili; Cobb, John W; Hagen, Mark E

2007-01-01

In order to build a bridge between the TeraGrid (TG), a national scale cyberinfrastructure resource, and neutron science, the Neutron Science TeraGrid Gateway (NSTG) is focused on introducing productive HPC usage to the neutron science community, primarily the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL). Monte Carlo simulations are used as a powerful tool for instrument design and optimization at SNS. One of the successful efforts of a collaboration team composed of NSTG HPC experts and SNS instrument scientists is the development of a software facility named PSoNI, Parallelizing Simulations of Neutron Instruments. Parallelizing the traditional serialmore » instrument simulation on TeraGrid resources, PSoNI quickly computes full instrument simulation at sufficient statistical levels in instrument de-sign. Upon SNS successful commissioning, to the end of 2007, three out of five commissioned instruments in SNS target station will be available for initial users. Advanced instrument study, proposal feasibility evalua-tion, and experiment planning are on the immediate schedule of SNS, which pose further requirements such as flexibility and high runtime efficiency on fast instrument simulation. PSoNI has been redesigned to meet the new challenges and a preliminary version is developed on TeraGrid. This paper explores the motivation and goals of the new design, and the improved software structure. Further, it describes the realized new fea-tures seen from MPI parallelized McStas running high resolution design simulations of the SEQUOIA and BSS instruments at SNS. A discussion regarding future work, which is targeted to do fast simulation for automated experiment adjustment and comparing models to data in analysis, is also presented.« less

When fast logic meets slow belief: Evidence for a parallel-processing model of belief bias.

PubMed

Trippas, Dries; Thompson, Valerie A; Handley, Simon J

2017-05-01

Two experiments pitted the default-interventionist account of belief bias against a parallel-processing model. According to the former, belief bias occurs because a fast, belief-based evaluation of the conclusion pre-empts a working-memory demanding logical analysis. In contrast, according to the latter both belief-based and logic-based responding occur in parallel. Participants were given deductive reasoning problems of variable complexity and instructed to decide whether the conclusion was valid on half the trials or to decide whether the conclusion was believable on the other half. When belief and logic conflict, the default-interventionist view predicts that it should take less time to respond on the basis of belief than logic, and that the believability of a conclusion should interfere with judgments of validity, but not the reverse. The parallel-processing view predicts that beliefs should interfere with logic judgments only if the processing required to evaluate the logical structure exceeds that required to evaluate the knowledge necessary to make a belief-based judgment, and vice versa otherwise. Consistent with this latter view, for the simplest reasoning problems (modus ponens), judgments of belief resulted in lower accuracy than judgments of validity, and believability interfered more with judgments of validity than the converse. For problems of moderate complexity (modus tollens and single-model syllogisms), the interference was symmetrical, in that validity interfered with belief judgments to the same degree that believability interfered with validity judgments. For the most complex (three-term multiple-model syllogisms), conclusion believability interfered more with judgments of validity than vice versa, in spite of the significant interference from conclusion validity on judgments of belief.

On a model of three-dimensional bursting and its parallel implementation

NASA Astrophysics Data System (ADS)

Tabik, S.; Romero, L. F.; Garzón, E. M.; Ramos, J. I.

2008-04-01

A mathematical model for the simulation of three-dimensional bursting phenomena and its parallel implementation are presented. The model consists of four nonlinearly coupled partial differential equations that include fast and slow variables, and exhibits bursting in the absence of diffusion. The differential equations have been discretized by means of a second-order accurate in both space and time, linearly-implicit finite difference method in equally-spaced grids. The resulting system of linear algebraic equations at each time level has been solved by means of the Preconditioned Conjugate Gradient (PCG) method. Three different parallel implementations of the proposed mathematical model have been developed; two of these implementations, i.e., the MPI and the PETSc codes, are based on a message passing paradigm, while the third one, i.e., the OpenMP code, is based on a shared space address paradigm. These three implementations are evaluated on two current high performance parallel architectures, i.e., a dual-processor cluster and a Shared Distributed Memory (SDM) system. A novel representation of the results that emphasizes the most relevant factors that affect the performance of the paralled implementations, is proposed. The comparative analysis of the computational results shows that the MPI and the OpenMP implementations are about twice more efficient than the PETSc code on the SDM system. It is also shown that, for the conditions reported here, the nonlinear dynamics of the three-dimensional bursting phenomena exhibits three stages characterized by asynchronous, synchronous and then asynchronous oscillations, before a quiescent state is reached. It is also shown that the fast system reaches steady state in much less time than the slow variables.

