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.

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.

Impact Damage on a Thin Glass Plate with a Thin Polycarbonate Backing

DTIC Science & Technology

2013-07-13

fixed and equals 0.25 in 3D (close to the soda-lime glass Poisson ratio of 0.22), and 1/3 in 2D, since the assumption is that material points interact...only through a pair-potential. The Poisson ratio limitation is removed in the state-based formulation of peridynamics (see Ref. [26]), however, here...we use the bond-based for simplicity. We note that, in dynamic fracture problems of the type considered in this work, the Poisson ratio value does not

Poisson noise removal with pyramidal multi-scale transforms

NASA Astrophysics Data System (ADS)

Woiselle, Arnaud; Starck, Jean-Luc; Fadili, Jalal M.

2013-09-01

In this paper, we introduce a method to stabilize the variance of decimated transforms using one or two variance stabilizing transforms (VST). These VSTs are applied to the 3-D Meyer wavelet pyramidal transform which is the core of the first generation 3D curvelets. This allows us to extend these 3-D curvelets to handle Poisson noise, that we apply to the denoising of a simulated cosmological volume.

Schrödinger-Poisson-Vlasov-Poisson correspondence

NASA Astrophysics Data System (ADS)

Mocz, Philip; Lancaster, Lachlan; Fialkov, Anastasia; Becerra, Fernando; Chavanis, Pierre-Henri

2018-04-01

The Schrödinger-Poisson equations describe the behavior of a superfluid Bose-Einstein condensate under self-gravity with a 3D wave function. As ℏ/m →0 , m being the boson mass, the equations have been postulated to approximate the collisionless Vlasov-Poisson equations also known as the collisionless Boltzmann-Poisson equations. The latter describe collisionless matter with a 6D classical distribution function. We investigate the nature of this correspondence with a suite of numerical test problems in 1D, 2D, and 3D along with analytic treatments when possible. We demonstrate that, while the density field of the superfluid always shows order unity oscillations as ℏ/m →0 due to interference and the uncertainty principle, the potential field converges to the classical answer as (ℏ/m )2. Thus, any dynamics coupled to the superfluid potential is expected to recover the classical collisionless limit as ℏ/m →0 . The quantum superfluid is able to capture rich phenomena such as multiple phase-sheets, shell-crossings, and warm distributions. Additionally, the quantum pressure tensor acts as a regularizer of caustics and singularities in classical solutions. This suggests the exciting prospect of using the Schrödinger-Poisson equations as a low-memory method for approximating the high-dimensional evolution of the Vlasov-Poisson equations. As a particular example we consider dark matter composed of ultralight axions, which in the classical limit (ℏ/m →0 ) is expected to manifest itself as collisionless cold dark matter.

Poisson Spot with Magnetic Levitation

ERIC Educational Resources Information Center

Hoover, Matthew; Everhart, Michael; D'Arruda, Jose

2010-01-01

In this paper we describe a unique method for obtaining the famous Poisson spot without adding obstacles to the light path, which could interfere with the effect. A Poisson spot is the interference effect from parallel rays of light diffracting around a solid spherical object, creating a bright spot in the center of the shadow.

Efficient three-dimensional Poisson solvers in open rectangular conducting pipe

NASA Astrophysics Data System (ADS)

Qiang, Ji

2016-06-01

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

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.

Multi-material Additive Manufacturing of Metamaterials with Giant, Tailorable Negative Poisson's Ratios.

PubMed

Chen, Da; Zheng, Xiaoyu

2018-06-14

Nature has evolved with a recurring strategy to achieve unusual mechanical properties through coupling variable elastic moduli from a few GPa to below KPa within a single tissue. The ability to produce multi-material, three-dimensional (3D) micro-architectures with high fidelity incorporating dissimilar components has been a major challenge in man-made materials. Here we show multi-modulus metamaterials whose architectural element is comprised of encoded elasticity ranging from rigid to soft. We found that, in contrast to ordinary architected materials whose negative Poisson's ratio is dictated by their geometry, these type of metamaterials are capable of displaying Poisson's ratios from extreme negative to zero, independent of their 3D micro-architecture. The resulting low density metamaterials is capable of achieving functionally graded, distributed strain amplification capabilities within the metamaterial with uniform micro-architectures. Simultaneous tuning of Poisson's ratio and moduli within the 3D multi-materials could open up a broad array of material by design applications ranging from flexible armor, artificial muscles, to actuators and bio-mimetic materials.

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.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

PubMed

Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G

2013-02-26

The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data.

Massively parallel algorithms for real-time wavefront control of a dense adaptive optics system

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

Fijany, A.; Milman, M.; Redding, D.

1994-12-31

In this paper massively parallel algorithms and architectures for real-time wavefront control of a dense adaptive optic system (SELENE) are presented. The authors have already shown that the computation of a near optimal control algorithm for SELENE can be reduced to the solution of a discrete Poisson equation on a regular domain. Although, this represents an optimal computation, due the large size of the system and the high sampling rate requirement, the implementation of this control algorithm poses a computationally challenging problem since it demands a sustained computational throughput of the order of 10 GFlops. They develop a novel algorithm,more » designated as Fast Invariant Imbedding algorithm, which offers a massive degree of parallelism with simple communication and synchronization requirements. Due to these features, this algorithm is significantly more efficient than other Fast Poisson Solvers for implementation on massively parallel architectures. The authors also discuss two massively parallel, algorithmically specialized, architectures for low-cost and optimal implementation of the Fast Invariant Imbedding algorithm.« less

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.

Derivation of the Navier-Stokes-Poisson System with Radiation for an Accretion Disk

NASA Astrophysics Data System (ADS)

Ducomet, Bernard; Nečasová, Šárka; Pokorný, Milan; Rodríguez-Bellido, M. Angeles

2018-01-01

We study the 3-D compressible barotropic radiation fluid dynamics system describing the motion of the compressible rotating viscous fluid with gravitation and radiation confined to a straight layer Ω _{ɛ } = ω × (0,ɛ ) , where ω is a 2-D domain. We show that weak solutions in the 3-D domain converge to the strong solution of—the rotating 2-D Navier-Stokes-Poisson system with radiation in ω as ɛ → 0 for all times less than the maximal life time of the strong solution of the 2-D system when the Froude number is small (Fr=O(√{ɛ })) ,—the rotating pure 2-D Navier-Stokes system with radiation in ω as ɛ → 0 when Fr=O(1).

Derivation of the Navier-Stokes-Poisson System with Radiation for an Accretion Disk

NASA Astrophysics Data System (ADS)

Ducomet, Bernard; Nečasová, Šárka; Pokorný, Milan; Rodríguez-Bellido, M. Angeles

2018-06-01

We study the 3-D compressible barotropic radiation fluid dynamics system describing the motion of the compressible rotating viscous fluid with gravitation and radiation confined to a straight layer Ω _{ɛ } = ω × (0,ɛ ) , where ω is a 2-D domain. We show that weak solutions in the 3-D domain converge to the strong solution of—the rotating 2-D Navier-Stokes-Poisson system with radiation in ω as ɛ → 0 for all times less than the maximal life time of the strong solution of the 2-D system when the Froude number is small (Fr={O}(√{ɛ })),—the rotating pure 2-D Navier-Stokes system with radiation in ω as ɛ → 0 when Fr={O}(1).

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.

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.

Pattern formation and filamentation in low temperature, magnetized plasmas - a numerical approach

NASA Astrophysics Data System (ADS)

Menati, Mohamad; Konopka, Uwe; Thomas, Edward

2017-10-01

In low-temperature discharges under the influence of high magnetic field, pattern and filament formation in the plasma has been reported by different groups. The phenomena present themselves as bright plasma columns (filaments) oriented parallel to the magnetic field lines at high magnetic field regime. The plasma structure can filament into different shapes from single columns to spiral and bright rings when viewed from the top. In spite of the extensive experimental observations, the observed effects lack a detailed theoretical and numerical description. In an attempt to numerically explain the plasma filamentation, we present a simplified model for the plasma discharge and power deposition into the plasma. Based on the model, 2-D and 3-D codes are being developed that solve Poisson's equation along with the fluid equations to obtain a self-consistent description of the plasma. The model and preliminary results applied to the specific plasma conditions will be presented. This work was supported by the US Dept. of Energy and NSF, DE-SC0016330, PHY-1613087.

Thermoelectrokinetic instability in micro/nanoscales

NASA Astrophysics Data System (ADS)

Ganchenko, Georgy; Ganchenko, Natalia

2016-11-01

A novel sophisticated type of electro-hydrodynamic instability in an electrolyte solution near ion-selective surfaces in an external electric field is discovered theoretically. The key mechanism of the instability is caused by Joule heating but dramatically differs from the well-known Raleigh-Benard convection. The investigation is based on the Nernst-Planck-Poisson-Navier-Stokes system along with the energy equation and corresponding BCs. The 1D quiescent steady state in microscales can be unstable with respect to either short-wave Rubinstein-Zaltzman or long-wave thermoelectokinenetic instability. The last one prevails in long microchannels and good enough thermal insulation of the system. In addition to the linear stability analysis a direct numerical simulation of the full 3D nonlinear system is fulfilled using a parallel computing. In the final coherent structures salt concentration, temperature and electric current are localized in narrow long fingers normal to the ion-selective surface while space charge forms crown-like micro-patterns. The investigation results can be useful in desalination problem.

Three-dimensional zonal grids about arbitrary shapes by Poisson's equation

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.

1988-01-01

A method for generating 3-D finite difference grids about or within arbitrary shapes is presented. The 3-D Poisson equations are solved numerically, with values for the inhomogeneous terms found automatically by the algorithm. Those inhomogeneous terms have the effect near boundaries of reducing cell skewness and imposing arbitrary cell height. The method allows the region of interest to be divided into zones (blocks), allowing the method to be applicable to almost any physical domain. A FORTRAN program called 3DGRAPE has been written to implement the algorithm. Lastly, a method for redistributing grid points along lines normal to boundaries will be described.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

PubMed Central

2013-01-01

Background The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Results Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. Conclusions In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. PMID:23442253

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.

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.

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.

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

Exploiting negative Poisson's ratio to design 3D-printed composites with enhanced mechanical properties

DOE PAGES

Li, Tiantian; Chen, Yanyu; Hu, Xiaoyi; ...

2018-02-03

Auxetic materials exhibiting a negative Poisson's ratio are shown to have better indentation resistance, impact shielding capability, and enhanced toughness. Here, we report a class of high-performance composites in which auxetic lattice structures are used as the reinforcements and the nearly incompressible soft material is employed as the matrix. This coupled geometry and material design concept is enabled by the state-of-the-art additive manufacturing technique. Guided by experimental tests and finite element analyses, we systematically study the compressive behavior of the 3D printed auxetics reinforced composites and achieve a significant enhancement of their stiffness and energy absorption. This improved mechanical performancemore » is due to the negative Poisson's ratio effect of the auxetic reinforcements, which makes the matrix in a state of biaxial compression and hence provides additional support. This mechanism is further supported by the investigation of the effect of auxetic degree on the stiffness and energy absorption capability. The findings reported here pave the way for developing a new class of auxetic composites that significantly expand their design space and possible applications through a combination of rational design and 3D printing.« less

Exploiting negative Poisson's ratio to design 3D-printed composites with enhanced mechanical properties

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

Li, Tiantian; Chen, Yanyu; Hu, Xiaoyi

Auxetic materials exhibiting a negative Poisson's ratio are shown to have better indentation resistance, impact shielding capability, and enhanced toughness. Here, we report a class of high-performance composites in which auxetic lattice structures are used as the reinforcements and the nearly incompressible soft material is employed as the matrix. This coupled geometry and material design concept is enabled by the state-of-the-art additive manufacturing technique. Guided by experimental tests and finite element analyses, we systematically study the compressive behavior of the 3D printed auxetics reinforced composites and achieve a significant enhancement of their stiffness and energy absorption. This improved mechanical performancemore » is due to the negative Poisson's ratio effect of the auxetic reinforcements, which makes the matrix in a state of biaxial compression and hence provides additional support. This mechanism is further supported by the investigation of the effect of auxetic degree on the stiffness and energy absorption capability. The findings reported here pave the way for developing a new class of auxetic composites that significantly expand their design space and possible applications through a combination of rational design and 3D printing.« less

Robust adaptive 3-D segmentation of vessel laminae from fluorescence confocal microscope images and parallel GPU implementation.

PubMed

Narayanaswamy, Arunachalam; Dwarakapuram, Saritha; Bjornsson, Christopher S; Cutler, Barbara M; Shain, William; Roysam, Badrinath

2010-03-01

This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8 x speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1-1.6) voxels per mesh face for peak signal-to-noise ratios from (110-28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively.

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

Incompressible SPH (ISPH) with fast Poisson solver on a GPU

NASA Astrophysics Data System (ADS)

Chow, Alex D.; Rogers, Benedict D.; Lind, Steven J.; Stansby, Peter K.

2018-05-01

This paper presents a fast incompressible SPH (ISPH) solver implemented to run entirely on a graphics processing unit (GPU) capable of simulating several millions of particles in three dimensions on a single GPU. The ISPH algorithm is implemented by converting the highly optimised open-source weakly-compressible SPH (WCSPH) code DualSPHysics to run ISPH on the GPU, combining it with the open-source linear algebra library ViennaCL for fast solutions of the pressure Poisson equation (PPE). Several challenges are addressed with this research: constructing a PPE matrix every timestep on the GPU for moving particles, optimising the limited GPU memory, and exploiting fast matrix solvers. The ISPH pressure projection algorithm is implemented as 4 separate stages, each with a particle sweep, including an algorithm for the population of the PPE matrix suitable for the GPU, and mixed precision storage methods. An accurate and robust ISPH boundary condition ideal for parallel processing is also established by adapting an existing WCSPH boundary condition for ISPH. A variety of validation cases are presented: an impulsively started plate, incompressible flow around a moving square in a box, and dambreaks (2-D and 3-D) which demonstrate the accuracy, flexibility, and speed of the methodology. Fragmentation of the free surface is shown to influence the performance of matrix preconditioners and therefore the PPE matrix solution time. The Jacobi preconditioner demonstrates robustness and reliability in the presence of fragmented flows. For a dambreak simulation, GPU speed ups demonstrate up to 10-18 times and 1.1-4.5 times compared to single-threaded and 16-threaded CPU run times respectively.

Advanced computational simulations of water waves interacting with wave energy converters

NASA Astrophysics Data System (ADS)

Pathak, Ashish; Freniere, Cole; Raessi, Mehdi

2017-03-01

Wave energy converter (WEC) devices harness the renewable ocean wave energy and convert it into useful forms of energy, e.g. mechanical or electrical. This paper presents an advanced 3D computational framework to study the interaction between water waves and WEC devices. The computational tool solves the full Navier-Stokes equations and considers all important effects impacting the device performance. To enable large-scale simulations in fast turnaround times, the computational solver was developed in an MPI parallel framework. A fast multigrid preconditioned solver is introduced to solve the computationally expensive pressure Poisson equation. The computational solver was applied to two surface-piercing WEC geometries: bottom-hinged cylinder and flap. Their numerically simulated response was validated against experimental data. Additional simulations were conducted to investigate the applicability of Froude scaling in predicting full-scale WEC response from the model experiments.

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.

AnisoVis: a MATLAB™ toolbox for the visualisation of elastic anisotropy

NASA Astrophysics Data System (ADS)

Healy, D.; Timms, N.; Pearce, M. A.

2016-12-01

The elastic properties of rocks and minerals vary with direction, and this has significant consequences for their physical response to acoustic waves and natural or imposed stresses. This anisotropy of elasticity is well described mathematically by 4th rank tensors of stiffness or compliance. These tensors are not easy to visualise in a single diagram or graphic, and visualising Poisson's ratio and shear modulus presents a further challenge in that their anisotropy depends on two principal directions. Students and researchers can easily underestimate the importance of elastic anisotropy. This presentation describes an open source toolbox of MATLAB scripts that aims to visualise elastic anisotropy in rocks and minerals. The code produces linked 2-D and 3-D representations of the standard elastic constants, such as Young's modulus, Poisson's ratio and shear modulus, all from a simple GUI. The 3-D plots can be manipulated by the user (rotated, panned, zoomed), to encourage investigation and a deeper understanding of directional variations in the fundamental properties. Examples are presented of common rock forming minerals, including those with negative Poisson's ratio (auxetic behaviour). We hope that an open source code base will encourage further enhancements from the rock physics and wider geoscience communities. Eventually, we hope to generate 3-D prints of these complex and beautiful natural surfaces to provide a tactile link to the underlying physics of elastic anisotropy.

Persistently Auxetic Materials: Engineering the Poisson Ratio of 2D Self-Avoiding Membranes under Conditions of Non-Zero Anisotropic Strain.

PubMed

Ulissi, Zachary W; Govind Rajan, Ananth; Strano, Michael S

2016-08-23

Entropic surfaces represented by fluctuating two-dimensional (2D) membranes are predicted to have desirable mechanical properties when unstressed, including a negative Poisson's ratio ("auxetic" behavior). Herein, we present calculations of the strain-dependent Poisson ratio of self-avoiding 2D membranes demonstrating desirable auxetic properties over a range of mechanical strain. Finite-size membranes with unclamped boundary conditions have positive Poisson's ratio due to spontaneous non-zero mean curvature, which can be suppressed with an explicit bending rigidity in agreement with prior findings. Applying longitudinal strain along a singular axis to this system suppresses this mean curvature and the entropic out-of-plane fluctuations, resulting in a molecular-scale mechanism for realizing a negative Poisson's ratio above a critical strain, with values significantly more negative than the previously observed zero-strain limit for infinite sheets. We find that auxetic behavior persists over surprisingly high strains of more than 20% for the smallest surfaces, with desirable finite-size scaling producing surfaces with negative Poisson's ratio over a wide range of strains. These results promise the design of surfaces and composite materials with tunable Poisson's ratio by prestressing platelet inclusions or controlling the surface rigidity of a matrix of 2D materials.

Computations of Wall Distances Based on Differential Equations

NASA Technical Reports Server (NTRS)

Tucker, Paul G.; Rumsey, Chris L.; Spalart, Philippe R.; Bartels, Robert E.; Biedron, Robert T.

2004-01-01

The use of differential equations such as Eikonal, Hamilton-Jacobi and Poisson for the economical calculation of the nearest wall distance d, which is needed by some turbulence models, is explored. Modifications that could palliate some turbulence-modeling anomalies are also discussed. Economy is of especial value for deforming/adaptive grid problems. For these, ideally, d is repeatedly computed. It is shown that the Eikonal and Hamilton-Jacobi equations can be easy to implement when written in implicit (or iterated) advection and advection-diffusion equation analogous forms, respectively. These, like the Poisson Laplacian term, are commonly occurring in CFD solvers, allowing the re-use of efficient algorithms and code components. The use of the NASA CFL3D CFD program to solve the implicit Eikonal and Hamilton-Jacobi equations is explored. The re-formulated d equations are easy to implement, and are found to have robust convergence. For accurate Eikonal solutions, upwind metric differences are required. The Poisson approach is also found effective, and easiest to implement. Modified distances are not found to affect global outputs such as lift and drag significantly, at least in common situations such as airfoil flows.

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

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

DOE PAGES

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

2013-01-01

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

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.

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.

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.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

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.

Poisson traces, D-modules, and symplectic resolutions

NASA Astrophysics Data System (ADS)

Etingof, Pavel; Schedler, Travis

2018-03-01

We survey the theory of Poisson traces (or zeroth Poisson homology) developed by the authors in a series of recent papers. The goal is to understand this subtle invariant of (singular) Poisson varieties, conditions for it to be finite-dimensional, its relationship to the geometry and topology of symplectic resolutions, and its applications to quantizations. The main technique is the study of a canonical D-module on the variety. In the case the variety has finitely many symplectic leaves (such as for symplectic singularities and Hamiltonian reductions of symplectic vector spaces by reductive groups), the D-module is holonomic, and hence, the space of Poisson traces is finite-dimensional. As an application, there are finitely many irreducible finite-dimensional representations of every quantization of the variety. Conjecturally, the D-module is the pushforward of the canonical D-module under every symplectic resolution of singularities, which implies that the space of Poisson traces is dual to the top cohomology of the resolution. We explain many examples where the conjecture is proved, such as symmetric powers of du Val singularities and symplectic surfaces and Slodowy slices in the nilpotent cone of a semisimple Lie algebra. We compute the D-module in the case of surfaces with isolated singularities and show it is not always semisimple. We also explain generalizations to arbitrary Lie algebras of vector fields, connections to the Bernstein-Sato polynomial, relations to two-variable special polynomials such as Kostka polynomials and Tutte polynomials, and a conjectural relationship with deformations of symplectic resolutions. In the appendix we give a brief recollection of the theory of D-modules on singular varieties that we require.

Poisson traces, D-modules, and symplectic resolutions.

PubMed

Etingof, Pavel; Schedler, Travis

2018-01-01

We survey the theory of Poisson traces (or zeroth Poisson homology) developed by the authors in a series of recent papers. The goal is to understand this subtle invariant of (singular) Poisson varieties, conditions for it to be finite-dimensional, its relationship to the geometry and topology of symplectic resolutions, and its applications to quantizations. The main technique is the study of a canonical D-module on the variety. In the case the variety has finitely many symplectic leaves (such as for symplectic singularities and Hamiltonian reductions of symplectic vector spaces by reductive groups), the D-module is holonomic, and hence, the space of Poisson traces is finite-dimensional. As an application, there are finitely many irreducible finite-dimensional representations of every quantization of the variety. Conjecturally, the D-module is the pushforward of the canonical D-module under every symplectic resolution of singularities, which implies that the space of Poisson traces is dual to the top cohomology of the resolution. We explain many examples where the conjecture is proved, such as symmetric powers of du Val singularities and symplectic surfaces and Slodowy slices in the nilpotent cone of a semisimple Lie algebra. We compute the D-module in the case of surfaces with isolated singularities and show it is not always semisimple. We also explain generalizations to arbitrary Lie algebras of vector fields, connections to the Bernstein-Sato polynomial, relations to two-variable special polynomials such as Kostka polynomials and Tutte polynomials, and a conjectural relationship with deformations of symplectic resolutions. In the appendix we give a brief recollection of the theory of D-modules on singular varieties that we require.

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.

ColDICE: A parallel Vlasov–Poisson solver using moving adaptive simplicial tessellation

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

Sousbie, Thierry, E-mail: tsousbie@gmail.com; Department of Physics, The University of Tokyo, Tokyo 113-0033; Research Center for the Early Universe, School of Science, The University of Tokyo, Tokyo 113-0033

2016-09-15

Resolving numerically Vlasov–Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm consisting in representing the phase-space sheet with a conforming, self-adaptive simplicial tessellation of which the vertices follow the Lagrangian equations of motion. The algorithm is implemented both in six- and four-dimensional phase-space. Refinement of the tessellation mesh is performed using the bisection method and a local representation of the phase-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the bestmore » way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincaré invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli [65–67] generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a “warm” dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.« less

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

PubMed Central

Pereira, N F; Sitek, A

2011-01-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated. PMID:20736496

Evaluation of a 3D point cloud tetrahedral tomographic reconstruction method

NASA Astrophysics Data System (ADS)

Pereira, N. F.; Sitek, A.

2010-09-01

Tomographic reconstruction on an irregular grid may be superior to reconstruction on a regular grid. This is achieved through an appropriate choice of the image space model, the selection of an optimal set of points and the use of any available prior information during the reconstruction process. Accordingly, a number of reconstruction-related parameters must be optimized for best performance. In this work, a 3D point cloud tetrahedral mesh reconstruction method is evaluated for quantitative tasks. A linear image model is employed to obtain the reconstruction system matrix and five point generation strategies are studied. The evaluation is performed using the recovery coefficient, as well as voxel- and template-based estimates of bias and variance measures, computed over specific regions in the reconstructed image. A similar analysis is performed for regular grid reconstructions that use voxel basis functions. The maximum likelihood expectation maximization reconstruction algorithm is used. For the tetrahedral reconstructions, of the five point generation methods that are evaluated, three use image priors. For evaluation purposes, an object consisting of overlapping spheres with varying activity is simulated. The exact parallel projection data of this object are obtained analytically using a parallel projector, and multiple Poisson noise realizations of these exact data are generated and reconstructed using the different point generation strategies. The unconstrained nature of point placement in some of the irregular mesh-based reconstruction strategies has superior activity recovery for small, low-contrast image regions. The results show that, with an appropriately generated set of mesh points, the irregular grid reconstruction methods can out-perform reconstructions on a regular grid for mathematical phantoms, in terms of the performance measures evaluated.

A 3D, fully Eulerian, VOF-based solver to study the interaction between two fluids and moving rigid bodies using the fictitious domain method

NASA Astrophysics Data System (ADS)

Pathak, Ashish; Raessi, Mehdi

2016-04-01

We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.

Development of a 3D parallel mechanism robot arm with three vertical-axial pneumatic actuators combined with a stereo vision system.

PubMed

Chiang, Mao-Hsiung; Lin, Hao-Ting

2011-01-01

This study aimed to develop a novel 3D parallel mechanism robot driven by three vertical-axial pneumatic actuators with a stereo vision system for path tracking control. The mechanical system and the control system are the primary novel parts for developing a 3D parallel mechanism robot. In the mechanical system, a 3D parallel mechanism robot contains three serial chains, a fixed base, a movable platform and a pneumatic servo system. The parallel mechanism are designed and analyzed first for realizing a 3D motion in the X-Y-Z coordinate system of the robot's end-effector. The inverse kinematics and the forward kinematics of the parallel mechanism robot are investigated by using the Denavit-Hartenberg notation (D-H notation) coordinate system. The pneumatic actuators in the three vertical motion axes are modeled. In the control system, the Fourier series-based adaptive sliding-mode controller with H(∞) tracking performance is used to design the path tracking controllers of the three vertical servo pneumatic actuators for realizing 3D path tracking control of the end-effector. Three optical linear scales are used to measure the position of the three pneumatic actuators. The 3D position of the end-effector is then calculated from the measuring position of the three pneumatic actuators by means of the kinematics. However, the calculated 3D position of the end-effector cannot consider the manufacturing and assembly tolerance of the joints and the parallel mechanism so that errors between the actual position and the calculated 3D position of the end-effector exist. In order to improve this situation, sensor collaboration is developed in this paper. A stereo vision system is used to collaborate with the three position sensors of the pneumatic actuators. The stereo vision system combining two CCD serves to measure the actual 3D position of the end-effector and calibrate the error between the actual and the calculated 3D position of the end-effector. Furthermore, to verify the feasibility of the proposed parallel mechanism robot driven by three vertical pneumatic servo actuators, a full-scale test rig of the proposed parallel mechanism pneumatic robot is set up. Thus, simulations and experiments for different complex 3D motion profiles of the robot end-effector can be successfully achieved. The desired, the actual and the calculated 3D position of the end-effector can be compared in the complex 3D motion control.

Development of a 3D Parallel Mechanism Robot Arm with Three Vertical-Axial Pneumatic Actuators Combined with a Stereo Vision System

PubMed Central

Chiang, Mao-Hsiung; Lin, Hao-Ting

2011-01-01

This study aimed to develop a novel 3D parallel mechanism robot driven by three vertical-axial pneumatic actuators with a stereo vision system for path tracking control. The mechanical system and the control system are the primary novel parts for developing a 3D parallel mechanism robot. In the mechanical system, a 3D parallel mechanism robot contains three serial chains, a fixed base, a movable platform and a pneumatic servo system. The parallel mechanism are designed and analyzed first for realizing a 3D motion in the X-Y-Z coordinate system of the robot’s end-effector. The inverse kinematics and the forward kinematics of the parallel mechanism robot are investigated by using the Denavit-Hartenberg notation (D-H notation) coordinate system. The pneumatic actuators in the three vertical motion axes are modeled. In the control system, the Fourier series-based adaptive sliding-mode controller with H∞ tracking performance is used to design the path tracking controllers of the three vertical servo pneumatic actuators for realizing 3D path tracking control of the end-effector. Three optical linear scales are used to measure the position of the three pneumatic actuators. The 3D position of the end-effector is then calculated from the measuring position of the three pneumatic actuators by means of the kinematics. However, the calculated 3D position of the end-effector cannot consider the manufacturing and assembly tolerance of the joints and the parallel mechanism so that errors between the actual position and the calculated 3D position of the end-effector exist. In order to improve this situation, sensor collaboration is developed in this paper. A stereo vision system is used to collaborate with the three position sensors of the pneumatic actuators. The stereo vision system combining two CCD serves to measure the actual 3D position of the end-effector and calibrate the error between the actual and the calculated 3D position of the end-effector. Furthermore, to verify the feasibility of the proposed parallel mechanism robot driven by three vertical pneumatic servo actuators, a full-scale test rig of the proposed parallel mechanism pneumatic robot is set up. Thus, simulations and experiments for different complex 3D motion profiles of the robot end-effector can be successfully achieved. The desired, the actual and the calculated 3D position of the end-effector can be compared in the complex 3D motion control. PMID:22247676

A statistical approach for inferring the 3D structure of the genome.

PubMed

Varoquaux, Nelle; Ay, Ferhat; Noble, William Stafford; Vert, Jean-Philippe

2014-06-15

Recent technological advances allow the measurement, in a single Hi-C experiment, of the frequencies of physical contacts among pairs of genomic loci at a genome-wide scale. The next challenge is to infer, from the resulting DNA-DNA contact maps, accurate 3D models of how chromosomes fold and fit into the nucleus. Many existing inference methods rely on multidimensional scaling (MDS), in which the pairwise distances of the inferred model are optimized to resemble pairwise distances derived directly from the contact counts. These approaches, however, often optimize a heuristic objective function and require strong assumptions about the biophysics of DNA to transform interaction frequencies to spatial distance, and thereby may lead to incorrect structure reconstruction. We propose a novel approach to infer a consensus 3D structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci. The method can automatically adjust the transfer function relating the spatial distance to the Poisson intensity and infer a genome structure that best explains the observed data. We compare two variants of our Poisson method, with or without optimization of the transfer function, to four different MDS-based algorithms-two metric MDS methods using different stress functions, a non-metric version of MDS and ChromSDE, a recently described, advanced MDS method-on a wide range of simulated datasets. We demonstrate that the Poisson models reconstruct better structures than all MDS-based methods, particularly at low coverage and high resolution, and we highlight the importance of optimizing the transfer function. On publicly available Hi-C data from mouse embryonic stem cells, we show that the Poisson methods lead to more reproducible structures than MDS-based methods when we use data generated using different restriction enzymes, and when we reconstruct structures at different resolutions. A Python implementation of the proposed method is available at http://cbio.ensmp.fr/pastis. © The Author 2014. Published by Oxford University Press.

Fast and Accurate Poisson Denoising With Trainable Nonlinear Diffusion.

PubMed

Feng, Wensen; Qiao, Peng; Chen, Yunjin; Wensen Feng; Peng Qiao; Yunjin Chen; Feng, Wensen; Chen, Yunjin; Qiao, Peng

2018-06-01

The degradation of the acquired signal by Poisson noise is a common problem for various imaging applications, such as medical imaging, night vision, and microscopy. Up to now, many state-of-the-art Poisson denoising techniques mainly concentrate on achieving utmost performance, with little consideration for the computation efficiency. Therefore, in this paper we aim to propose an efficient Poisson denoising model with both high computational efficiency and recovery quality. To this end, we exploit the newly developed trainable nonlinear reaction diffusion (TNRD) model which has proven an extremely fast image restoration approach with performance surpassing recent state-of-the-arts. However, the straightforward direct gradient descent employed in the original TNRD-based denoising task is not applicable in this paper. To solve this problem, we resort to the proximal gradient descent method. We retrain the model parameters, including the linear filters and influence functions by taking into account the Poisson noise statistics, and end up with a well-trained nonlinear diffusion model specialized for Poisson denoising. The trained model provides strongly competitive results against state-of-the-art approaches, meanwhile bearing the properties of simple structure and high efficiency. Furthermore, our proposed model comes along with an additional advantage, that the diffusion process is well-suited for parallel computation on graphics processing units (GPUs). For images of size , our GPU implementation takes less than 0.1 s to produce state-of-the-art Poisson denoising performance.

Hole-ness of point clouds

NASA Astrophysics Data System (ADS)

Gronz, Oliver; Seeger, Manuel; Klaes, Björn; Casper, Markus C.; Ries, Johannes B.

2015-04-01

Accurate and dense 3D models of soil surfaces can be used in various ways: They can be used as initial shapes for erosion models. They can be used as benchmark shapes for erosion model outputs. They can be used to derive metrics, such as random roughness... One easy and low-cost method to produce these models is structure from motion (SfM). Using this method, two questions arise: Does the soil moisture, which changes the colour, albedo and reflectivity of the soil, influence the model quality? How can the model quality be evaluated? To answer these questions, a suitable data set has been produced: soil has been placed on a tray and areas with different roughness structures have been formed. For different moisture states - dry, medium, saturated - and two different lighting conditions - direct and indirect - sets of high-resolution images at the same camera positions have been taken. From the six image sets, 3D point clouds have been produced using VisualSfM. The visual inspection of the 3D models showed that all models have different areas, where holes of different sizes occur. But it is obviously a subjective task to determine the model's quality by visual inspection. One typical approach to evaluate model quality objectively is to estimate the point density on a regular, two-dimensional grid: the number of 3D points in each grid cell projected on a plane is calculated. This works well for surfaces that do not show vertical structures. Along vertical structures, many points will be projected on the same grid cell and thus the point density rather depends on the shape of the surface but less on the quality of the model. Another approach has been applied by using the points resulting from Poisson Surface Reconstructions. One of this algorithm's properties is the filling of holes: new points are interpolated inside the holes. Using the original 3D point cloud and the interpolated Poisson point set, two analyses have been performed: For all Poisson points, the distance to the closest original point cloud member has been calculated. For the resulting set of distances, histograms have been produced that show the distribution of point distances. As the Poisson points also make up a connected mesh, the size and distribution of single holes can also be estimated by labeling Poisson points that belong to the same hole: each hole gets a specific number. Afterwards, the area of the mesh formed by each set of Poisson hole points can be calculated. The result is a set of distinctive holes and their sizes. The two approaches showed that the hole-ness of the point cloud depends on the soil moisture respectively the reflectivity: the distance distribution of the model of the saturated soil shows the smallest number of large distances. The histogram of the medium state shows more large distances and the dry model shows the largest distances. Models resulting from indirect lighting are better than the models resulting from direct light for all moisture states.

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

Design and Performance of a 1 ms High-Speed Vision Chip with 3D-Stacked 140 GOPS Column-Parallel PEs †.

PubMed

Nose, Atsushi; Yamazaki, Tomohiro; Katayama, Hironobu; Uehara, Shuji; Kobayashi, Masatsugu; Shida, Sayaka; Odahara, Masaki; Takamiya, Kenichi; Matsumoto, Shizunori; Miyashita, Leo; Watanabe, Yoshihiro; Izawa, Takashi; Muramatsu, Yoshinori; Nitta, Yoshikazu; Ishikawa, Masatoshi

2018-04-24

We have developed a high-speed vision chip using 3D stacking technology to address the increasing demand for high-speed vision chips in diverse applications. The chip comprises a 1/3.2-inch, 1.27 Mpixel, 500 fps (0.31 Mpixel, 1000 fps, 2 × 2 binning) vision chip with 3D-stacked column-parallel Analog-to-Digital Converters (ADCs) and 140 Giga Operation per Second (GOPS) programmable Single Instruction Multiple Data (SIMD) column-parallel PEs for new sensing applications. The 3D-stacked structure and column parallel processing architecture achieve high sensitivity, high resolution, and high-accuracy object positioning.

Fast l₁-SPIRiT compressed sensing parallel imaging MRI: scalable parallel implementation and clinically feasible runtime.

PubMed

Murphy, Mark; Alley, Marcus; Demmel, James; Keutzer, Kurt; Vasanawala, Shreyas; Lustig, Michael

2012-06-01

We present l₁-SPIRiT, a simple algorithm for auto calibrating parallel imaging (acPI) and compressed sensing (CS) that permits an efficient implementation with clinically-feasible runtimes. We propose a CS objective function that minimizes cross-channel joint sparsity in the wavelet domain. Our reconstruction minimizes this objective via iterative soft-thresholding, and integrates naturally with iterative self-consistent parallel imaging (SPIRiT). Like many iterative magnetic resonance imaging reconstructions, l₁-SPIRiT's image quality comes at a high computational cost. Excessively long runtimes are a barrier to the clinical use of any reconstruction approach, and thus we discuss our approach to efficiently parallelizing l₁-SPIRiT and to achieving clinically-feasible runtimes. We present parallelizations of l₁-SPIRiT for both multi-GPU systems and multi-core CPUs, and discuss the software optimization and parallelization decisions made in our implementation. The performance of these alternatives depends on the processor architecture, the size of the image matrix, and the number of parallel imaging channels. Fundamentally, achieving fast runtime requires the correct trade-off between cache usage and parallelization overheads. We demonstrate image quality via a case from our clinical experimentation, using a custom 3DFT spoiled gradient echo (SPGR) sequence with up to 8× acceleration via Poisson-disc undersampling in the two phase-encoded directions.