High-speed spectral domain optical coherence tomography using non-uniform fast Fourier transform

PubMed Central

Chan, Kenny K. H.; Tang, Shuo

2010-01-01

The useful imaging range in spectral domain optical coherence tomography (SD-OCT) is often limited by the depth dependent sensitivity fall-off. Processing SD-OCT data with the non-uniform fast Fourier transform (NFFT) can improve the sensitivity fall-off at maximum depth by greater than 5dB concurrently with a 30 fold decrease in processing time compared to the fast Fourier transform with cubic spline interpolation method. NFFT can also improve local signal to noise ratio (SNR) and reduce image artifacts introduced in post-processing. Combined with parallel processing, NFFT is shown to have the ability to process up to 90k A-lines per second. High-speed SD-OCT imaging is demonstrated at camera-limited 100 frames per second on an ex-vivo squid eye. PMID:21258551

The solution of large multi-dimensional Poisson problems

NASA Technical Reports Server (NTRS)

Stone, H. S.

1974-01-01

The Buneman algorithm for solving Poisson problems can be adapted to solve large Poisson problems on computers with a rotating drum memory so that the computation is done with very little time lost due to rotational latency of the drum.

3D Compton scattering imaging and contour reconstruction for a class of Radon transforms

NASA Astrophysics Data System (ADS)

Rigaud, Gaël; Hahn, Bernadette N.

2018-07-01

Compton scattering imaging is a nascent concept arising from the current development of high-sensitive energy detectors and is devoted to exploit the scattering radiation to image the electron density of the studied medium. Such detectors are able to collect incoming photons in terms of energy. This paper introduces potential 3D modalities in Compton scattering imaging (CSI). The associated measured data are modeled using a class of generalized Radon transforms. The study of this class of operators leads to build a filtered back-projection kind algorithm preserving the contours of the sought-for function and offering a fast approach to partially solve the associated inverse problems. Simulation results including Poisson noise demonstrate the potential of this new imaging concept as well as the proposed image reconstruction approach.

Solution of elliptic partial differential equations by fast Poisson solvers using a local relaxation factor. 1: One-step method

NASA Technical Reports Server (NTRS)

Chang, S. C.

1986-01-01

An algorithm for solving a large class of two- and three-dimensional nonseparable elliptic partial differential equations (PDE's) is developed and tested. It uses a modified D'Yakanov-Gunn iterative procedure in which the relaxation factor is grid-point dependent. It is easy to implement and applicable to a variety of boundary conditions. It is also computationally efficient, as indicated by the results of numerical comparisons with other established methods. Furthermore, the current algorithm has the advantage of possessing two important properties which the traditional iterative methods lack; that is: (1) the convergence rate is relatively insensitive to grid-cell size and aspect ratio, and (2) the convergence rate can be easily estimated by using the coefficient of the PDE being solved.

Solution of elliptic PDEs by fast Poisson solvers using a local relaxation factor

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung

1986-01-01

A large class of two- and three-dimensional, nonseparable elliptic partial differential equations (PDEs) is presently solved by means of novel one-step (D'Yakanov-Gunn) and two-step (accelerated one-step) iterative procedures, using a local, discrete Fourier analysis. In addition to being easily implemented and applicable to a variety of boundary conditions, these procedures are found to be computationally efficient on the basis of the results of numerical comparison with other established methods, which lack the present one's: (1) insensitivity to grid cell size and aspect ratio, and (2) ease of convergence rate estimation by means of the coefficient of the PDE being solved. The two-step procedure is numerically demonstrated to outperform the one-step procedure in the case of PDEs with variable coefficients.

Efficient multitasking of Choleski matrix factorization on CRAY supercomputers

NASA Technical Reports Server (NTRS)

Overman, Andrea L.; Poole, Eugene L.

1991-01-01

A Choleski method is described and used to solve linear systems of equations that arise in large scale structural analysis. The method uses a novel variable-band storage scheme and is structured to exploit fast local memory caches while minimizing data access delays between main memory and vector registers. Several parallel implementations of this method are described for the CRAY-2 and CRAY Y-MP computers demonstrating the use of microtasking and autotasking directives. A portable parallel language, FORCE, is used for comparison with the microtasked and autotasked implementations. Results are presented comparing the matrix factorization times for three representative structural analysis problems from runs made in both dedicated and multi-user modes on both computers. CPU and wall clock timings are given for the parallel implementations and are compared to single processor timings of the same algorithm.

Parallel, stochastic measurement of molecular surface area.

PubMed

Juba, Derek; Varshney, Amitabh

2008-08-01

Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy.

Parallel momentum input by tangential neutral beam injections in stellarator and heliotron plasmas

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

Nishimura, S., E-mail: nishimura.shin@lhd.nifs.ac.jp; Nakamura, Y.; Nishioka, K.

The configuration dependence of parallel momentum inputs to target plasma particle species by tangentially injected neutral beams is investigated in non-axisymmetric stellarator/heliotron model magnetic fields by assuming the existence of magnetic flux-surfaces. In parallel friction integrals of the full Rosenbluth-MacDonald-Judd collision operator in thermal particles' kinetic equations, numerically obtained eigenfunctions are used for excluding trapped fast ions that cannot contribute to the friction integrals. It is found that the momentum inputs to thermal ions strongly depend on magnetic field strength modulations on the flux-surfaces, while the input to electrons is insensitive to the modulation. In future plasma flow studies requiringmore » flow calculations of all particle species in more general non-symmetric toroidal configurations, the eigenfunction method investigated here will be useful.« less

The fast and the slow of skilled bimanual rhythm production: parallel versus integrated timing.

PubMed

Krampe, R T; Kliegl, R; Mayr, U; Engbert, R; Vorberg, D

2000-02-01

Professional pianists performed 2 bimanual rhythms at a wide range of different tempos. The polyrhythmic task required the combination of 2 isochronous sequences (3 against 4) between the hands; in the syncopated rhythm task successive keystrokes formed intervals of identical (isochronous) durations. At slower tempos, pianists relied on integrated timing control merging successive intervals between the hands into a common reference frame. A timer-motor model is proposed based on the concepts of rate fluctuation and the distinction between target specification and timekeeper execution processes as a quantitative account of performance at slow tempos. At rapid rates expert pianists used hand-independent, parallel timing control. In alternative to a model based on a single central clock, findings support a model of flexible control structures with multiple timekeepers that can work in parallel to accommodate specific task constraints.

A rapid parallelization of cone-beam projection and back-projection operator based on texture fetching interpolation

NASA Astrophysics Data System (ADS)

Xie, Lizhe; Hu, Yining; Chen, Yang; Shi, Luyao

2015-03-01

Projection and back-projection are the most computational consuming parts in Computed Tomography (CT) reconstruction. Parallelization strategies using GPU computing techniques have been introduced. We in this paper present a new parallelization scheme for both projection and back-projection. The proposed method is based on CUDA technology carried out by NVIDIA Corporation. Instead of build complex model, we aimed on optimizing the existing algorithm and make it suitable for CUDA implementation so as to gain fast computation speed. Besides making use of texture fetching operation which helps gain faster interpolation speed, we fixed sampling numbers in the computation of projection, to ensure the synchronization of blocks and threads, thus prevents the latency caused by inconsistent computation complexity. Experiment results have proven the computational efficiency and imaging quality of the proposed method.