Fast ℓ1-SPIRiT Compressed Sensing Parallel Imaging MRI: Scalable Parallel Implementation and Clinically Feasible Runtime

PubMed Central

Murphy, Mark; Alley, Marcus; Demmel, James; Keutzer, Kurt; Vasanawala, Shreyas; Lustig, Michael

2012-01-01

We present ℓ1-SPIRiT, a simple algorithm for auto calibrating parallel imaging (acPI) and compressed sensing (CS) that permits an efficient implementation with clinically-feasible runtimes. We propose a CS objective function that minimizes cross-channel joint sparsity in the Wavelet domain. Our reconstruction minimizes this objective via iterative soft-thresholding, and integrates naturally with iterative Self-Consistent Parallel Imaging (SPIRiT). Like many iterative MRI reconstructions, ℓ1-SPIRiT’s image quality comes at a high computational cost. Excessively long runtimes are a barrier to the clinical use of any reconstruction approach, and thus we discuss our approach to efficiently parallelizing ℓ1-SPIRiT and to achieving clinically-feasible runtimes. We present parallelizations of ℓ1-SPIRiT for both multi-GPU systems and multi-core CPUs, and discuss the software optimization and parallelization decisions made in our implementation. The performance of these alternatives depends on the processor architecture, the size of the image matrix, and the number of parallel imaging channels. Fundamentally, achieving fast runtime requires the correct trade-off between cache usage and parallelization overheads. We demonstrate image quality via a case from our clinical experimentation, using a custom 3DFT Spoiled Gradient Echo (SPGR) sequence with up to 8× acceleration via poisson-disc undersampling in the two phase-encoded directions. PMID:22345529

Identification d’une Classe de Processus de Poisson Filtres (Identification of a Class of Filtered Poisson Processes).

DTIC Science & Technology

1983-05-20

Poisson processes is introduced: the amplitude has a law which is spherically invariant and the filter is real, linear and causal. It is shown how such a model can be identified from experimental data. (Author)

A 3D staggered-grid finite difference scheme for poroelastic wave equation

NASA Astrophysics Data System (ADS)

Zhang, Yijie; Gao, Jinghuai

2014-10-01

Three dimensional numerical modeling has been a viable tool for understanding wave propagation in real media. The poroelastic media can better describe the phenomena of hydrocarbon reservoirs than acoustic and elastic media. However, the numerical modeling in 3D poroelastic media demands significantly more computational capacity, including both computational time and memory. In this paper, we present a 3D poroelastic staggered-grid finite difference (SFD) scheme. During the procedure, parallel computing is implemented to reduce the computational time. Parallelization is based on domain decomposition, and communication between processors is performed using message passing interface (MPI). Parallel analysis shows that the parallelized SFD scheme significantly improves the simulation efficiency and 3D decomposition in domain is the most efficient. We also analyze the numerical dispersion and stability condition of the 3D poroelastic SFD method. Numerical results show that the 3D numerical simulation can provide a real description of wave propagation.

Parallelization of PANDA discrete ordinates code using spatial decomposition

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

Humbert, P.

2006-07-01

We present the parallel method, based on spatial domain decomposition, implemented in the 2D and 3D versions of the discrete Ordinates code PANDA. The spatial mesh is orthogonal and the spatial domain decomposition is Cartesian. For 3D problems a 3D Cartesian domain topology is created and the parallel method is based on a domain diagonal plane ordered sweep algorithm. The parallel efficiency of the method is improved by directions and octants pipelining. The implementation of the algorithm is straightforward using MPI blocking point to point communications. The efficiency of the method is illustrated by an application to the 3D-Ext C5G7more » benchmark of the OECD/NEA. (authors)« 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

On the Geometry of the Hamilton-Jacobi Equation and Generating Functions

NASA Astrophysics Data System (ADS)

Ferraro, Sebastián; de León, Manuel; Marrero, Juan Carlos; Martín de Diego, David; Vaquero, Miguel

2017-10-01

In this paper we develop a geometric version of the Hamilton-Jacobi equation in the Poisson setting. Specifically, we "geometrize" what is usually called a complete solution of the Hamilton-Jacobi equation. We use some well-known results about symplectic groupoids, in particular cotangent groupoids, as a keystone for the construction of our framework. Our methodology follows the ambitious program proposed by Weinstein (In Mechanics day (Waterloo, ON, 1992), volume 7 of fields institute communications, American Mathematical Society, Providence, 1996) in order to develop geometric formulations of the dynamical behavior of Lagrangian and Hamiltonian systems on Lie algebroids and Lie groupoids. This procedure allows us to take symmetries into account, and, as a by-product, we recover results from Channell and Scovel (Phys D 50(1):80-88, 1991), Ge (Indiana Univ. Math. J. 39(3):859-876, 1990), Ge and Marsden (Phys Lett A 133(3):134-139, 1988), but even in these situations our approach is new. A theory of generating functions for the Poisson structures considered here is also developed following the same pattern, solving a longstanding problem of the area: how to obtain a generating function for the identity transformation and the nearby Poisson automorphisms of Poisson manifolds. A direct application of our results gives the construction of a family of Poisson integrators, that is, integrators that conserve the underlying Poisson geometry. These integrators are implemented in the paper in benchmark problems. Some conclusions, current and future directions of research are shown at the end of the paper.

Design studies of the Ku-band, wide-band Gyro-TWT amplifier

NASA Astrophysics Data System (ADS)

Jung, Sang Wook; Lee, Han Seul; Jang, Kwong Ho; Choi, Jin Joo; Hong, Yong Jun; Shin, Jin Woo; So, Jun Ho; Won, Jong Hyo

2014-02-01

This paper reports a Ku-band, wide band Gyrotron-Traveling-wave-tube(Gyro-TWT) that is currently being developed at Kwangwoon University. The Gyro-TWT has a two stage linear tapered interaction circuit to obtain a wide operating bandwidth. The linearly-tapered interaction circuit and nonlinearly-tapered magnetic field gives the Gyro-TWT a wide operating bandwidth. The Gyro-TWT bandwidth is 23%. The 2d-Particle-in-cell(PIC) and MAGIC2d code simulation results are 17.3 dB and 24.34 kW, respectively for the maximum saturated output power. A double anode MIG was simulated with E-Gun code. The results were 0.7 for the transvers to the axial beam velocity ratio (=alpha) and a 2.3% axial velocity spread at 50 kV and 4 A. A magnetic field profile simulation was performed by using the Poisson code to obtain the grazing magnetic field of the entire interaction circuit with Poisson code.

High order solution of Poisson problems with piecewise constant coefficients and interface jumps

NASA Astrophysics Data System (ADS)

Marques, Alexandre Noll; Nave, Jean-Christophe; Rosales, Rodolfo Ruben

2017-04-01

We present a fast and accurate algorithm to solve Poisson problems in complex geometries, using regular Cartesian grids. We consider a variety of configurations, including Poisson problems with interfaces across which the solution is discontinuous (of the type arising in multi-fluid flows). The algorithm is based on a combination of the Correction Function Method (CFM) and Boundary Integral Methods (BIM). Interface and boundary conditions can be treated in a fast and accurate manner using boundary integral equations, and the associated BIM. Unfortunately, BIM can be costly when the solution is needed everywhere in a grid, e.g. fluid flow problems. We use the CFM to circumvent this issue. The solution from the BIM is used to rewrite the problem as a series of Poisson problems in rectangular domains-which requires the BIM solution at interfaces/boundaries only. These Poisson problems involve discontinuities at interfaces, of the type that the CFM can handle. Hence we use the CFM to solve them (to high order of accuracy) with finite differences and a Fast Fourier Transform based fast Poisson solver. We present 2-D examples of the algorithm applied to Poisson problems involving complex geometries, including cases in which the solution is discontinuous. We show that the algorithm produces solutions that converge with either 3rd or 4th order of accuracy, depending on the type of boundary condition and solution discontinuity.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code.

NASA Astrophysics Data System (ADS)

Chacon, L.; Knoll, D. A.

2004-11-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended primitive-variable MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field, non-dissipative, and stable in the absence of physical dissipation.(L. Chacón , phComput. Phys. Comm.) submitted (2004) PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, first and second-order implicit schemes are available, although higher-order temporal implicit schemes can be effortlessly implemented within the Newton-Krylov framework. A successful, scalable, MG physics-based preconditioning strategy, similar in concept to previous 2D MHD efforts,(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002); phJ. Comput. Phys., 188 (2), 573-592 (2003) has been developed. We are currently in the process of parallelizing the code using the PETSc library, and a Newton-Krylov-Schwarz approach for the parallel treatment of the preconditioner. In this poster, we will report on both the serial and parallel performance of PIXIE3D, focusing primarily on scalability and CPU speedup vs. an explicit approach.

Casimir force in O(n) systems with a diffuse interface.

PubMed

Dantchev, Daniel; Grüneberg, Daniel

2009-04-01

We study the behavior of the Casimir force in O(n) systems with a diffuse interface and slab geometry infinity;{d-1}xL , where 2infinity limit of O(n) models with antiperiodic boundary conditions applied along the finite dimension L of the film. We observe that the Casimir amplitude Delta_{Casimir}(dmid R:J_{ perpendicular},J_{ parallel}) of the anisotropic d -dimensional system is related to that of the isotropic system Delta_{Casimir}(d) via Delta_{Casimir}(dmid R:J_{ perpendicular},J_{ parallel})=(J_{ perpendicular}J_{ parallel});{(d-1)2}Delta_{Casimir}(d) . For d=3 we derive the exact Casimir amplitude Delta_{Casimir}(3,mid R:J_{ perpendicular},J_{ parallel})=[Cl_{2}(pi3)3-zeta(3)(6pi)](J_{ perpendicular}J_{ parallel}) , as well as the exact scaling functions of the Casimir force and of the helicity modulus Upsilon(T,L) . We obtain that beta_{c}Upsilon(T_{c},L)=(2pi;{2})[Cl_{2}(pi3)3+7zeta(3)(30pi)](J_{ perpendicular}J_{ parallel})L;{-1} , where T_{c} is the critical temperature of the bulk system. We find that the contributions in the excess free energy due to the existence of a diffuse interface result in a repulsive Casimir force in the whole temperature region.

On time-dependent Hamiltonian realizations of planar and nonplanar systems

NASA Astrophysics Data System (ADS)

Esen, Oğul; Guha, Partha

2018-04-01

In this paper, we elucidate the key role played by the cosymplectic geometry in the theory of time dependent Hamiltonian systems in 2 D. We generalize the cosymplectic structures to time-dependent Nambu-Poisson Hamiltonian systems and corresponding Jacobi's last multiplier for 3 D systems. We illustrate our constructions with various examples.

Identification of lithology in Gulf of Mexico Miocene rocks

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

Hilterman, F.J.; Sherwood, J.W.C.; Schellhorn, R.

1996-12-31

In the Gulf of Mexico, many gas-saturated sands are not Bright Spots and thus are difficult to detect on conventional 3D seismic data. These small amplitude reflections occur frequently in Pliocene-Miocene exploration plays when the acoustic impedances of the gas-saturated sands and shales are approximately the same. In these areas, geophysicists have had limited success using AVO to reduce the exploration risk. The interpretation of the conventional AVO attributes is often difficult and contains questionable relationships to the physical properties of the media. A 3D AVO study was conducted utilizing numerous well-log suites, core analyses, and production histories to helpmore » calibrate the seismic response to the petrophysical properties. This study resulted in an extension of the AVO method to a technique that now displays Bright spots when very clean sands and gas-saturated sands occur. These litho-stratigraphic reflections on the new AVO technique are related to Poisson`s ratio, a petrophysical property that is normally mixed with the acoustic impedance on conventional 3D migrated data.« less

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

An efficient parallel algorithm: Poststack and prestack Kirchhoff 3D depth migration using flexi-depth iterations

NASA Astrophysics Data System (ADS)

Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh

2015-07-01

This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.

A convergent 2D finite-difference scheme for the Dirac–Poisson system and the simulation of graphene

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

Brinkman, D., E-mail: Daniel.Brinkman@asu.edu; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287; Heitzinger, C., E-mail: Clemens.Heitzinger@asu.edu

2014-01-15

We present a convergent finite-difference scheme of second order in both space and time for the 2D electromagnetic Dirac equation. We apply this method in the self-consistent Dirac–Poisson system to the simulation of graphene. The model is justified for low energies, where the particles have wave vectors sufficiently close to the Dirac points. In particular, we demonstrate that our method can be used to calculate solutions of the Dirac–Poisson system where potentials act as beam splitters or Veselago lenses.

Quasineutral plasma expansion into infinite vacuum as a model for parallel ELM transport

NASA Astrophysics Data System (ADS)

Moulton, D.; Ghendrih, Ph; Fundamenski, W.; Manfredi, G.; Tskhakaya, D.

2013-08-01

An analytic solution for the expansion of a plasma into vacuum is assessed for its relevance to the parallel transport of edge localized mode (ELM) filaments along field lines. This solution solves the 1D1V Vlasov-Poisson equations for the adiabatic (instantaneous source), collisionless expansion of a Gaussian plasma bunch into an infinite space in the quasineutral limit. The quasineutral assumption is found to hold as long as λD0/σ0 ≲ 0.01 (where λD0 is the initial Debye length at peak density and σ0 is the parallel length of the Gaussian filament), a condition that is physically realistic. The inclusion of a boundary at x = L and consequent formation of a target sheath is found to have a negligible effect when L/σ0 ≳ 5, a condition that is physically plausible. Under the same condition, the target flux densities predicted by the analytic solution are well approximated by the ‘free-streaming’ equations used in previous experimental studies, strengthening the notion that these simple equations are physically reasonable. Importantly, the analytic solution predicts a zero heat flux density so that a fluid approach to the problem can be used equally well, at least when the source is instantaneous. It is found that, even for JET-like pedestal parameters, collisions can affect the expansion dynamics via electron temperature isotropization, although this is probably a secondary effect. Finally, the effect of a finite duration, τsrc, for the plasma source is investigated. As is found for an instantaneous source, when L/σ0 ≳ 5 the presence of a target sheath has a negligible effect, at least up to the explored range of τsrc = L/cs (where cs is the sound speed at the initial temperature).

A Fourier spectral-discontinuous Galerkin method for time-dependent 3-D Schrödinger-Poisson equations with discontinuous potentials

NASA Astrophysics Data System (ADS)

Lu, Tiao; Cai, Wei

2008-10-01

In this paper, we propose a high order Fourier spectral-discontinuous Galerkin method for time-dependent Schrödinger-Poisson equations in 3-D spaces. The Fourier spectral Galerkin method is used for the two periodic transverse directions and a high order discontinuous Galerkin method for the longitudinal propagation direction. Such a combination results in a diagonal form for the differential operators along the transverse directions and a flexible method to handle the discontinuous potentials present in quantum heterojunction and supperlattice structures. As the derivative matrices are required for various time integration schemes such as the exponential time differencing and Crank Nicholson methods, explicit derivative matrices of the discontinuous Galerkin method of various orders are derived. Numerical results, using the proposed method with various time integration schemes, are provided to validate the method.

A Parallel Numerical Algorithm To Solve Linear Systems Of Equations Emerging From 3D Radiative Transfer

NASA Astrophysics Data System (ADS)

Wichert, Viktoria; Arkenberg, Mario; Hauschildt, Peter H.

2016-10-01

Highly resolved state-of-the-art 3D atmosphere simulations will remain computationally extremely expensive for years to come. In addition to the need for more computing power, rethinking coding practices is necessary. We take a dual approach by introducing especially adapted, parallel numerical methods and correspondingly parallelizing critical code passages. In the following, we present our respective work on PHOENIX/3D. With new parallel numerical algorithms, there is a big opportunity for improvement when iteratively solving the system of equations emerging from the operator splitting of the radiative transfer equation J = ΛS. The narrow-banded approximate Λ-operator Λ* , which is used in PHOENIX/3D, occurs in each iteration step. By implementing a numerical algorithm which takes advantage of its characteristic traits, the parallel code's efficiency is further increased and a speed-up in computational time can be achieved.

3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

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

Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.

1997-12-31

The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle.more » The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.« less

A Kullback-Leibler approach for 3D reconstruction of spectral CT data corrupted by Poisson noise

NASA Astrophysics Data System (ADS)

Hohweiller, Tom; Ducros, Nicolas; Peyrin, Françoise; Sixou, Bruno

2017-09-01

While standard computed tomography (CT) data do not depend on energy, spectral computed tomography (SPCT) acquire energy-resolved data, which allows material decomposition of the object of interest. Decompo- sitions in the projection domain allow creating projection mass density (PMD) per materials. From decomposed projections, a tomographic reconstruction creates 3D material density volume. The decomposition is made pos- sible by minimizing a cost function. The variational approach is preferred since this is an ill-posed non-linear inverse problem. Moreover, noise plays a critical role when decomposing data. That is why in this paper, a new data fidelity term is used to take into account of the photonic noise. In this work two data fidelity terms were investigated: a weighted least squares (WLS) term, adapted to Gaussian noise, and the Kullback-Leibler distance (KL), adapted to Poisson noise. A regularized Gauss-Newton algorithm minimizes the cost function iteratively. Both methods decompose materials from a numerical phantom of a mouse. Soft tissues and bones are decomposed in the projection domain; then a tomographic reconstruction creates a 3D material density volume for each material. Comparing relative errors, KL is shown to outperform WLS for low photon counts, in 2D and 3D. This new method could be of particular interest when low-dose acquisitions are performed.

The development of a scalable parallel 3-D CFD algorithm for turbomachinery. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Luke, Edward Allen

1993-01-01

Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.

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

Hybrid parallel computing architecture for multiview phase shifting

NASA Astrophysics Data System (ADS)

Zhong, Kai; Li, Zhongwei; Zhou, Xiaohui; Shi, Yusheng; Wang, Congjun

2014-11-01

The multiview phase-shifting method shows its powerful capability in achieving high resolution three-dimensional (3-D) shape measurement. Unfortunately, this ability results in very high computation costs and 3-D computations have to be processed offline. To realize real-time 3-D shape measurement, a hybrid parallel computing architecture is proposed for multiview phase shifting. In this architecture, the central processing unit can co-operate with the graphic processing unit (GPU) to achieve hybrid parallel computing. The high computation cost procedures, including lens distortion rectification, phase computation, correspondence, and 3-D reconstruction, are implemented in GPU, and a three-layer kernel function model is designed to simultaneously realize coarse-grained and fine-grained paralleling computing. Experimental results verify that the developed system can perform 50 fps (frame per second) real-time 3-D measurement with 260 K 3-D points per frame. A speedup of up to 180 times is obtained for the performance of the proposed technique using a NVIDIA GT560Ti graphics card rather than a sequential C in a 3.4 GHZ Inter Core i7 3770.