On the Determination of Poisson Statistics for Haystack Radar Observations of Orbital Debris

NASA Technical Reports Server (NTRS)

Stokely, Christopher L.; Benbrook, James R.; Horstman, Matt

2007-01-01

A convenient and powerful method is used to determine if radar detections of orbital debris are observed according to Poisson statistics. This is done by analyzing the time interval between detection events. For Poisson statistics, the probability distribution of the time interval between events is shown to be an exponential distribution. This distribution is a special case of the Erlang distribution that is used in estimating traffic loads on telecommunication networks. Poisson statistics form the basis of many orbital debris models but the statistical basis of these models has not been clearly demonstrated empirically until now. Interestingly, during the fiscal year 2003 observations with the Haystack radar in a fixed staring mode, there are no statistically significant deviations observed from that expected with Poisson statistics, either independent or dependent of altitude or inclination. One would potentially expect some significant clustering of events in time as a result of satellite breakups, but the presence of Poisson statistics indicates that such debris disperse rapidly with respect to Haystack's very narrow radar beam. An exception to Poisson statistics is observed in the months following the intentional breakup of the Fengyun satellite in January 2007.

Bayesian inference on multiscale models for poisson intensity estimation: applications to photon-limited image denoising.

PubMed

Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George

2009-08-01

We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.

A numerical analysis of plasma non-uniformity in the parallel plate VHF-CCP and the comparison among various model

NASA Astrophysics Data System (ADS)

Sawada, Ikuo

2012-10-01

We measured the radial distribution of electron density in a 200 mm parallel plate CCP and compared it with results from numerical simulations. The experiments were conducted with pure Ar gas with pressures ranging from 15 to 100 mTorr and 60 MHz applied at the top electrode with powers from 500 to 2000W. The measured electron profile is peaked in the center, and the relative non-uniformity is higher at 100 mTorr than at 15 mTorr. We compare the experimental results with simulations with both HPEM and Monte-Carlo/PIC codes. In HPEM simulations, we used either fluid or electron Monte-Carlo module, and the Poisson or the Electromagnetic solver. None of the models were able to duplicate the experimental results quantitatively. However, HPEM with the electron Monte-Carlo module and PIC qualitatively matched the experimental results. We will discuss the results from these models and how they illuminate the mechanism of enhanced electron central peak.[4pt] [1] T. Oshita, M. Matsukuma, S.Y. Kang, I. Sawada: The effect of non-uniform RF voltage in a CCP discharge, The 57^th JSAP Spring Meeting 2010[4pt] [2] I. Sawada, K. Matsuzaki, S.Y. Kang, T. Ohshita, M. Kawakami, S. Segawa: 1-st IC-PLANTS, 2008

Data-Driven Significance Estimation for Precise Spike Correlation

PubMed Central

Grün, Sonja

2009-01-01

The mechanisms underlying neuronal coding and, in particular, the role of temporal spike coordination are hotly debated. However, this debate is often confounded by an implicit discussion about the use of appropriate analysis methods. To avoid incorrect interpretation of data, the analysis of simultaneous spike trains for precise spike correlation needs to be properly adjusted to the features of the experimental spike trains. In particular, nonstationarity of the firing of individual neurons in time or across trials, a spike train structure deviating from Poisson, or a co-occurrence of such features in parallel spike trains are potent generators of false positives. Problems can be avoided by including these features in the null hypothesis of the significance test. In this context, the use of surrogate data becomes increasingly important, because the complexity of the data typically prevents analytical solutions. This review provides an overview of the potential obstacles in the correlation analysis of parallel spike data and possible routes to overcome them. The discussion is illustrated at every stage of the argument by referring to a specific analysis tool (the Unitary Events method). The conclusions, however, are of a general nature and hold for other analysis techniques. Thorough testing and calibration of analysis tools and the impact of potentially erroneous preprocessing stages are emphasized. PMID:19129298

Simulation Methods for Poisson Processes in Nonstationary Systems.

DTIC Science & Technology

1978-08-01

for simulation of nonhomogeneous Poisson processes is stated with log-linear rate function. The method is based on an identity relating the...and relatively efficient new method for simulation of one-dimensional and two-dimensional nonhomogeneous Poisson processes is described. The method is

Poisson geometry from a Dirac perspective

NASA Astrophysics Data System (ADS)

Meinrenken, Eckhard

2018-03-01

We present proofs of classical results in Poisson geometry using techniques from Dirac geometry. This article is based on mini-courses at the Poisson summer school in Geneva, June 2016, and at the workshop Quantum Groups and Gravity at the University of Waterloo, April 2016.

Identification of a Class of Filtered Poisson Processes.

DTIC Science & Technology

1981-01-01

LD-A135 371 IDENTIFICATION OF A CLASS OF FILERED POISSON PROCESSES I AU) NORTH CAROLINA UNIV AT CHAPEL HIL DEPT 0F STATISTICS D DE RRUC ET AL 1981...STNO&IO$ !tt ~ 4.s " . , ".7" -L N ~ TITLE :IDENTIFICATION OF A CLASS OF FILTERED POISSON PROCESSES Authors : DE BRUCQ Denis - GUALTIEROTTI Antonio...filtered Poisson processes is intro- duced : the amplitude has a law which is spherically invariant and the filter is real, linear and causal. It is shown

Interactive Graphic Simulation of Rolling Element Bearings. Phase I. Low Frequency Phenomenon and RAPIDREB Development.

DTIC Science & Technology

1981-11-01

RDRER413 C EH 11-22 HOUSING ELASTIC MODUJLUS (F/L**2). RDRE8415 C PO4 ?3-34 HOUSING POISSON-S PATTO . PDPR416 C DENH 35-46 HOUSING MATERIAL DFNSITY (MA/L...23-34 CAGE POISSON-S PATTO . RDPRE427 C DENC 35-46 CAC7E MATFRIAL DENSITY (MA/L-03), PDPEP4?8 C RDRER4?9 C CARD 11 RDRE9430 C ---- ROPER431 C JF 11-16

Minimum risk wavelet shrinkage operator for Poisson image denoising.

PubMed

Cheng, Wu; Hirakawa, Keigo

2015-05-01

The pixel values of images taken by an image sensor are said to be corrupted by Poisson noise. To date, multiscale Poisson image denoising techniques have processed Haar frame and wavelet coefficients--the modeling of coefficients is enabled by the Skellam distribution analysis. We extend these results by solving for shrinkage operators for Skellam that minimizes the risk functional in the multiscale Poisson image denoising setting. The minimum risk shrinkage operator of this kind effectively produces denoised wavelet coefficients with minimum attainable L2 error.

Cumulative Poisson Distribution Program

NASA Technical Reports Server (NTRS)

Bowerman, Paul N.; Scheuer, Ernest M.; Nolty, Robert

1990-01-01

Overflow and underflow in sums prevented. Cumulative Poisson Distribution Program, CUMPOIS, one of two computer programs that make calculations involving cumulative Poisson distributions. Both programs, CUMPOIS (NPO-17714) and NEWTPOIS (NPO-17715), used independently of one another. CUMPOIS determines cumulative Poisson distribution, used to evaluate cumulative distribution function (cdf) for gamma distributions with integer shape parameters and cdf for X (sup2) distributions with even degrees of freedom. Used by statisticians and others concerned with probabilities of independent events occurring over specific units of time, area, or volume. Written in C.

Poly-symplectic Groupoids and Poly-Poisson Structures

NASA Astrophysics Data System (ADS)

Martinez, Nicolas

2015-05-01

We introduce poly-symplectic groupoids, which are natural extensions of symplectic groupoids to the context of poly-symplectic geometry, and define poly-Poisson structures as their infinitesimal counterparts. We present equivalent descriptions of poly-Poisson structures, including one related with AV-Dirac structures. We also discuss symmetries and reduction in the setting of poly-symplectic groupoids and poly-Poisson structures, and use our viewpoint to revisit results and develop new aspects of the theory initiated in Iglesias et al. (Lett Math Phys 103:1103-1133, 2013).

Exploiting Symmetry on Parallel Architectures.

NASA Astrophysics Data System (ADS)

Stiller, Lewis Benjamin

1995-01-01

This thesis describes techniques for the design of parallel programs that solve well-structured problems with inherent symmetry. Part I demonstrates the reduction of such problems to generalized matrix multiplication by a group-equivariant matrix. Fast techniques for this multiplication are described, including factorization, orbit decomposition, and Fourier transforms over finite groups. Our algorithms entail interaction between two symmetry groups: one arising at the software level from the problem's symmetry and the other arising at the hardware level from the processors' communication network. Part II illustrates the applicability of our symmetry -exploitation techniques by presenting a series of case studies of the design and implementation of parallel programs. First, a parallel program that solves chess endgames by factorization of an associated dihedral group-equivariant matrix is described. This code runs faster than previous serial programs, and discovered it a number of results. Second, parallel algorithms for Fourier transforms for finite groups are developed, and preliminary parallel implementations for group transforms of dihedral and of symmetric groups are described. Applications in learning, vision, pattern recognition, and statistics are proposed. Third, parallel implementations solving several computational science problems are described, including the direct n-body problem, convolutions arising from molecular biology, and some communication primitives such as broadcast and reduce. Some of our implementations ran orders of magnitude faster than previous techniques, and were used in the investigation of various physical phenomena.