3D Kirchhoff depth migration algorithm: A new scalable approach for parallelization on multicore CPU based cluster

NASA Astrophysics Data System (ADS)

Rastogi, Richa; Londhe, Ashutosh; Srivastava, Abhishek; Sirasala, Kirannmayi M.; Khonde, Kiran

2017-03-01

In this article, a new scalable 3D Kirchhoff depth migration algorithm is presented on state of the art multicore CPU based cluster. Parallelization of 3D Kirchhoff depth migration is challenging due to its high demand of compute time, memory, storage and I/O along with the need of their effective management. The most resource intensive modules of the algorithm are traveltime calculations and migration summation which exhibit an inherent trade off between compute time and other resources. The parallelization strategy of the algorithm largely depends on the storage of calculated traveltimes and its feeding mechanism to the migration process. The presented work is an extension of our previous work, wherein a 3D Kirchhoff depth migration application for multicore CPU based parallel system had been developed. Recently, we have worked on improving parallel performance of this application by re-designing the parallelization approach. The new algorithm is capable to efficiently migrate both prestack and poststack 3D data. It exhibits flexibility for migrating large number of traces within the available node memory and with minimal requirement of storage, I/O and inter-node communication. The resultant application is tested using 3D Overthrust data on PARAM Yuva II, which is a Xeon E5-2670 based multicore CPU cluster with 16 cores/node and 64 GB shared memory. Parallel performance of the algorithm is studied using different numerical experiments and the scalability results show striking improvement over its previous version. An impressive 49.05X speedup with 76.64% efficiency is achieved for 3D prestack data and 32.00X speedup with 50.00% efficiency for 3D poststack data, using 64 nodes. The results also demonstrate the effectiveness and robustness of the improved algorithm with high scalability and efficiency on a multicore CPU cluster.

An efficient implementation of 3D high-resolution imaging for large-scale seismic data with GPU/CPU heterogeneous parallel computing

NASA Astrophysics Data System (ADS)

Xu, Jincheng; Liu, Wei; Wang, Jin; Liu, Linong; Zhang, Jianfeng

2018-02-01

De-absorption pre-stack time migration (QPSTM) compensates for the absorption and dispersion of seismic waves by introducing an effective Q parameter, thereby making it an effective tool for 3D, high-resolution imaging of seismic data. Although the optimal aperture obtained via stationary-phase migration reduces the computational cost of 3D QPSTM and yields 3D stationary-phase QPSTM, the associated computational efficiency is still the main problem in the processing of 3D, high-resolution images for real large-scale seismic data. In the current paper, we proposed a division method for large-scale, 3D seismic data to optimize the performance of stationary-phase QPSTM on clusters of graphics processing units (GPU). Then, we designed an imaging point parallel strategy to achieve an optimal parallel computing performance. Afterward, we adopted an asynchronous double buffering scheme for multi-stream to perform the GPU/CPU parallel computing. Moreover, several key optimization strategies of computation and storage based on the compute unified device architecture (CUDA) were adopted to accelerate the 3D stationary-phase QPSTM algorithm. Compared with the initial GPU code, the implementation of the key optimization steps, including thread optimization, shared memory optimization, register optimization and special function units (SFU), greatly improved the efficiency. A numerical example employing real large-scale, 3D seismic data showed that our scheme is nearly 80 times faster than the CPU-QPSTM algorithm. Our GPU/CPU heterogeneous parallel computing framework significant reduces the computational cost and facilitates 3D high-resolution imaging for large-scale seismic data.

Evaluation of usefulness of 3D views for clinical photography.

PubMed

Jinnin, Masatoshi; Fukushima, Satoshi; Masuguchi, Shinichi; Tanaka, Hiroki; Kawashita, Yoshio; Ishihara, Tsuyoshi; Ihn, Hironobu

2011-01-01

This is the first report investigating the usefulness of a 3D viewing technique (parallel viewing and cross-eyed viewing) for presenting clinical photography. Using the technique, we can grasp 3D structure of various lesions (e.g. tumors, wounds) or surgical procedures (e.g. lymph node dissection, flap) much more easily even without any cost and optical aids compared to 2D photos. Most recently 3D cameras started to be commercially available, but they may not be useful for presentation in scientific papers or poster sessions. To create a stereogram, two different pictures were taken from the right and left eye views using a digital camera. Then, the two pictures were placed next to one another. Using 9 stereograms, we performed a questionnaire-based survey. Our survey revealed 57.7% of the doctors/students had acquired the 3D viewing technique and an additional 15.4% could learn parallel viewing with 10 minutes training. Among the subjects capable of 3D views, 73.7% used the parallel view technique whereas only 26.3% chose the cross-eyed view. There was no significant difference in the results of the questionnaire about the efficiency and usefulness of 3D views between parallel view users and cross-eyed users. Almost all subjects (94.7%) answered that the technique is useful. Lesions with multiple undulations are a good application. 3D views, especially parallel viewing, are likely to be common and easy enough to consider for practical use in doctors/students. The wide use of the technique may revolutionize presentation of clinical pictures in meetings, educational lectures, or manuscripts.

Parallelization of Program to Optimize Simulated Trajectories (POST3D)

NASA Technical Reports Server (NTRS)

Hammond, Dana P.; Korte, John J. (Technical Monitor)

2001-01-01

This paper describes the parallelization of the Program to Optimize Simulated Trajectories (POST3D). POST3D uses a gradient-based optimization algorithm that reaches an optimum design point by moving from one design point to the next. The gradient calculations required to complete the optimization process, dominate the computational time and have been parallelized using a Single Program Multiple Data (SPMD) on a distributed memory NUMA (non-uniform memory access) architecture. The Origin2000 was used for the tests presented.

3D printed soft parallel actuator

NASA Astrophysics Data System (ADS)

Zolfagharian, Ali; Kouzani, Abbas Z.; Khoo, Sui Yang; Noshadi, Amin; Kaynak, Akif

2018-04-01

This paper presents a 3-dimensional (3D) printed soft parallel contactless actuator for the first time. The actuator involves an electro-responsive parallel mechanism made of two segments namely active chain and passive chain both 3D printed. The active chain is attached to the ground from one end and constitutes two actuator links made of responsive hydrogel. The passive chain, on the other hand, is attached to the active chain from one end and consists of two rigid links made of polymer. The actuator links are printed using an extrusion-based 3D-Bioplotter with polyelectrolyte hydrogel as printer ink. The rigid links are also printed by a 3D fused deposition modelling (FDM) printer with acrylonitrile butadiene styrene (ABS) as print material. The kinematics model of the soft parallel actuator is derived via transformation matrices notations to simulate and determine the workspace of the actuator. The printed soft parallel actuator is then immersed into NaOH solution with specific voltage applied to it via two contactless electrodes. The experimental data is then collected and used to develop a parametric model to estimate the end-effector position and regulate kinematics model in response to specific input voltage over time. It is observed that the electroactive actuator demonstrates expected behaviour according to the simulation of its kinematics model. The use of 3D printing for the fabrication of parallel soft actuators opens a new chapter in manufacturing sophisticated soft actuators with high dexterity and mechanical robustness for biomedical applications such as cell manipulation and drug release.

Higher-Order Compact Schemes for Numerical Simulation of Incompressible Flows

NASA Technical Reports Server (NTRS)

Wilson, Robert V.; Demuren, Ayodeji O.; Carpenter, Mark

1998-01-01

A higher order accurate numerical procedure has been developed for solving incompressible Navier-Stokes equations for 2D or 3D fluid flow problems. It is based on low-storage Runge-Kutta schemes for temporal discretization and fourth and sixth order compact finite-difference schemes for spatial discretization. The particular difficulty of satisfying the divergence-free velocity field required in incompressible fluid flow is resolved by solving a Poisson equation for pressure. It is demonstrated that for consistent global accuracy, it is necessary to employ the same order of accuracy in the discretization of the Poisson equation. Special care is also required to achieve the formal temporal accuracy of the Runge-Kutta schemes. The accuracy of the present procedure is demonstrated by application to several pertinent benchmark problems.

Parallel CE/SE Computations via Domain Decomposition

NASA Technical Reports Server (NTRS)

Himansu, Ananda; Jorgenson, Philip C. E.; Wang, Xiao-Yen; Chang, Sin-Chung

2000-01-01

This paper describes the parallelization strategy and achieved parallel efficiency of an explicit time-marching algorithm for solving conservation laws. The Space-Time Conservation Element and Solution Element (CE/SE) algorithm for solving the 2D and 3D Euler equations is parallelized with the aid of domain decomposition. The parallel efficiency of the resultant algorithm on a Silicon Graphics Origin 2000 parallel computer is checked.

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.

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

Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

Ion flux through membrane channels--an enhanced algorithm for the Poisson-Nernst-Planck model.

PubMed

Dyrka, Witold; Augousti, Andy T; Kotulska, Malgorzata

2008-09-01

A novel algorithmic scheme for numerical solution of the 3D Poisson-Nernst-Planck model is proposed. The algorithmic improvements are universal and independent of the detailed physical model. They include three major steps: an adjustable gradient-based step value, an adjustable relaxation coefficient, and an optimized segmentation of the modeled space. The enhanced algorithm significantly accelerates the speed of computation and reduces the computational demands. The theoretical model was tested on a regular artificial channel and validated on a real protein channel-alpha-hemolysin, proving its efficiency. (c) 2008 Wiley Periodicals, Inc.

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

Determination of oral mucosal Poisson's ratio and coefficient of friction from in-vivo contact pressure measurements.

PubMed

Chen, Junning; Suenaga, Hanako; Hogg, Michael; Li, Wei; Swain, Michael; Li, Qing

2016-01-01

Despite their considerable importance to biomechanics, there are no existing methods available to directly measure apparent Poisson's ratio and friction coefficient of oral mucosa. This study aimed to develop an inverse procedure to determine these two biomechanical parameters by utilizing in vivo experiment of contact pressure between partial denture and beneath mucosa through nonlinear finite element (FE) analysis and surrogate response surface (RS) modelling technique. First, the in vivo denture-mucosa contact pressure was measured by a tactile electronic sensing sheet. Second, a 3D FE model was constructed based on the patient CT images. Third, a range of apparent Poisson's ratios and the coefficients of friction from literature was considered as the design variables in a series of FE runs for constructing a RS surrogate model. Finally, the discrepancy between computed in silico and measured in vivo results was minimized to identify the best matching Poisson's ratio and coefficient of friction. The established non-invasive methodology was demonstrated effective to identify such biomechanical parameters of oral mucosa and can be potentially used for determining the biomaterial properties of other soft biological tissues.

Time-Resolved 3D Quantitative Flow MRI of the Major Intracranial Vessels: Initial Experience and Comparative Evaluation at 1.5T and 3.0T in Combination With Parallel Imaging

PubMed Central

Bammer, Roland; Hope, Thomas A.; Aksoy, Murat; Alley, Marcus T.

2012-01-01

Exact knowledge of blood flow characteristics in the major cerebral vessels is of great relevance for diagnosing cerebrovascular abnormalities. This involves the assessment of hemodynamically critical areas as well as the derivation of biomechanical parameters such as wall shear stress and pressure gradients. A time-resolved, 3D phase-contrast (PC) MRI method using parallel imaging was implemented to measure blood flow in three dimensions at multiple instances over the cardiac cycle. The 4D velocity data obtained from 14 healthy volunteers were used to investigate dynamic blood flow with the use of multiplanar reformatting, 3D streamlines, and 4D particle tracing. In addition, the effects of magnetic field strength, parallel imaging, and temporal resolution on the data were investigated in a comparative evaluation at 1.5T and 3T using three different parallel imaging reduction factors and three different temporal resolutions in eight of the 14 subjects. Studies were consistently performed faster at 3T than at 1.5T because of better parallel imaging performance. A high temporal resolution (65 ms) was required to follow dynamic processes in the intracranial vessels. The 4D flow measurements provided a high degree of vascular conspicuity. Time-resolved streamline analysis provided features that have not been reported previously for the intracranial vasculature. PMID:17195166

High Performance Programming Using Explicit Shared Memory Model on the Cray T3D

NASA Technical Reports Server (NTRS)

Saini, Subhash; Simon, Horst D.; Lasinski, T. A. (Technical Monitor)

1994-01-01

The Cray T3D is the first-phase system in Cray Research Inc.'s (CRI) three-phase massively parallel processing program. In this report we describe the architecture of the T3D, as well as the CRAFT (Cray Research Adaptive Fortran) programming model, and contrast it with PVM, which is also supported on the T3D We present some performance data based on the NAS Parallel Benchmarks to illustrate both architectural and software features of the T3D.

Statistical shape analysis using 3D Poisson equation--A quantitatively validated approach.

PubMed

Gao, Yi; Bouix, Sylvain

2016-05-01

Statistical shape analysis has been an important area of research with applications in biology, anatomy, neuroscience, agriculture, paleontology, etc. Unfortunately, the proposed methods are rarely quantitatively evaluated, and as shown in recent studies, when they are evaluated, significant discrepancies exist in their outputs. In this work, we concentrate on the problem of finding the consistent location of deformation between two population of shapes. We propose a new shape analysis algorithm along with a framework to perform a quantitative evaluation of its performance. Specifically, the algorithm constructs a Signed Poisson Map (SPoM) by solving two Poisson equations on the volumetric shapes of arbitrary topology, and statistical analysis is then carried out on the SPoMs. The method is quantitatively evaluated on synthetic shapes and applied on real shape data sets in brain structures. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Koniges, A.E.

The author describes the new T3D parallel computer at NERSC. The adaptive mesh ICF3D code is one of the current applications being ported and developed for use on the T3D. It has been stressed in other papers in this proceedings that the development environment and tools available on the parallel computer is similar to any planned for the future including networks of workstations.

Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals

NASA Astrophysics Data System (ADS)

Lu, Benzhuo; Cheng, Xiaolin; Hou, Tingjun; McCammon, J. Andrew

2005-08-01

The electrostatic interaction among molecules solvated in ionic solution is governed by the Poisson-Boltzmann equation (PBE). Here the hypersingular integral technique is used in a boundary element method (BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell stress tensor on the solvated molecular surface, and then the PB forces and torques can be obtained from the stress tensor. Compared with the variational method (also in a BEM frame) that we proposed recently, this method provides an even more efficient way to calculate the full intermolecular electrostatic interaction force, especially for macromolecular systems. Thus, it may be more suitable for the application of Brownian dynamics methods to study the dynamics of protein/protein docking as well as the assembly of large 3D architectures involving many diffusing subunits. The method has been tested on two simple cases to demonstrate its reliability and efficiency, and also compared with our previous variational method used in BEM.

Finite element 3D modeling of mechanical behavior of mineralized collagen microfibrils.

PubMed

Barkaoui, Abdelwahed; Hambli, Ridha

2011-01-01

The aim of this work is to develop a 3D finite elements model to study the nanomechanical behavior of mineralized collagen microfibrils, which consists of three phases, (i) collagen phase formed by five tropocollagen (TC) molecules linked together with cross-links, (ii) a mineral phase (Hydroxyapatite), and (iii) impure mineral phase, and to investigate the important role of individual properties of every constituent. The mechanical and geometric properties (TC molecule diameter) of both tropocollagen and mineral were taken into consideration as well as cross-links, which was represented by spring elements with adjusted properties based on experimental data. In this paper an equivalent homogenized model was developed to assess the whole microfibril mechanical properties (Young's modulus and Poisson's ratio) under varying mechanical properties of each phase. In this study, both equivalent Young's modulus and Poisson's ratio, which were expressed as functions of Young's modulus of each phase, were obtained under tensile load with symmetric and periodic boundary conditions.

Parallelization of ARC3D with Computer-Aided Tools

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; Hribar, Michelle; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

Evaluation of myocardial defect detection between parallel-hole and fan-beam SPECT using the Hotelling trace

NASA Astrophysics Data System (ADS)

Wollenweber, S. D.; Tsui, B. M. W.; Lalush, D. S.; Frey, E. C.; Gullberg, G. T.

1998-08-01

The objective of this study was to implement the Hotelling trace (HT) to evaluate the potential increase in defect detection in myocardial SPECT using high-resolution fan-beam (HRF) versus parallel-hole (HRP) collimation and compare results to a previously reported human observer study (G.K. Gregoriou et al., ibid., vol. 42, p. 1267-75, 1995). Projection data from the 3D MCAT torso phantom were simulated including the effects of attenuation, collimator-detector response blurring and scatter. Poisson noise fluctuations were then simulated. The HRP and HRF collimators had the same spatial resolution at 20 cm. The total counts in the projection data sets were proportional to the detection efficiencies of the collimators and on the order of that found in clinical Tc-99m studies. In six left-ventricular defect locations, the HT found for HRF was superior to that for HRP collimation. For HRF collimation, the HT was calculated for reconstructed images using 64/spl times/64, 128/spl times/128 and 192/spl times/192 grid sizes. The results demonstrate substantial improvement in myocardial defect detection when the grid size was increased from 64/spl times/64 to 128/spl times/128 and slight improvement from 128/spl times/128 to 192/spl times/192. Also, the performance of the Hotelling observer in terms of the HT at the different grid sizes correlates at better than 0.95 to that found in human observers in a previously reported observer experiment and ROC study.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

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

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

C1 finite elements on non-tensor-product 2d and 3d manifolds.

PubMed

Nguyen, Thien; Karčiauskas, Kęstutis; Peters, Jörg

2016-01-01

Geometrically continuous ( G k ) constructions naturally yield families of finite elements for isogeometric analysis (IGA) that are C k also for non-tensor-product layout. This paper describes and analyzes one such concrete C 1 geometrically generalized IGA element (short: gIGA element) that generalizes bi-quadratic splines to quad meshes with irregularities. The new gIGA element is based on a recently-developed G 1 surface construction that recommends itself by its a B-spline-like control net, low (least) polynomial degree, good shape properties and reproduction of quadratics at irregular (extraordinary) points. Remarkably, for Poisson's equation on the disk using interior vertices of valence 3 and symmetric layout, we observe O ( h 3 ) convergence in the L ∞ norm for this family of elements. Numerical experiments confirm the elements to be effective for solving the trivariate Poisson equation on the solid cylinder, deformations thereof (a turbine blade), modeling and computing geodesics on smooth free-form surfaces via the heat equation, for solving the biharmonic equation on the disk and for Koiter-type thin-shell analysis.

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.

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.

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

Crashworthiness simulations with DYNA3D

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

Schauer, D.A.; Hoover, C.G.; Kay, G.J.

1996-04-01

Current progress in parallel algorithm research and applications in vehicle crash simulation is described for the explicit, finite element algorithms in DYNA3D. Problem partitioning methods and parallel algorithms for contact at material interfaces are the two challenging algorithm research problems that are addressed. Two prototype parallel contact algorithms have been developed for treating the cases of local and arbitrary contact. Demonstration problems for local contact are crashworthiness simulations with 222 locally defined contact surfaces and a vehicle/barrier collision modeled with arbitrary contact. A simulation of crash tests conducted for a vehicle impacting a U-channel small sign post embedded in soilmore » has been run on both the serial and parallel versions of DYNA3D. A significant reduction in computational time has been observed when running these problems on the parallel version. However, to achieve maximum efficiency, complex problems must be appropriately partitioned, especially when contact dominates the computation.« less

Multichannel Poisson denoising and deconvolution 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.

2012-10-01

A multiscale representation-based denoising method for spherical data contaminated with Poisson noise, the multiscale variance stabilizing transform on the sphere (MS-VSTS), has been previously proposed. This paper first extends this MS-VSTS to spherical two and one dimensions data (2D-1D), where the two first dimensions are longitude and latitude, and the third dimension is a meaningful physical index such as energy or time. We then introduce a novel multichannel deconvolution built upon the 2D-1D MS-VSTS, which allows us to get rid of both the noise and the blur introduced by the point spread function (PSF) in each energy (or time) band. The method is applied to simulated data from the Large Area Telescope (LAT), the main instrument of the Fermi Gamma-ray Space Telescope, which detects high energy gamma-rays in a very wide energy range (from 20 MeV to more than 300 GeV), and whose PSF is strongly energy-dependent (from about 3.5 at 100 MeV to less than 0.1 at 10 GeV).

Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code

NASA Astrophysics Data System (ADS)

Longoni, Gianluca; Anderson, Stanwood L.

2009-08-01

The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.

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

Finite element solution of torsion and other 2-D Poisson equations

NASA Technical Reports Server (NTRS)

Everstine, G. C.

1982-01-01

The NASTRAN structural analysis computer program may be used, without modification, to solve two dimensional Poisson equations such as arise in the classical Saint Venant torsion problem. The nonhomogeneous term (the right-hand side) in the Poisson equation can be handled conveniently by specifying a gravitational load in a "structural" analysis. The use of an analogy between the equations of elasticity and those of classical mathematical physics is summarized in detail.

3D Data Denoising via Nonlocal Means Filter by Using Parallel GPU Strategies

PubMed Central

Cuomo, Salvatore; De Michele, Pasquale; Piccialli, Francesco

2014-01-01

Nonlocal Means (NLM) algorithm is widely considered as a state-of-the-art denoising filter in many research fields. Its high computational complexity leads researchers to the development of parallel programming approaches and the use of massively parallel architectures such as the GPUs. In the recent years, the GPU devices had led to achieving reasonable running times by filtering, slice-by-slice, and 3D datasets with a 2D NLM algorithm. In our approach we design and implement a fully 3D NonLocal Means parallel approach, adopting different algorithm mapping strategies on GPU architecture and multi-GPU framework, in order to demonstrate its high applicability and scalability. The experimental results we obtained encourage the usability of our approach in a large spectrum of applicative scenarios such as magnetic resonance imaging (MRI) or video sequence denoising. PMID:25045397

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.

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers

DOE PAGES

Wang, Bei; Ethier, Stephane; Tang, William; ...

2017-06-29

The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability ofmore » the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon Phi (MIC) co-processors and performance comparisons with state-of-the-art homogeneous HPC systems such as Blue Gene/Q. New discovery science capabilities in the magnetic fusion energy application domain are enabled, including investigations of Ion-Temperature-Gradient (ITG) driven turbulence simulations with unprecedented spatial resolution and long temporal duration. Performance studies with realistic fusion experimental parameters are carried out on multiple supercomputing systems spanning a wide range of cache capacities, cache-sharing configurations, memory bandwidth, interconnects and network topologies. These performance comparisons using a realistic discovery-science-capable domain application code provide valuable insights on optimization techniques across one of the broadest sets of current high-end computing platforms worldwide.« less

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers

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

Wang, Bei; Ethier, Stephane; Tang, William

The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability ofmore » the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon Phi (MIC) co-processors and performance comparisons with state-of-the-art homogeneous HPC systems such as Blue Gene/Q. New discovery science capabilities in the magnetic fusion energy application domain are enabled, including investigations of Ion-Temperature-Gradient (ITG) driven turbulence simulations with unprecedented spatial resolution and long temporal duration. Performance studies with realistic fusion experimental parameters are carried out on multiple supercomputing systems spanning a wide range of cache capacities, cache-sharing configurations, memory bandwidth, interconnects and network topologies. These performance comparisons using a realistic discovery-science-capable domain application code provide valuable insights on optimization techniques across one of the broadest sets of current high-end computing platforms worldwide.« less

Progress report on PIXIE3D, a fully implicit 3D extended MHD solver

NASA Astrophysics Data System (ADS)

Chacon, Luis

2008-11-01

Recently, invited talk at DPP07 an optimal, massively parallel implicit algorithm for 3D resistive magnetohydrodynamics (PIXIE3D) was demonstrated. Excellent algorithmic and parallel results were obtained with up to 4096 processors and 138 million unknowns. While this is a remarkable result, further developments are still needed for PIXIE3D to become a 3D extended MHD production code in general geometries. In this poster, we present an update on the status of PIXIE3D on several fronts. On the physics side, we will describe our progress towards the full Braginskii model, including: electron Hall terms, anisotropic heat conduction, and gyroviscous corrections. Algorithmically, we will discuss progress towards a robust, optimal, nonlinear solver for arbitrary geometries, including preconditioning for the new physical effects described, the implementation of a coarse processor-grid solver (to maintain optimal algorithmic performance for an arbitrarily large number of processors in massively parallel computations), and of a multiblock capability to deal with complicated geometries. L. Chac'on, Phys. Plasmas 15, 056103 (2008);

High Performance Programming Using Explicit Shared Memory Model on Cray T3D1

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Saini, Subhash; Grassi, Charles

1994-01-01

The Cray T3D system is the first-phase system in Cray Research, Inc.'s (CRI) three-phase massively parallel processing (MPP) program. This system features a heterogeneous architecture that closely couples DEC's Alpha microprocessors and CRI's parallel-vector technology, i.e., the Cray Y-MP and Cray C90. An overview of the Cray T3D hardware and available programming models is presented. Under Cray Research adaptive Fortran (CRAFT) model four programming methods (data parallel, work sharing, message-passing using PVM, and explicit shared memory model) are available to the users. However, at this time data parallel and work sharing programming models are not available to the user community. The differences between standard PVM and CRI's PVM are highlighted with performance measurements such as latencies and communication bandwidths. We have found that the performance of neither standard PVM nor CRI s PVM exploits the hardware capabilities of the T3D. The reasons for the bad performance of PVM as a native message-passing library are presented. This is illustrated by the performance of NAS Parallel Benchmarks (NPB) programmed in explicit shared memory model on Cray T3D. In general, the performance of standard PVM is about 4 to 5 times less than obtained by using explicit shared memory model. This degradation in performance is also seen on CM-5 where the performance of applications using native message-passing library CMMD on CM-5 is also about 4 to 5 times less than using data parallel methods. The issues involved (such as barriers, synchronization, invalidating data cache, aligning data cache etc.) while programming in explicit shared memory model are discussed. Comparative performance of NPB using explicit shared memory programming model on the Cray T3D and other highly parallel systems such as the TMC CM-5, Intel Paragon, Cray C90, IBM-SP1, etc. is presented.

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.

Vlasov Simulation of Mixing in Antihydrogen Formation

NASA Astrophysics Data System (ADS)

So, Chukman; Fajans, Joel; Friedland, Lazar; Wurtele, Jonathan; Alpha Collaboration

2011-10-01

In the ALPHA apparatus, low temperature antiprotons (p) and positrons (e+) are prepared adjacent to each other in a nested Penning trap. To create trappable antihydrogen (H), the two species must be mixed such that some resultant H atoms have sub-Kelvin kinetic energy. A new simulation has been developed to study and optimize the autoresonant mixing, in ALPHA. The p dynamics are governed by their own self- field, the e+ plasma field, and the external fields. The e+ 's are handled quasi-statically with a Poisson-Boltzmann solver. p 's are handled by multiple time dependent 1D Vlasov-Poisson solvers, each representing a radial slice of the plasma. The 1D simulatiuons couple through the 2D Poisson equation. We neglect radial transport due to the strong solenoidal field. The advantages and disadvantages of different descretization schemes, comparisons of simulation with experiment, and techniques for optimizing mixing, will be presented.

Parallel 3D Finite Element Numerical Modelling of DC Electron Guns

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

Prudencio, E.; Candel, A.; Ge, L.

2008-02-04

In this paper we present Gun3P, a parallel 3D finite element application that the Advanced Computations Department at the Stanford Linear Accelerator Center is developing for the analysis of beam formation in DC guns and beam transport in klystrons. Gun3P is targeted specially to complex geometries that cannot be described by 2D models and cannot be easily handled by finite difference discretizations. Its parallel capability allows simulations with more accuracy and less processing time than packages currently available. We present simulation results for the L-band Sheet Beam Klystron DC gun, in which case Gun3P is able to reduce simulation timemore » from days to some hours.« 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.

Guidelines for Use of the Approximate Beta-Poisson Dose-Response Model.

PubMed

Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie

2017-07-01

For dose-response analysis in quantitative microbial risk assessment (QMRA), the exact beta-Poisson model is a two-parameter mechanistic dose-response model with parameters α>0 and β>0, which involves the Kummer confluent hypergeometric function. Evaluation of a hypergeometric function is a computational challenge. Denoting PI(d) as the probability of infection at a given mean dose d, the widely used dose-response model PI(d)=1-(1+dβ)-α is an approximate formula for the exact beta-Poisson model. Notwithstanding the required conditions α<β and β>1, issues related to the validity and approximation accuracy of this approximate formula have remained largely ignored in practice, partly because these conditions are too general to provide clear guidance. Consequently, this study proposes a probability measure Pr(0 < r < 1 | α̂, β̂) as a validity measure (r is a random variable that follows a gamma distribution; α̂ and β̂ are the maximum likelihood estimates of α and β in the approximate model); and the constraint conditions β̂>(22α̂)0.50 for 0.02<α̂<2 as a rule of thumb to ensure an accurate approximation (e.g., Pr(0 < r < 1 | α̂, β̂) >0.99) . This validity measure and rule of thumb were validated by application to all the completed beta-Poisson models (related to 85 data sets) from the QMRA community portal (QMRA Wiki). The results showed that the higher the probability Pr(0 < r < 1 | α̂, β̂), the better the approximation. The results further showed that, among the total 85 models examined, 68 models were identified as valid approximate model applications, which all had a near perfect match to the corresponding exact beta-Poisson model dose-response curve. © 2016 Society for Risk Analysis.

Vortex-induced vibration of two parallel risers: Experimental test and numerical simulation

NASA Astrophysics Data System (ADS)

Huang, Weiping; Zhou, Yang; Chen, Haiming

2016-04-01

The vortex-induced vibration of two identical rigidly mounted risers in a parallel arrangement was studied using Ansys- CFX and model tests. The vortex shedding and force were recorded to determine the effect of spacing on the two-degree-of-freedom oscillation of the risers. CFX was used to study the single riser and two parallel risers in 2-8 D spacing considering the coupling effect. Because of the limited width of water channel, only three different riser spacings, 2 D, 3 D, and 4 D, were tested to validate the characteristics of the two parallel risers by comparing to the numerical simulation. The results indicate that the lift force changes significantly with the increase in spacing, and in the case of 3 D spacing, the lift force of the two parallel risers reaches the maximum. The vortex shedding of the risers in 3 D spacing shows that a variable velocity field with the same frequency as the vortex shedding is generated in the overlapped area, thus equalizing the period of drag force to that of lift force. It can be concluded that the interaction between the two parallel risers is significant when the risers are brought to a small distance between them because the trajectory of riser changes from oval to curve 8 as the spacing is increased. The phase difference of lift force between the two risers is also different as the spacing changes.

Reconstruction for time-domain in vivo EPR 3D multigradient oximetric imaging--a parallel processing perspective.

PubMed

Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C

2009-01-01

Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

Parallel ALLSPD-3D: Speeding Up Combustor Analysis Via Parallel Processing

NASA Technical Reports Server (NTRS)

Fricker, David M.

1997-01-01

The ALLSPD-3D Computational Fluid Dynamics code for reacting flow simulation was run on a set of benchmark test cases to determine its parallel efficiency. These test cases included non-reacting and reacting flow simulations with varying numbers of processors. Also, the tests explored the effects of scaling the simulation with the number of processors in addition to distributing a constant size problem over an increasing number of processors. The test cases were run on a cluster of IBM RS/6000 Model 590 workstations with ethernet and ATM networking plus a shared memory SGI Power Challenge L workstation. The results indicate that the network capabilities significantly influence the parallel efficiency, i.e., a shared memory machine is fastest and ATM networking provides acceptable performance. The limitations of ethernet greatly hamper the rapid calculation of flows using ALLSPD-3D.

An application of queueing theory to the design of channel requirements for special purpose communications satellites. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Hein, G. F.

1974-01-01

Special purpose satellites are very cost sensitive to the number of broadcast channels, usually will have Poisson arrivals, fairly low utilization (less than 35%), and a very high availability requirement. To solve the problem of determining the effects of limiting C the number of channels, the Poisson arrival, infinite server queueing model will be modified to describe the many server case. The model is predicated on the reproductive property of the Poisson distribution.

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.

Parallel fabrication of macroporous scaffolds.

PubMed

Dobos, Andrew; Grandhi, Taraka Sai Pavan; Godeshala, Sudhakar; Meldrum, Deirdre R; Rege, Kaushal

2018-07-01

Scaffolds generated from naturally occurring and synthetic polymers have been investigated in several applications because of their biocompatibility and tunable chemo-mechanical properties. Existing methods for generation of 3D polymeric scaffolds typically cannot be parallelized, suffer from low throughputs, and do not allow for quick and easy removal of the fragile structures that are formed. Current molds used in hydrogel and scaffold fabrication using solvent casting and porogen leaching are often single-use and do not facilitate 3D scaffold formation in parallel. Here, we describe a simple device and related approaches for the parallel fabrication of macroporous scaffolds. This approach was employed for the generation of macroporous and non-macroporous materials in parallel, in higher throughput and allowed for easy retrieval of these 3D scaffolds once formed. In addition, macroporous scaffolds with interconnected as well as non-interconnected pores were generated, and the versatility of this approach was employed for the generation of 3D scaffolds from diverse materials including an aminoglycoside-derived cationic hydrogel ("Amikagel"), poly(lactic-co-glycolic acid) or PLGA, and collagen. Macroporous scaffolds generated using the device were investigated for plasmid DNA binding and cell loading, indicating the use of this approach for developing materials for different applications in biotechnology. Our results demonstrate that the device-based approach is a simple technology for generating scaffolds in parallel, which can enhance the toolbox of current fabrication techniques. © 2018 Wiley Periodicals, Inc.

Gust Acoustics Computation with a Space-Time CE/SE Parallel 3D Solver

NASA Technical Reports Server (NTRS)

Wang, X. Y.; Himansu, A.; Chang, S. C.; Jorgenson, P. C. E.; Reddy, D. R. (Technical Monitor)

2002-01-01

The benchmark Problem 2 in Category 3 of the Third Computational Aero-Acoustics (CAA) Workshop is solved using the space-time conservation element and solution element (CE/SE) method. This problem concerns the unsteady response of an isolated finite-span swept flat-plate airfoil bounded by two parallel walls to an incident gust. The acoustic field generated by the interaction of the gust with the flat-plate airfoil is computed by solving the 3D (three-dimensional) Euler equations in the time domain using a parallel version of a 3D CE/SE solver. The effect of the gust orientation on the far-field directivity is studied. Numerical solutions are presented and compared with analytical solutions, showing a reasonable agreement.

Wakefield Computations for the CLIC PETS using the Parallel Finite Element Time-Domain Code T3P

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

Candel, A; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the high-performance parallel 3D electromagnetic time-domain code, T3P, for simulations of wakefields and transients in complex accelerator structures. T3P is based on advanced higher-order Finite Element methods on unstructured grids with quadratic surface approximation. Optimized for large-scale parallel processing on leadership supercomputing facilities, T3P allows simulations of realistic 3D structures with unprecedented accuracy, aiding the design of the next generation of accelerator facilities. Applications to the Compact Linear Collider (CLIC) Power Extraction and Transfer Structure (PETS) are presented.

Performance of fully-coupled algebraic multigrid preconditioners for large-scale VMS resistive MHD

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

Lin, P. T.; Shadid, J. N.; Hu, J. J.

Here, we explore the current performance and scaling of a fully-implicit stabilized unstructured finite element (FE) variational multiscale (VMS) capability for large-scale simulations of 3D incompressible resistive magnetohydrodynamics (MHD). The large-scale linear systems that are generated by a Newton nonlinear solver approach are iteratively solved by preconditioned Krylov subspace methods. The efficiency of this approach is critically dependent on the scalability and performance of the algebraic multigrid preconditioner. Our study considers the performance of the numerical methods as recently implemented in the second-generation Trilinos implementation that is 64-bit compliant and is not limited by the 32-bit global identifiers of themore » original Epetra-based Trilinos. The study presents representative results for a Poisson problem on 1.6 million cores of an IBM Blue Gene/Q platform to demonstrate very large-scale parallel execution. Additionally, results for a more challenging steady-state MHD generator and a transient solution of a benchmark MHD turbulence calculation for the full resistive MHD system are also presented. These results are obtained on up to 131,000 cores of a Cray XC40 and one million cores of a BG/Q system.« less

Performance of fully-coupled algebraic multigrid preconditioners for large-scale VMS resistive MHD

DOE PAGES

Lin, P. T.; Shadid, J. N.; Hu, J. J.; ...