Parallel imaging of knee cartilage at 3 Tesla.

PubMed

Zuo, Jin; Li, Xiaojuan; Banerjee, Suchandrima; Han, Eric; Majumdar, Sharmila

2007-10-01

To evaluate the feasibility and reproducibility of quantitative cartilage imaging with parallel imaging at 3T and to determine the impact of the acceleration factor (AF) on morphological and relaxation measurements. An eight-channel phased-array knee coil was employed for conventional and parallel imaging on a 3T scanner. The imaging protocol consisted of a T2-weighted fast spin echo (FSE), a 3D-spoiled gradient echo (SPGR), a custom 3D-SPGR T1rho, and a 3D-SPGR T2 sequence. Parallel imaging was performed with an array spatial sensitivity technique (ASSET). The left knees of six healthy volunteers were scanned with both conventional and parallel imaging (AF = 2). Morphological parameters and relaxation maps from parallel imaging methods (AF = 2) showed comparable results with conventional method. The intraclass correlation coefficient (ICC) of the two methods for cartilage volume, mean cartilage thickness, T1rho, and T2 were 0.999, 0.977, 0.964, and 0.969, respectively, while demonstrating excellent reproducibility. No significant measurement differences were found when AF reached 3 despite the low signal-to-noise ratio (SNR). The study demonstrated that parallel imaging can be applied to current knee cartilage quantification at AF = 2 without degrading measurement accuracy with good reproducibility while effectively reducing scan time. Shorter imaging times can be achieved with higher AF at the cost of SNR. (c) 2007 Wiley-Liss, Inc.

Fractional poisson--a simple dose-response model for human norovirus.

PubMed

Messner, Michael J; Berger, Philip; Nappier, Sharon P

2014-10-01

This study utilizes old and new Norovirus (NoV) human challenge data to model the dose-response relationship for human NoV infection. The combined data set is used to update estimates from a previously published beta-Poisson dose-response model that includes parameters for virus aggregation and for a beta-distribution that describes variable susceptibility among hosts. The quality of the beta-Poisson model is examined and a simpler model is proposed. The new model (fractional Poisson) characterizes hosts as either perfectly susceptible or perfectly immune, requiring a single parameter (the fraction of perfectly susceptible hosts) in place of the two-parameter beta-distribution. A second parameter is included to account for virus aggregation in the same fashion as it is added to the beta-Poisson model. Infection probability is simply the product of the probability of nonzero exposure (at least one virus or aggregate is ingested) and the fraction of susceptible hosts. The model is computationally simple and appears to be well suited to the data from the NoV human challenge studies. The model's deviance is similar to that of the beta-Poisson, but with one parameter, rather than two. As a result, the Akaike information criterion favors the fractional Poisson over the beta-Poisson model. At low, environmentally relevant exposure levels (<100), estimation error is small for the fractional Poisson model; however, caution is advised because no subjects were challenged at such a low dose. New low-dose data would be of great value to further clarify the NoV dose-response relationship and to support improved risk assessment for environmentally relevant exposures. © 2014 Society for Risk Analysis Published 2014. This article is a U.S. Government work and is in the public domain for the U.S.A.

Modeling animal-vehicle collisions using diagonal inflated bivariate Poisson regression.