2017-11-06

Here, we explore the current performance and scaling of a fully-implicit stabilized unstructured finite element (FE) variational multiscale (VMS) capability for large-scale simulations of 3D incompressible resistive magnetohydrodynamics (MHD). The large-scale linear systems that are generated by a Newton nonlinear solver approach are iteratively solved by preconditioned Krylov subspace methods. The efficiency of this approach is critically dependent on the scalability and performance of the algebraic multigrid preconditioner. Our study considers the performance of the numerical methods as recently implemented in the second-generation Trilinos implementation that is 64-bit compliant and is not limited by the 32-bit global identifiers of themore » original Epetra-based Trilinos. The study presents representative results for a Poisson problem on 1.6 million cores of an IBM Blue Gene/Q platform to demonstrate very large-scale parallel execution. Additionally, results for a more challenging steady-state MHD generator and a transient solution of a benchmark MHD turbulence calculation for the full resistive MHD system are also presented. These results are obtained on up to 131,000 cores of a Cray XC40 and one million cores of a BG/Q system.« less

Anisotropic upper critical magnetic fields in Rb 2 Cr 3 As 3 superconductor

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

Tang, Zhang-Tu; Liu, Yi; Bao, Jin-Ke

Rb2Cr3As3 is a structurally one-dimensional superconductor containing Cr3As3 chains with a superconducting transition temperature of T-c = 4.8 K. Here we report the electrical resistance measurements for Rb2Cr3As3 single crystals, under magnetic fields up to 29.5 T and at temperatures down to 0.36 K, from which the upper critical fields, H-c2(T), can be obtained in a broad temperature range. For field parallel to the Cr3As3 chains, H-c2(parallel to)(T) is paramagnetically limited with an initial slope of mu(0)dH(c2)(parallel to)/dT|T-c = - 16 T K-1 and a zero-temperature upper critical field of mu H-0(c2)parallel to(0) = 17.5 T. For field perpendicular tomore » the Cr3As3 chains, however, H-c2(perpendicular to)(T) is only limited by orbital pair-breaking effect with mu(0)dH(c2)(perpendicular to)/dT|(Tc) = - 3 T K-1. As a consequence, the anisotropy gamma H = H-c2(parallel to)/H-c2(perpendicular to) decreases sharply near T-c and reverses below 2 K. Remarkably, the low- temperature H-c2(perpendicular to)(T) down to 0.075 T-c remains to increase linearly up to over three times the Pauli paramagnetic limit, which strongly suggests dominant spin-triplet superconductivity in Rb2Cr3As3.« less

Transport of Multivalent Electrolyte Mixtures in Micro- and Nanochannels

DTIC Science & Technology

2013-11-08

equations for this process are the unsteady Navier-Stokes equations along with continuity and the Poisson- Nernst -Planck system for the electro- static part...about five times the Debye screening length D (the 1/e lengthscale for the potential from the solution of the linearized Poisson- Boltzmann equation

Simulation of neoclassical transport with the continuum gyrokinetic code COGENT

DOE PAGES

Dorf, M. A.; Cohen, R. H.; Dorr, M.; ...

2013-01-25

The development of the continuum gyrokinetic code COGENT for edge plasma simulations is reported. The present version of the code models a nonlinear axisymmetric 4D (R, v∥, μ) gyrokinetic equation coupled to the long-wavelength limit of the gyro-Poisson equation. Here, R is the particle gyrocenter coordinate in the poloidal plane, and v∥ and μ are the guiding center velocity parallel to the magnetic field and the magnetic moment, respectively. The COGENT code utilizes a fourth-order finite-volume (conservative) discretization combined with arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy.more » Furthermore, topics presented are the implementation of increasingly detailed model collision operators, and the results of neoclassical transport simulations including the effects of a strong radial electric field characteristic of a tokamak pedestal under H-mode conditions.« less

Numerical simulation of two-phase filtration in the near well bore zone

NASA Astrophysics Data System (ADS)

Maksat, Kalimoldayev; Kalipa, Kuspanova; Kulyash, Baisalbayeva; Orken, Mamyrbayev; Assel, Abdildayeva

2018-04-01

On the basis of the fundamental laws of energy conservation, nonstationary processes of filtration of two-phase liquids in multilayered reservoirs in the near well bore zone are considered. Number of reservoirs, fluid pressure in the given reservoirs, reservoir permeability, oil viscosity, etc. are taken into account upon that. Plane-parallel flow and axisymmetric cases have been studied. In the numerical solution, non-structured meshes are used. Closer to the well, the meshes thicken. The integration step over time is defined by the generalized Courant inequality. As a result, there are no large oscillations in the numerical solutions obtained. Oil production rates, Poisson's ratios, D-diameters of the well, filter height, filter permeability, and cumulative thickness of the filter cake and the area have been taken as the main inputs in numerical simulation of non-stationary processes of two-phase filtration.

Development of the PARVMEC Code for Rapid Analysis of 3D MHD Equilibrium

NASA Astrophysics Data System (ADS)

Seal, Sudip; Hirshman, Steven; Cianciosa, Mark; Wingen, Andreas; Unterberg, Ezekiel; Wilcox, Robert; ORNL Collaboration

2015-11-01

The VMEC three-dimensional (3D) MHD equilibrium has been used extensively for designing stellarator experiments and analyzing experimental data in such strongly 3D systems. Recent applications of VMEC include 2D systems such as tokamaks (in particular, the D3D experiment), where application of very small (delB/B ~ 10-3) 3D resonant magnetic field perturbations render the underlying assumption of axisymmetry invalid. In order to facilitate the rapid analysis of such equilibria (for example, for reconstruction purposes), we have undertaken the task of parallelizing the VMEC code (PARVMEC) to produce a scalable and temporally rapidly convergent equilibrium code for use on parallel distributed memory platforms. The parallelization task naturally splits into three distinct parts 1) radial surfaces in the fixed-boundary part of the calculation; 2) two 2D angular meshes needed to compute the Green's function integrals over the plasma boundary for the free-boundary part of the code; and 3) block tridiagonal matrix needed to compute the full (3D) pre-conditioner near the final equilibrium state. Preliminary results show that scalability is achieved for tasks 1 and 3, with task 2 still nearing completion. The impact of this work on the rapid reconstruction of D3D plasmas using PARVMEC in the V3FIT code will be discussed. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

Scalable Computing of the Mesh Size Effect on Modeling Damage Mechanics in Woven Armor Composites

DTIC Science & Technology

2008-12-01

manner of a user defined material subroutine to provide overall stress increments to, the parallel LS-DYNA3D a Lagrangian explicit code used in...finite element code, as a user defined material subroutine . The ability of this subroutine to model the effect of the progressions of a select number...is added as a user defined material subroutine to parallel LS-DYNA3D. The computations of the global mesh are handled by LS-DYNA3D and are spread

Sparse Poisson noisy image deblurring.

PubMed

Carlavan, Mikael; Blanc-Féraud, Laure

2012-04-01

Deblurring noisy Poisson images has recently been a subject of an increasing amount of works in many areas such as astronomy and biological imaging. In this paper, we focus on confocal microscopy, which is a very popular technique for 3-D imaging of biological living specimens that gives images with a very good resolution (several hundreds of nanometers), although degraded by both blur and Poisson noise. Deconvolution methods have been proposed to reduce these degradations, and in this paper, we focus on techniques that promote the introduction of an explicit prior on the solution. One difficulty of these techniques is to set the value of the parameter, which weights the tradeoff between the data term and the regularizing term. Only few works have been devoted to the research of an automatic selection of this regularizing parameter when considering Poisson noise; therefore, it is often set manually such that it gives the best visual results. We present here two recent methods to estimate this regularizing parameter, and we first propose an improvement of these estimators, which takes advantage of confocal images. Following these estimators, we secondly propose to express the problem of the deconvolution of Poisson noisy images as the minimization of a new constrained problem. The proposed constrained formulation is well suited to this application domain since it is directly expressed using the antilog likelihood of the Poisson distribution and therefore does not require any approximation. We show how to solve the unconstrained and constrained problems using the recent alternating-direction technique, and we present results on synthetic and real data using well-known priors, such as total variation and wavelet transforms. Among these wavelet transforms, we specially focus on the dual-tree complex wavelet transform and on the dictionary composed of curvelets and an undecimated wavelet transform.

Parallel Anisotropic Tetrahedral Adaptation

NASA Technical Reports Server (NTRS)

Park, Michael A.; Darmofal, David L.

2008-01-01

An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

NRL Plasma Formulary. Revision

DTIC Science & Technology

1990-01-01

Description SI Gaussian 9B 1l0B Faraday’s law V x E -- V x E =-- at c Ot c9D 10D 4wr Ampere’s law V x H + J V x H =- + -J at c Ot c Poisson equation V - D = p...Froude Fr V/(g L) 1/ 2 t(Inertial force/gravitational or V/NL buoyancy force) 1 /2 Gay- Lussac Ga 1/fOAT Inverse of relative change in volume during... law heat coefficient, k = crAT0ax Volumetric expansion coefficient, dV/V = )3dT Bulk modulus (units kg m 1 s - 2) 6R, AV, Ap, AT Imposed difference in

Structure, stability, and thermodynamics of lamellar DNA-lipid complexes.

PubMed Central

Harries, D; May, S; Gelbart, W M; Ben-Shaul, A

1998-01-01

We develop a statistical thermodynamic model for the phase evolution of DNA-cationic lipid complexes in aqueous solution, as a function of the ratios of charged to neutral lipid and charged lipid to DNA. The complexes consist of parallel strands of DNA intercalated in the water layers of lamellar stacks of mixed lipid bilayers, as determined by recent synchrotron x-ray measurements. Elastic deformations of the DNA and the lipid bilayers are neglected, but DNA-induced spatial inhomogeneities in the bilayer charge densities are included. The relevant nonlinear Poisson-Boltzmann equation is solved numerically, including self-consistent treatment of the boundary conditions at the polarized membrane surfaces. For a wide range of lipid compositions, the phase evolution is characterized by three regions of lipid to DNA charge ratio, rho: 1) for low rho, the complexes coexist with excess DNA, and the DNA-DNA spacing in the complex, d, is constant; 2) for intermediate rho, including the isoelectric point rho = 1, all of the lipid and DNA in solution is incorporated into the complex, whose inter-DNA distance d increases linearly with rho; and 3) for high rho, the complexes coexist with excess liposomes (whose lipid composition is different from that in the complex), and their spacing d is nearly, but not completely, independent of rho. These results can be understood in terms of a simple charging model that reflects the competition between counterion entropy and inter-DNA (rho < 1) and interbilayer (rho > 1) repulsions. Finally, our approach and conclusions are compared with theoretical work by others, and with relevant experiments. PMID:9649376

2-D Modeling of Nanoscale MOSFETs: Non-Equilibrium Green's Function Approach

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

2001-01-01

We have developed physical approximations and computer code capable of realistically simulating 2-D nanoscale transistors, using the non-equilibrium Green's function (NEGF) method. This is the most accurate full quantum model yet applied to 2-D device simulation. Open boundary conditions and oxide tunneling are treated on an equal footing. Electrons in the ellipsoids of the conduction band are treated within the anisotropic effective mass approximation. Electron-electron interaction is treated within Hartree approximation by solving NEGF and Poisson equations self-consistently. For the calculations presented here, parallelization is performed by distributing the solution of NEGF equations to various processors, energy wise. We present simulation of the "benchmark" MIT 25nm and 90nm MOSFETs and compare our results to those from the drift-diffusion simulator and the quantum-corrected results available. In the 25nm MOSFET, the channel length is less than ten times the electron wavelength, and the electron scattering time is comparable to its transit time. Our main results are: (1) Simulated drain subthreshold current characteristics are shown, where the potential profiles are calculated self-consistently by the corresponding simulation methods. The current predicted by our quantum simulation has smaller subthreshold slope of the Vg dependence which results in higher threshold voltage. (2) When gate oxide thickness is less than 2 nm, gate oxide leakage is a primary factor which determines off-current of a MOSFET (3) Using our 2-D NEGF simulator, we found several ways to drastically decrease oxide leakage current without compromising drive current. (4) Quantum mechanically calculated electron density is much smaller than the background doping density in the poly silicon gate region near oxide interface. This creates an additional effective gate voltage. Different ways to. include this effect approximately will be discussed.

Poisson's spot and Gouy phase

NASA Astrophysics Data System (ADS)

da Paz, I. G.; Soldati, Rodolfo; Cabral, L. A.; de Oliveira, J. G. G.; Sampaio, Marcos

2016-12-01

Recently there have been experimental results on Poisson spot matter-wave interferometry followed by theoretical models describing the relative importance of the wave and particle behaviors for the phenomenon. We propose an analytical theoretical model for Poisson's spot with matter waves based on the Babinet principle, in which we use the results for free propagation and single-slit diffraction. We take into account effects of loss of coherence and finite detection area using the propagator for a quantum particle interacting with an environment. We observe that the matter-wave Gouy phase plays a role in the existence of the central peak and thus corroborates the predominantly wavelike character of the Poisson's spot. Our model shows remarkable agreement with the experimental data for deuterium (D2) molecules.

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

Development of a Stereo Vision Measurement System for a 3D Three-Axial Pneumatic Parallel Mechanism Robot Arm

PubMed Central

Chiang, Mao-Hsiung; Lin, Hao-Ting; Hou, Chien-Lun

2011-01-01

In this paper, a stereo vision 3D position measurement system for a three-axial pneumatic parallel mechanism robot arm is presented. The stereo vision 3D position measurement system aims to measure the 3D trajectories of the end-effector of the robot arm. To track the end-effector of the robot arm, the circle detection algorithm is used to detect the desired target and the SAD algorithm is used to track the moving target and to search the corresponding target location along the conjugate epipolar line in the stereo pair. After camera calibration, both intrinsic and extrinsic parameters of the stereo rig can be obtained, so images can be rectified according to the camera parameters. Thus, through the epipolar rectification, the stereo matching process is reduced to a horizontal search along the conjugate epipolar line. Finally, 3D trajectories of the end-effector are computed by stereo triangulation. The experimental results show that the stereo vision 3D position measurement system proposed in this paper can successfully track and measure the fifth-order polynomial trajectory and sinusoidal trajectory of the end-effector of the three- axial pneumatic parallel mechanism robot arm. PMID:22319408

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.

An Elliptic PDE Approach for Shape Characterization

PubMed Central

Haidar, Haissam; Bouix, Sylvain; Levitt, James; McCarley, Robert W.; Shenton, Martha E.; Soul, Janet S.

2009-01-01

This paper presents a novel approach to analyze the shape of anatomical structures. Our methodology is rooted in classical physics and in particular Poisson's equation, a fundamental partial differential equation [1]. The solution to this equation and more specifically its equipotential surfaces display properties that are useful for shape analysis. We present a numerical algorithm to calculate the length of streamlines formed by the gradient field of the solution to this equation for 2D and 3D objects. The length of the streamlines along the equipotential surfaces was used to build a new function which can characterize the shape of objects. We illustrate our method on 2D synthetic and natural shapes as well as 3D medical data. PMID:17271986

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.

3D motion picture of transparent gas flow by parallel phase-shifting digital holography

NASA Astrophysics Data System (ADS)

Awatsuji, Yasuhiro; Fukuda, Takahito; Wang, Yexin; Xia, Peng; Kakue, Takashi; Nishio, Kenzo; Matoba, Osamu

2018-03-01

Parallel phase-shifting digital holography is a technique capable of recording three-dimensional (3D) motion picture of dynamic object, quantitatively. This technique can record single hologram of an object with an image sensor having a phase-shift array device and reconstructs the instantaneous 3D image of the object with a computer. In this technique, a single hologram in which the multiple holograms required for phase-shifting digital holography are multiplexed by using space-division multiplexing technique pixel by pixel. We demonstrate 3D motion picture of dynamic and transparent gas flow recorded and reconstructed by the technique. A compressed air duster was used to generate the gas flow. A motion picture of the hologram of the gas flow was recorded at 180,000 frames/s by parallel phase-shifting digital holography. The phase motion picture of the gas flow was reconstructed from the motion picture of the hologram. The Abel inversion was applied to the phase motion picture and then the 3D motion picture of the gas flow was obtained.

Bistatic scattering from a three-dimensional object above a two-dimensional randomly rough surface modeled with the parallel FDTD approach.

PubMed

Guo, L-X; Li, J; Zeng, H

2009-11-01

We present an investigation of the electromagnetic scattering from a three-dimensional (3-D) object above a two-dimensional (2-D) randomly rough surface. A Message Passing Interface-based parallel finite-difference time-domain (FDTD) approach is used, and the uniaxial perfectly matched layer (UPML) medium is adopted for truncation of the FDTD lattices, in which the finite-difference equations can be used for the total computation domain by properly choosing the uniaxial parameters. This makes the parallel FDTD algorithm easier to implement. The parallel performance with different number of processors is illustrated for one rough surface realization and shows that the computation time of our parallel FDTD algorithm is dramatically reduced relative to a single-processor implementation. Finally, the composite scattering coefficients versus scattered and azimuthal angle are presented and analyzed for different conditions, including the surface roughness, the dielectric constants, the polarization, and the size of the 3-D object.

OSIRIS - an object-oriented parallel 3D PIC code for modeling laser and particle beam-plasma interaction

NASA Astrophysics Data System (ADS)

Hemker, Roy

1999-11-01

The advances in computational speed make it now possible to do full 3D PIC simulations of laser plasma and beam plasma interactions, but at the same time the increased complexity of these problems makes it necessary to apply modern approaches like object oriented programming to the development of simulation codes. We report here on our progress in developing an object oriented parallel 3D PIC code using Fortran 90. In its current state the code contains algorithms for 1D, 2D, and 3D simulations in cartesian coordinates and for 2D cylindrically-symmetric geometry. For all of these algorithms the code allows for a moving simulation window and arbitrary domain decomposition for any number of dimensions. Recent 3D simulation results on the propagation of intense laser and electron beams through plasmas will be presented.

Statistical analysis of electroconvection near an ion-selective membrane in the highly chaotic regime

NASA Astrophysics Data System (ADS)

Druzgalski, Clara; Mani, Ali

2016-11-01

We investigate electroconvection and its impact on ion transport in a model system comprised of an ion-selective membrane, an aqueous electrolyte, and an external electric field applied normal to the membrane. We develop a direct numerical simulation code to solve the governing Poisson-Nernst-Planck and Navier-Stokes equations in three dimensions using a specialized parallel numerical algorithm and sufficient resolution to capture the high frequency and high wavenumber physics. We show a comprehensive statistical analysis of the transport phenomena in the highly chaotic regime. Qualitative and quantitative comparisons of two-dimensional (2D) and 3D simulations include prediction of the mean concentration fields as well as the spectra of concentration, charge density, and velocity signals. Our analyses reveal a significant quantitative difference between 2D and 3D electroconvection. Furthermore, we show that high-intensity yet short-lived current density hot spots appear randomly on the membrane surface, contributing significantly to the mean current density. By examining cross correlations between current density on the membrane and other field quantities we explore the physical mechanisms leading to current hot spots. We also present analysis of transport fluxes in the context of ensemble-averaged equations. Our analysis reveals that in the highly chaotic regime the mixing layer (ML), which spans the majority of the domain extent, is governed by advective fluctuations. Furthermore, we show that in the ML the mean electromigration fluxes cancel out for positive and negative ions, indicating that the mean transport of total salt content within the ML can be represented via the electroneutral approximation. Finally, we present an assessment of the importance of different length scales in enhancing transport by computing the cross covariance of concentration and velocity fluctuations in the wavenumber space. Our analysis indicates that in the majority of the domain the large scales contribute most significantly to transport, while the effects of small scales become more appreciable in regions very near the membrane.

Rinne test: does the tuning fork position affect the sound amplitude at the ear?

PubMed

Butskiy, Oleksandr; Ng, Denny; Hodgson, Murray; Nunez, Desmond A

2016-03-24

Guidelines and text-book descriptions of the Rinne test advise orienting the tuning fork tines in parallel with the longitudinal axis of the external auditory canal (EAC), presumably to maximise the amplitude of the air conducted sound signal at the ear. Whether the orientation of the tuning fork tines affects the amplitude of the sound signal at the ear in clinical practice has not been previously reported. The present study had two goals: determine if (1) there is clinician variability in tuning fork placement when presenting the air-conduction stimulus during the Rinne test; (2) the orientation of the tuning fork tines, parallel versus perpendicular to the EAC, affects the sound amplitude at the ear. To assess the variability in performing the Rinne test, the Canadian Society of Otolaryngology - Head and Neck Surgery members were surveyed. The amplitudes of the sound delivered to the tympanic membrane with the activated tuning fork tines held in parallel, and perpendicular to, the longitudinal axis of the EAC were measured using a Knowles Electronics Mannequin for Acoustic Research (KEMAR) with the microphone of a sound level meter inserted in the pinna insert. 47.4 and 44.8% of 116 survey responders reported placing the fork parallel and perpendicular to the EAC respectively. The sound intensity (sound-pressure level) recorded at the tympanic membrane with the 512 Hz tuning fork tines in parallel with as opposed to perpendicular to the EAC was louder by 2.5 dB (95% CI: 1.35, 3.65 dB; p < 0.0001) for the fundamental frequency (512 Hz), and by 4.94 dB (95% CI: 3.10, 6.78 dB; p < 0.0001) and 3.70 dB (95% CI: 1.62, 5.78 dB; p = .001) for the two harmonic (non-fundamental) frequencies (1 and 3.15 kHz), respectively. The 256 Hz tuning fork in parallel with the EAC as opposed to perpendicular to was louder by 0.83 dB (95% CI: -0.26, 1.93 dB; p = 0.14) for the fundamental frequency (256 Hz), and by 4.28 dB (95% CI: 2.65, 5.90 dB; p < 0.001) and 1.93 dB (95% CI: 0.26, 3.61 dB; p = .02) for the two harmonic frequencies (500 and 4 kHz) respectively. Clinicians vary in their orientation of the tuning fork tines in relation to the EAC when performing the Rinne test. Placement of the tuning fork tines in parallel as opposed to perpendicular to the EAC results in a higher sound amplitude at the level of the tympanic membrane.

3D hyperpolarized C-13 EPI with calibrationless parallel imaging

NASA Astrophysics Data System (ADS)

Gordon, Jeremy W.; Hansen, Rie B.; Shin, Peter J.; Feng, Yesu; Vigneron, Daniel B.; Larson, Peder E. Z.

2018-04-01

With the translation of metabolic MRI with hyperpolarized 13C agents into the clinic, imaging approaches will require large volumetric FOVs to support clinical applications. Parallel imaging techniques will be crucial to increasing volumetric scan coverage while minimizing RF requirements and temporal resolution. Calibrationless parallel imaging approaches are well-suited for this application because they eliminate the need to acquire coil profile maps or auto-calibration data. In this work, we explored the utility of a calibrationless parallel imaging method (SAKE) and corresponding sampling strategies to accelerate and undersample hyperpolarized 13C data using 3D blipped EPI acquisitions and multichannel receive coils, and demonstrated its application in a human study of [1-13C]pyruvate metabolism.

Parallel microfluidic synthesis of size-tunable polymeric nanoparticles using 3D flow focusing towards in vivo study

PubMed Central

Lim, Jong-Min; Bertrand, Nicolas; Valencia, Pedro M.; Rhee, Minsoung; Langer, Robert; Jon, Sangyong; Farokhzad, Omid C.; Karnik, Rohit

2014-01-01

Microfluidic synthesis of nanoparticles (NPs) can enhance the controllability and reproducibility in physicochemical properties of NPs compared to bulk synthesis methods. However, applications of microfluidic synthesis are typically limited to in vitro studies due to low production rates. Herein, we report the parallelization of NP synthesis by 3D hydrodynamic flow focusing (HFF) using a multilayer microfluidic system to enhance the production rate without losing the advantages of reproducibility, controllability, and robustness. Using parallel 3D HFF, polymeric poly(lactide-co-glycolide)-b-polyethyleneglycol (PLGA-PEG) NPs with sizes tunable in the range of 13–150 nm could be synthesized reproducibly with high production rate. As a proof of concept, we used this system to perform in vivo pharmacokinetic and biodistribution study of small (20 nm diameter) PLGA-PEG NPs that are otherwise difficult to synthesize. Microfluidic parallelization thus enables synthesis of NPs with tunable properties with production rates suitable for both in vitro and in vivo studies. PMID:23969105

Parallel Rendering of Large Time-Varying Volume Data

NASA Technical Reports Server (NTRS)

Garbutt, Alexander E.

2005-01-01

Interactive visualization of large time-varying 3D volume datasets has been and still is a great challenge to the modem computational world. It stretches the limits of the memory capacity, the disk space, the network bandwidth and the CPU speed of a conventional computer. In this SURF project, we propose to develop a parallel volume rendering program on SGI's Prism, a cluster computer equipped with state-of-the-art graphic hardware. The proposed program combines both parallel computing and hardware rendering in order to achieve an interactive rendering rate. We use 3D texture mapping and a hardware shader to implement 3D volume rendering on each workstation. We use SGI's VisServer to enable remote rendering using Prism's graphic hardware. And last, we will integrate this new program with ParVox, a parallel distributed visualization system developed at JPL. At the end of the project, we Will demonstrate remote interactive visualization using this new hardware volume renderer on JPL's Prism System using a time-varying dataset from selected JPL applications.

The Effect of Fluid and Solid Properties on the Auxetic Behavior of Porous Materials Having Rock-like Microstructures

NASA Astrophysics Data System (ADS)

Wollner, U.; Vanorio, T.; Kiss, A. M.

2017-12-01

Materials with a negative Poisson's Ratio (PR), known as auxetics, exhibit the counterintuitive behavior of becoming wider when uniaxially stretched and thinner when compressed. Though negative PR is characteristic of polymer foams or cellular solids, tight as well as highly porous rocks have also been reported to exhibit a negative Poisson's ratio, both from dynamic (PRd) and static measurements. We propose a novel auxetic structure based on pore-space configuration observed in rocks. First, we performed 2D and 3D imaging of a pumice and tight basalt to analyze their rock microstructure as well as similarities to natural structures of auxetic materials - e.g., cork. Based on these analyses, we developed a theoretical auxetic 3D model consisting of rotating rigid bodies having pore configurations similar to those observed in rocks. To alleviate the mechanical assumption of rotating bodies, the theoretical model was modified to include crack-like features being represented by intersecting, elliptic cylinders. We then used a 3D printer to create a physical version of the modified model, whose PRd was tested. We also numerically explored how the compressibility of fluids located in the pore-space of the modified model as well as how the elastic properties of the material from which the model is made of affect its auxetic behavior. We conclude that for a porous medium composed of a single material saturated with a single fluid (a) the more compliant the fluid is and (b) the lower the PR of the solid material, the lower the PR value of the composite material.

A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

PubMed

Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

2007-01-01

The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

Simulation of bipolar charge transport in nanocomposite polymer films

NASA Astrophysics Data System (ADS)

Lean, Meng H.; Chu, Wei-Ping L.

2015-03-01

This paper describes 3D particle-in-cell simulation of bipolar charge injection and transport through nanocomposite film comprised of ferroelectric ceramic nanofillers in an amorphous polymer matrix. The classical electrical double layer (EDL) model for a monopolar core is extended (eEDL) to represent the nanofiller by replacing it with a dipolar core. Charge injection at the electrodes assumes metal-polymer Schottky emission at low to moderate fields and Fowler-Nordheim tunneling at high fields. Injected particles migrate via field-dependent Poole-Frenkel mobility and recombine with Monte Carlo selection. The simulation algorithm uses a boundary integral equation method for solution of the Poisson equation coupled with a second-order predictor-corrector scheme for robust time integration of the equations of motion. The stability criterion of the explicit algorithm conforms to the Courant-Friedrichs-Levy limit assuring robust and rapid convergence. The model is capable of simulating a wide dynamic range spanning leakage current to pre-breakdown. Simulation results for BaTiO3 nanofiller in amorphous polymer matrix indicate that charge transport behavior depend on nanoparticle polarization with anti-parallel orientation showing the highest leakage conduction and therefore lowest level of charge trapping in the interaction zone. Charge recombination is also highest, at the cost of reduced leakage conduction charge. The eEDL model predicts the meandering pathways of charge particle trajectories.

Research on ponderomotive driven Vlasov–Poisson system in electron acoustic wave parametric region

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

Xiao, C. Z.; Huang, T. W.; Liu, Z. J.

2014-03-15

Theoretical analysis and corresponding 1D Particle-in-Cell (PIC) simulations of ponderomotive driven Vlasov–Poisson system in electron acoustic wave (EAW) parametric region are demonstrated. Theoretical analysis identifies that under the resonant condition, a monochromatic EAW can be excited when the wave number of the drive ponderomotive force satisfies 0.26≲k{sub d}λ{sub D}≲0.53. If k{sub d}λ{sub D}≲0.26, nonlinear superposition of harmonic waves can be resonantly excited, called kinetic electrostatic electron nonlinear waves. Numerical simulations have demonstrated these wave excitation and evolution dynamics, in consistence with the theoretical predictions. The physical nature of these two waves is supposed to be interaction of harmonic waves, andmore » their similar phase space properties are also discussed.« less

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.

Parallel phase-sensitive three-dimensional imaging camera

DOEpatents

Smithpeter, Colin L.; Hoover, Eddie R.; Pain, Bedabrata; Hancock, Bruce R.; Nellums, Robert O.

2007-09-25

An apparatus is disclosed for generating a three-dimensional (3-D) image of a scene illuminated by a pulsed light source (e.g. a laser or light-emitting diode). The apparatus, referred to as a phase-sensitive 3-D imaging camera utilizes a two-dimensional (2-D) array of photodetectors to receive light that is reflected or scattered from the scene and processes an electrical output signal from each photodetector in the 2-D array in parallel using multiple modulators, each having inputs of the photodetector output signal and a reference signal, with the reference signal provided to each modulator having a different phase delay. The output from each modulator is provided to a computational unit which can be used to generate intensity and range information for use in generating a 3-D image of the scene. The 3-D camera is capable of generating a 3-D image using a single pulse of light, or alternately can be used to generate subsequent 3-D images with each additional pulse of light.

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.

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.

Amplification of perpendicular and parallel magnetic fields by cosmic ray currents

NASA Astrophysics Data System (ADS)

Matthews, J. H.; Bell, A. R.; Blundell, K. M.; Araudo, A. T.

2017-08-01

Cosmic ray (CR) currents through magnetized plasma drive strong instabilities producing amplification of the magnetic field. This amplification helps explain the CR energy spectrum as well as observations of supernova remnants and radio galaxy hotspots. Using magnetohydrodynamic simulations, we study the behaviour of the non-resonant hybrid (NRH) instability (also known as the Bell instability) in the case of CR currents perpendicular and parallel to the initial magnetic field. We demonstrate that extending simulations of the perpendicular case to 3D reveals a different character to the turbulence from that observed in 2D. Despite these differences, in 3D the perpendicular NRH instability still grows exponentially far into the non-linear regime with a similar growth rate to both the 2D perpendicular and 3D parallel situations. We introduce some simple analytical models to elucidate the physical behaviour, using them to demonstrate that the transition to the non-linear regime is governed by the growth of thermal pressure inside dense filaments at the edges of the expanding loops. We discuss our results in the context of supernova remnants and jets in radio galaxies. Our work shows that the NRH instability can amplify magnetic fields to many times their initial value in parallel and perpendicular shocks.

Effect of solid distribution on elastic properties of open-cell cellular solids using numerical and experimental methods.

PubMed

Zargarian, A; Esfahanian, M; Kadkhodapour, J; Ziaei-Rad, S

2014-09-01

Effect of solid distribution between edges and vertices of three-dimensional cellular solid with an open-cell structure was investigated both numerically and experimentally. Finite element analysis (FEA) with continuum elements and appropriate periodic boundary condition was employed to calculate the elastic properties of cellular solids using tetrakaidecahedral (Kelvin) unit cell. Relative densities between 0.01 and 0.1 and various values of solid fractions were considered. In order to validate the numerical model, three scaffolds with the relative density of 0.08, but different amounts of solid in vertices, were fabricated via 3-D printing technique. Good agreement was observed between numerical simulation and experimental results. Results of numerical simulation showed that, at low relative densities (<0.03), Young׳s modulus increased by shifting materials away from edges to vertices at first and then decreased after reaching a critical point. However, for the high values of relative density, Young׳s modulus increased monotonically. Mechanisms of such a behavior were discussed in detail. Results also indicated that Poisson׳s ratio decreased by increasing relative density and solid fraction in vertices. By fitting a curve to the data obtained from the numerical simulation and considering the relative density and solid fraction in vertices, empirical relations were derived for Young׳s modulus and Poisson׳s ratio. Copyright © 2014 Elsevier Ltd. All rights reserved.

Three-dimensional FEM model of FBGs in PANDA fibers with experimentally determined model parameters

NASA Astrophysics Data System (ADS)

Lindner, Markus; Hopf, Barbara; Koch, Alexander W.; Roths, Johannes

2017-04-01

A 3D-FEM model has been developed to improve the understanding of multi-parameter sensing with Bragg gratings in attached or embedded polarization maintaining fibers. The material properties of the fiber, especially Young's modulus and Poisson's ratio of the fiber's stress applying parts, are crucial for accurate simulations, but are usually not provided by the manufacturers. A methodology is presented to determine the unknown parameters by using experimental characterizations of the fiber and iterative FEM simulations. The resulting 3D-Model is capable of describing the change in birefringence of the free fiber when exposed to longitudinal strain. In future studies the 3D-FEM model will be employed to study the interaction of PANDA fibers with the surrounding materials in which they are embedded.

Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU

PubMed Central

Xia, Yong; Zhang, Henggui

2015-01-01

Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations. PMID:26581957

Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU.

PubMed

Xia, Yong; Wang, Kuanquan; Zhang, Henggui

2015-01-01

Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.

Reduced-thickness backlighter for autostereoscopic display and display using the backlighter

NASA Technical Reports Server (NTRS)

Eichenlaub, Jesse B (Inventor); Gruhlke, Russell W (Inventor)

1999-01-01

A reduced-thickness backlighter for an autostereoscopic display is disclosed having a lightguide and at least one light source parallel to an edge of the lightguide so as to be substantially coplanar with the lightguide. The lightguide is provided with a first surface which has a plurality of reflective linear regions, such as elongated grooves or glossy lines, parallel to the illuminated edge of the lightguide. Preferably the lightguide further has a second surface which has a plurality of lenticular lenses for reimaging the reflected light from the linear regions into a series of thin vertical lines outside the guide. Because of the reduced thickness of the backlighter system, autostereoscopic viewing is enabled in applications requiring thin backlighter systems. In addition to taking up less space, the reduced-thickness backlighter uses less lamps and less power. For accommodating 2-D applications, a 2-D diffuser plate or a 2-D lightguide parallel to the 3-D backlighter is disclosed for switching back and forth between 3-D viewing and 2-D viewing.

3D Printed, Microgroove Pattern-Driven Generation of Oriented Ligamentous Architectures.

PubMed

Park, Chan Ho; Kim, Kyoung-Hwa; Lee, Yong-Moo; Giannobile, William V; Seol, Yang-Jo

2017-09-08

Specific orientations of regenerated ligaments are crucially required for mechanoresponsive properties and various biomechanical adaptations, which are the key interplay to support mineralized tissues. Although various 2D platforms or 3D printing systems can guide cellular activities or aligned organizations, it remains a challenge to develop ligament-guided, 3D architectures with the angular controllability for parallel, oblique or perpendicular orientations of cells required for biomechanical support of organs. Here, we show the use of scaffold design by additive manufacturing for specific topographies or angulated microgroove patterns to control cell orientations such as parallel (0°), oblique (45°) and perpendicular (90°) angulations. These results demonstrate that ligament cells displayed highly predictable and controllable orientations along microgroove patterns on 3D biopolymeric scaffolds. Our findings demonstrate that 3D printed topographical approaches can regulate spatiotemporal cell organizations that offer strong potential for adaptation to complex tissue defects to regenerate ligament-bone complexes.

Absolute and relative nonlinear optical coefficients of KDP, KD(asterisk)P, BaB2O4, LiIO3, MgO:LiNbO3, and KTP measured by phase-matched second-harmonic generation

NASA Technical Reports Server (NTRS)

Eckardt, Robert C.; Byer, Robert L.; Masuda, Hisashi; Fan, Yuan Xuan

1990-01-01

Both absolute and relative nonlinear optical coefficients of six nonlinear materials measured by second-harmonic generation are discussed. A single-mode, injection-seeded, Q-switched Nd:YAG laser with spatially filtered output was used to generate the 1.064-micron fundamental radiation. The following results were obtained: d36(KDP) = 0.38 pm/V, d36(KD/asterisk/P) = 0.37 pm/V, (parallel)d22(BaB2O4)(parallel) = 2.2 pm/V, d31(LiIO3) = -4.1 pm/V, d31(5 percentMgO:MgO LiNbO3) = -4.7 pm/V, and d(eff)(KTP) = 3.2 pm/V. The accuracy of these measurements is estimated to be better than 10 percent.

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

Dynamics of kinetic geodesic-acoustic modes and the radial electric field in tokamak neoclassical plasmas

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Belli, E.; Bodi, K.; Candy, J.; Chang, C. S.; Cohen, R. H.; Colella, P.; Dimits, A. M.; Dorr, M. R.; Gao, Z.; Hittinger, J. A.; Ko, S.; Krasheninnikov, S.; McKee, G. R.; Nevins, W. M.; Rognlien, T. D.; Snyder, P. B.; Suh, J.; Umansky, M. V.