PubMed

Lao, Yunteng; Wu, Yao-Jan; Corey, Jonathan; Wang, Yinhai

2011-01-01

Two types of animal-vehicle collision (AVC) data are commonly adopted for AVC-related risk analysis research: reported AVC data and carcass removal data. One issue with these two data sets is that they were found to have significant discrepancies by previous studies. In order to model these two types of data together and provide a better understanding of highway AVCs, this study adopts a diagonal inflated bivariate Poisson regression method, an inflated version of bivariate Poisson regression model, to fit the reported AVC and carcass removal data sets collected in Washington State during 2002-2006. The diagonal inflated bivariate Poisson model not only can model paired data with correlation, but also handle under- or over-dispersed data sets as well. Compared with three other types of models, double Poisson, bivariate Poisson, and zero-inflated double Poisson, the diagonal inflated bivariate Poisson model demonstrates its capability of fitting two data sets with remarkable overlapping portions resulting from the same stochastic process. Therefore, the diagonal inflated bivariate Poisson model provides researchers a new approach to investigating AVCs from a different perspective involving the three distribution parameters (λ(1), λ(2) and λ(3)). The modeling results show the impacts of traffic elements, geometric design and geographic characteristics on the occurrences of both reported AVC and carcass removal data. It is found that the increase of some associated factors, such as speed limit, annual average daily traffic, and shoulder width, will increase the numbers of reported AVCs and carcass removals. Conversely, the presence of some geometric factors, such as rolling and mountainous terrain, will decrease the number of reported AVCs. Published by Elsevier Ltd.

Parallel image reconstruction for 3D positron emission tomography from incomplete 2D projection data

NASA Astrophysics Data System (ADS)

Guerrero, Thomas M.; Ricci, Anthony R.; Dahlbom, Magnus; Cherry, Simon R.; Hoffman, Edward T.

1993-07-01

The problem of excessive computational time in 3D Positron Emission Tomography (3D PET) reconstruction is defined, and we present an approach for solving this problem through the construction of an inexpensive parallel processing system and the adoption of the FAVOR algorithm. Currently, the 3D reconstruction of the 610 images of a total body procedure would require 80 hours and the 3D reconstruction of the 620 images of a dynamic study would require 110 hours. An inexpensive parallel processing system for 3D PET reconstruction is constructed from the integration of board level products from multiple vendors. The system achieves its computational performance through the use of 6U VME four i860 processor boards, the processor boards from five manufacturers are discussed from our perspective. The new 3D PET reconstruction algorithm FAVOR, FAst VOlume Reconstructor, that promises a substantial speed improvement is adopted. Preliminary results from parallelizing FAVOR are utilized in formulating architectural improvements for this problem. In summary, we are addressing the problem of excessive computational time in 3D PET image reconstruction, through the construction of an inexpensive parallel processing system and the parallelization of a 3D reconstruction algorithm that uses the incomplete data set that is produced by current PET systems.

YAPPA: a Compiler-Based Parallelization Framework for Irregular Applications on MPSoCs

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

Lovergine, Silvia; Tumeo, Antonino; Villa, Oreste

Modern embedded systems include hundreds of cores. Because of the difficulty in providing a fast, coherent memory architecture, these systems usually rely on non-coherent, non-uniform memory architectures with private memories for each core. However, programming these systems poses significant challenges. The developer must extract large amounts of parallelism, while orchestrating communication among cores to optimize application performance. These issues become even more significant with irregular applications, which present data sets difficult to partition, unpredictable memory accesses, unbalanced control flow and fine grained communication. Hand-optimizing every single aspect is hard and time-consuming, and it often does not lead to the expectedmore » performance. There is a growing gap between such complex and highly-parallel architectures and the high level languages used to describe the specification, which were designed for simpler systems and do not consider these new issues. In this paper we introduce YAPPA (Yet Another Parallel Programming Approach), a compilation framework for the automatic parallelization of irregular applications on modern MPSoCs based on LLVM. We start by considering an efficient parallel programming approach for irregular applications on distributed memory systems. We then propose a set of transformations that can reduce the development and optimization effort. The results of our initial prototype confirm the correctness of the proposed approach.« less

Parallel versus Sequential Processing in Print and Braille Reading

ERIC Educational Resources Information Center

Veispak, Anneli; Boets, Bart; Ghesquiere, Pol

2012-01-01

In the current study we investigated word, pseudoword and story reading in Dutch speaking braille and print readers. To examine developmental patterns, these reading skills were assessed in both children and adults. The results reveal that braille readers read less accurately and fast than print readers. While item length has no impact on word…