2009-06-01

We present edge gyrokinetic simulations of tokamak plasmas using the fully non-linear (full-f) continuum code TEMPEST. A non-linear Boltzmann model is used for the electrons. The electric field is obtained by solving the 2D gyrokinetic Poisson equation. We demonstrate the following. (1) High harmonic resonances (n > 2) significantly enhance geodesic-acoustic mode (GAM) damping at high q (tokamak safety factor), and are necessary to explain the damping observed in our TEMPEST q-scans and consistent with the experimental measurements of the scaling of the GAM amplitude with edge q95 in the absence of obvious evidence that there is a strong q-dependence of the turbulent drive and damping of the GAM. (2) The kinetic GAM exists in the edge for steep density and temperature gradients in the form of outgoing waves, its radial scale is set by the ion temperature profile, and ion temperature inhomogeneity is necessary for GAM radial propagation. (3) The development of the neoclassical electric field evolves through different phases of relaxation, including GAMs, their radial propagation and their long-time collisional decay. (4) Natural consequences of orbits in the pedestal and scrape-off layer region in divertor geometry are substantial non-Maxwellian ion distributions and parallel flow characteristics qualitatively like those observed in experiments.

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.

Investigation of the line arrangement of 2D resistivity surveys for 3D inversion*

NASA Astrophysics Data System (ADS)

Inoue, Keisuke; Nakazato, Hiroomi; Takeuchi, Mutsuo; Sugimoto, Yoshihiro; Kim, Hee Joon; Yoshisako, Hiroshi; Konno, Michiaki; Shoda, Daisuke

2018-03-01

We have conducted numerical and field experiments to investigate the applicability of electrode configurations and line layouts commonly used for two-dimensional (2D) resistivity surveys to 3D inversion. We examined three kinds of electrode configurations and two types of line arrangements, for 16 resistivity models of a conductive body in a homogeneous half-space. The results of the numerical experiment revealed that the parallel-line arrangement was effective in identifying the approximate location of the conductive body. The orthogonal-line arrangement was optimal for identifying a target body near the line intersection. As a result, we propose that parallel lines are useful to highlight areas of particular interest where further detailed work with an intersecting line could be carried out. In the field experiment, 2D resistivity data were measured on a loam layer with a backfilled pit. The reconstructed resistivity image derived from parallel-line data showed a low-resistivity portion near the backfilled pit. When an orthogonal line was added to the parallel lines, the newly estimated location of the backfilled pit coincided well with the actual location. In a further field application, we collected several 2D resistivity datasets in the Nojima Fault area in Awaji Island. The 3D inversion of these datasets provided a resistivity distribution corresponding to the geological structure. In particular, the Nojima Fault was imaged as the western boundary of a low-resistivity belt, from only two orthogonal lines.

An Artificial Neural Networks Method for Solving Partial Differential Equations

NASA Astrophysics Data System (ADS)

Alharbi, Abir

2010-09-01

While there already exists many analytical and numerical techniques for solving PDEs, this paper introduces an approach using artificial neural networks. The approach consists of a technique developed by combining the standard numerical method, finite-difference, with the Hopfield neural network. The method is denoted Hopfield-finite-difference (HFD). The architecture of the nets, energy function, updating equations, and algorithms are developed for the method. The HFD method has been used successfully to approximate the solution of classical PDEs, such as the Wave, Heat, Poisson and the Diffusion equations, and on a system of PDEs. The software Matlab is used to obtain the results in both tabular and graphical form. The results are similar in terms of accuracy to those obtained by standard numerical methods. In terms of speed, the parallel nature of the Hopfield nets methods makes them easier to implement on fast parallel computers while some numerical methods need extra effort for parallelization.

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.

Leveraging the Cloud for Integrated Network Experimentation

DTIC Science & Technology

2014-03-01

kernel settings, or any of the low-level subcomponents. 3. Scalable Solutions: Businesses can build scalable solutions for their clients , ranging from...values. These values 13 can assume several distributions that include normal, Pareto , uniform, exponential and Poisson, among others [21]. Additionally, D...communication, the web client establishes a connection to the server before traffic begins to flow. Web servers do not initiate connections to clients in

Computational Challenges of 3D Radiative Transfer in Atmospheric Models

NASA Astrophysics Data System (ADS)

Jakub, Fabian; Bernhard, Mayer

2017-04-01

The computation of radiative heating and cooling rates is one of the most expensive components in todays atmospheric models. The high computational cost stems not only from the laborious integration over a wide range of the electromagnetic spectrum but also from the fact that solving the integro-differential radiative transfer equation for monochromatic light is already rather involved. This lead to the advent of numerous approximations and parameterizations to reduce the cost of the solver. One of the most prominent one is the so called independent pixel approximations (IPA) where horizontal energy transfer is neglected whatsoever and radiation may only propagate in the vertical direction (1D). Recent studies implicate that the IPA introduces significant errors in high resolution simulations and affects the evolution and development of convective systems. However, using fully 3D solvers such as for example MonteCarlo methods is not even on state of the art supercomputers feasible. The parallelization of atmospheric models is often realized by a horizontal domain decomposition, and hence, horizontal transfer of energy necessitates communication. E.g. a cloud's shadow at a low zenith angle will cast a long shadow and potentially needs to communication through a multitude of processors. Especially light in the solar spectral range may travel long distances through the atmosphere. Concerning highly parallel simulations, it is vital that 3D radiative transfer solvers put a special emphasis on parallel scalability. We will present an introduction to intricacies computing 3D radiative heating and cooling rates as well as report on the parallel performance of the TenStream solver. The TenStream is a 3D radiative transfer solver using the PETSc framework to iteratively solve a set of partial differential equation. We investigate two matrix preconditioners, (a) geometric algebraic multigrid preconditioning(MG+GAMG) and (b) block Jacobi incomplete LU (ILU) factorization. The TenStream solver is tested for up to 4096 cores and shows a parallel scaling efficiency of 80-90% on various supercomputers.

Mineral lineation produced by 3-D rotation of rigid inclusions in confined viscous simple shear

NASA Astrophysics Data System (ADS)

Marques, Fernando O.

2016-08-01

The solid-state flow of rocks commonly produces a parallel arrangement of elongate minerals with their longest axes coincident with the direction of flow-a mineral lineation. However, this does not conform to Jeffery's theory of the rotation of rigid ellipsoidal inclusions (REIs) in viscous simple shear, because rigid inclusions rotate continuously with applied shear. In 2-dimensional (2-D) flow, the REI's greatest axis (e1) is already in the shear direction; therefore, the problem is to find mechanisms that can prevent the rotation of the REI about one axis, the vorticity axis. In 3-D flow, the problem is to find a mechanism that can make e1 rotate towards the shear direction, and so generate a mineral lineation by rigid rotation about two axes. 3-D analogue and numerical modelling was used to test the effects of confinement on REI rotation and, for narrow channels (shear zone thickness over inclusion's least axis, Wr < 2), the results show that: (1) the rotational behaviour deviates greatly from Jeffery's model; (2) inclusions with aspect ratio Ar (greatest over least principle axis, e1/e3) > 1 can rotate backwards from an initial orientation w e1 parallel to the shear plane, in great contrast to Jeffery's model; (3) back rotation is limited because inclusions reach a stable equilibrium orientation; (4) most importantly and, in contrast to Jeffery's model and to the 2-D simulations, in 3-D, the confined REI gradually rotated about an axis orthogonal to the shear plane towards an orientation with e1 parallel to the shear direction, thus producing a lineation parallel to the shear direction. The modelling results lead to the conclusion that confined simple shear can be responsible for the mineral alignment (lineation) observed in ductile shear zones.

Measurement and modeling of electric field and space-charge distributions in obstructed helium discharge

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

Fendel, Peter; Ganguly, Biswa N.; Bletzinger, Peter

Axial and radial variations of electric field have been measured in dielectric shielded 0.025 m diameter parallel plate electrode with 0.0065 m gap for 1.6 mA, 2260 V helium dc discharge at 1.75 Torr. The axial and radial electric field profiles have been measured from the Stark splitting of 2{sup 1}S→11 {sup 1}P transition through collision induced fluorescence from 4{sup 3}D→2{sup 3}P. The electric field values showed a strong radial variation peaking to 500 kV/m near the cathode radial boundary, and decreasing to about 100 kV/m near the anode edge, suggesting the formation of an obstructed discharge for this low nd condition, where n is the gasmore » density and d is the gap distance. The off-axis Stark spectra showed that the electric field vector deviates from normal to the cathode surface which permits longer path electron trajectories in the inter-electrode gap. Also, the on-axis electric field gradient was very small and off-axis electric field gradient was large indicating a radially non-uniform current density. In order to obtain information about the space charge distribution in this obstructed discharge, it was modeled using the 2-d axisymmetric Poisson solver with the COMSOL finite element modeling program. The best fit to the measured electric field distribution was obtained with a space charge variation of ρ(r) = ρ{sub 0}(r/r{sub 0}){sup 3}, where ρ(r) is the local space charge density, ρ{sub 0} = 6 × 10{sup −3} Coulomb/m{sup 3}, r is the local radial value, and r{sub 0} is the radius of the electrode.« less

Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration

NASA Astrophysics Data System (ADS)

Zhang, Y.; Key, K.; Ovall, J.; Holst, M.

2014-12-01

We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented adaptive refinement code named MARE2DEM. We demonstrate the performance and parallel scaling of this algorithm on a medium-scale computing cluster with a marine controlled-source EM example that includes a 3D array of receivers located over a 3D model that includes significant seafloor bathymetry variations and a heterogeneous subsurface.

Massive parallelization of a 3D finite difference electromagnetic forward solution using domain decomposition methods on multiple CUDA enabled GPUs

NASA Astrophysics Data System (ADS)

Schultz, A.

2010-12-01

3D forward solvers lie at the core of inverse formulations used to image the variation of electrical conductivity within the Earth's interior. This property is associated with variations in temperature, composition, phase, presence of volatiles, and in specific settings, the presence of groundwater, geothermal resources, oil/gas or minerals. The high cost of 3D solutions has been a stumbling block to wider adoption of 3D methods. Parallel algorithms for modeling frequency domain 3D EM problems have not achieved wide scale adoption, with emphasis on fairly coarse grained parallelism using MPI and similar approaches. The communications bandwidth as well as the latency required to send and receive network communication packets is a limiting factor in implementing fine grained parallel strategies, inhibiting wide adoption of these algorithms. Leading Graphics Processor Unit (GPU) companies now produce GPUs with hundreds of GPU processor cores per die. The footprint, in silicon, of the GPU's restricted instruction set is much smaller than the general purpose instruction set required of a CPU. Consequently, the density of processor cores on a GPU can be much greater than on a CPU. GPUs also have local memory, registers and high speed communication with host CPUs, usually through PCIe type interconnects. The extremely low cost and high computational power of GPUs provides the EM geophysics community with an opportunity to achieve fine grained (i.e. massive) parallelization of codes on low cost hardware. The current generation of GPUs (e.g. NVidia Fermi) provides 3 billion transistors per chip die, with nearly 500 processor cores and up to 6 GB of fast (DDR5) GPU memory. This latest generation of GPU supports fast hardware double precision (64 bit) floating point operations of the type required for frequency domain EM forward solutions. Each Fermi GPU board can sustain nearly 1 TFLOP in double precision, and multiple boards can be installed in the host computer system. We describe our ongoing efforts to achieve massive parallelization on a novel hybrid GPU testbed machine currently configured with 12 Intel Westmere Xeon CPU cores (or 24 parallel computational threads) with 96 GB DDR3 system memory, 4 GPU subsystems which in aggregate contain 960 NVidia Tesla GPU cores with 16 GB dedicated DDR3 GPU memory, and a second interleved bank of 4 GPU subsystems containing in aggregate 1792 NVidia Fermi GPU cores with 12 GB dedicated DDR5 GPU memory. We are applying domain decomposition methods to a modified version of Weiss' (2001) 3D frequency domain full physics EM finite difference code, an open source GPL licensed f90 code available for download from www.OpenEM.org. This will be the core of a new hybrid 3D inversion that parallelizes frequencies across CPUs and individual forward solutions across GPUs. We describe progress made in modifying the code to use direct solvers in GPU cores dedicated to each small subdomain, iteratively improving the solution by matching adjacent subdomain boundary solutions, rather than iterative Krylov space sparse solvers as currently applied to the whole domain.

A Generalized QMRA Beta-Poisson Dose-Response Model.

PubMed

Xie, Gang; Roiko, Anne; Stratton, Helen; Lemckert, Charles; Dunn, Peter K; Mengersen, Kerrie

2016-10-01

Quantitative microbial risk assessment (QMRA) is widely accepted for characterizing the microbial risks associated with food, water, and wastewater. Single-hit dose-response models are the most commonly used dose-response models in QMRA. Denoting PI(d) as the probability of infection at a given mean dose d, a three-parameter generalized QMRA beta-Poisson dose-response model, PI(d|α,β,r*), is proposed in which the minimum number of organisms required for causing infection, K min , is not fixed, but a random variable following a geometric distribution with parameter 0

Waveform inversion for 3-D earth structure using the Direct Solution Method implemented on vector-parallel supercomputer

NASA Astrophysics Data System (ADS)

Hara, Tatsuhiko

2004-08-01

We implement the Direct Solution Method (DSM) on a vector-parallel supercomputer and show that it is possible to significantly improve its computational efficiency through parallel computing. We apply the parallel DSM calculation to waveform inversion of long period (250-500 s) surface wave data for three-dimensional (3-D) S-wave velocity structure in the upper and uppermost lower mantle. We use a spherical harmonic expansion to represent lateral variation with the maximum angular degree 16. We find significant low velocities under south Pacific hot spots in the transition zone. This is consistent with other seismological studies conducted in the Superplume project, which suggests deep roots of these hot spots. We also perform simultaneous waveform inversion for 3-D S-wave velocity and Q structure. Since resolution for Q is not good, we develop a new technique in which power spectra are used as data for inversion. We find good correlation between long wavelength patterns of Vs and Q in the transition zone such as high Vs and high Q under the western Pacific.

NRL Plasma Formulary

DTIC Science & Technology

2007-01-01

1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no...β/α3 (h̄c)−1 Resistance 4πǫ0/α (ǫ0/µ0) 1/2 Time 1 c Velocity α c−1 18 MAXWELL’S EQUATIONS Name or Description SI Gaussian Faraday’s law ∇ × E = −∂B...t ∇ × E = − 1 c ∂B ∂t Ampere’s law ∇ × H = ∂D ∂t + J ∇ × H = 1 c ∂D ∂t + 4π c J Poisson equation ∇ · D = ρ ∇ · D = 4πρ [Absence of magnetic ∇ · B = 0

NRL: Plasma Formulary

DTIC Science & Technology

2004-12-01

Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no person...Pressure β/α3 (h̄c)−1 Resistance 4π0/α (0/µ0) 1/2 Time 1 c Velocity α c−1 19 MAXWELL’S EQUATIONS Name or Description SI Gaussian Faraday’s law ∇ × E = −∂B...t ∇ × E = − 1 c ∂B ∂t Ampere’s law ∇ × H = ∂D ∂t + J ∇ × H = 1 c ∂D ∂t + 4π c J Poisson equation ∇ · D = ρ ∇ · D = 4πρ [Absence of magnetic ∇ · B = 0

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.

Advanced Numerical Techniques of Performance Evaluation. Volume 1

DTIC Science & Technology

1990-06-01

system scheduling3thread. The scheduling thread then runs any other ready thread that can be found. A thread can only sleep or switch out on itself...Polychronopoulos and D.J. Kuck. Guided Self- Scheduling : A Practical Scheduling Scheme for Parallel Supercomputers. IEEE Transactions on Computers C...Kuck 1987] C.D. Polychronopoulos and D.J. Kuck. Guided Self- Scheduling : A Practical Scheduling Scheme for Parallel Supercomputers. IEEE Trans. on Comp

Properties of plane discrete Poisson-Voronoi tessellations on triangular tiling formed by the Kolmogorov-Johnson-Mehl-Avrami growth of triangular islands

NASA Astrophysics Data System (ADS)

Korobov, A.

2011-08-01

Discrete uniform Poisson-Voronoi tessellations of two-dimensional triangular tilings resulting from the Kolmogorov-Johnson-Mehl-Avrami (KJMA) growth of triangular islands have been studied. This shape of tiles and islands, rarely considered in the field of random tessellations, is prompted by the birth-growth process of Ir(210) faceting. The growth mode determines a triangular metric different from the Euclidean metric. Kinetic characteristics of tessellations appear to be metric sensitive, in contrast to area distributions. The latter have been studied for the variant of nuclei growth to the first impingement in addition to the conventional case of complete growth. Kiang conjecture works in both cases. The averaged number of neighbors is six for all studied densities of random tessellations, but neighbors appear to be mainly different in triangular and Euclidean metrics. Also, the applicability of the obtained results for simulating birth-growth processes when the 2D nucleation and impingements are combined with the 3D growth in the particular case of similar shape and the same orientation of growing nuclei is briefly discussed.

Properties of plane discrete Poisson-Voronoi tessellations on triangular tiling formed by the Kolmogorov-Johnson-Mehl-Avrami growth of triangular islands.

PubMed

Korobov, A

2011-08-01

Discrete uniform Poisson-Voronoi tessellations of two-dimensional triangular tilings resulting from the Kolmogorov-Johnson-Mehl-Avrami (KJMA) growth of triangular islands have been studied. This shape of tiles and islands, rarely considered in the field of random tessellations, is prompted by the birth-growth process of Ir(210) faceting. The growth mode determines a triangular metric different from the Euclidean metric. Kinetic characteristics of tessellations appear to be metric sensitive, in contrast to area distributions. The latter have been studied for the variant of nuclei growth to the first impingement in addition to the conventional case of complete growth. Kiang conjecture works in both cases. The averaged number of neighbors is six for all studied densities of random tessellations, but neighbors appear to be mainly different in triangular and Euclidean metrics. Also, the applicability of the obtained results for simulating birth-growth processes when the 2D nucleation and impingements are combined with the 3D growth in the particular case of similar shape and the same orientation of growing nuclei is briefly discussed.

Influence of deflection on a fold-to-fault progression: field evidence from near Marietta, South Carolina

USGS Publications Warehouse

Clendenin, C.W.; Garihan, J.M.

2006-01-01

Four periods of deformation (D1-D4) are recognized in the Lion Park Road borrow pit near Marietta, South Carolina. Although each period is characterized by distinct structures, D3 produced two structural styles (D3a, D3b) resulting from layer-parallel shortening. D3a is characterized by detachment folding at the tip of an underlying thrust. D3b is a fold-to-fault progression that was localized by east-dipping, quartz-filled gash fractures. The fold-to-fault progression demonstrates the influence of a mechanical anisotropy on ramp development. The early stages of D3b were formed by deflection of northwest-directed, layer-parallel shortening and active, down-section propagation of folds and thrusts. Following connection with a splay of basal detachment, later D3b stages resulted from up-section movement that produced kink folding and a throughgoing thrust. This up-section movement deformed and modified the geometries of older, down-section structures. Detailed mesoscopic field observations, integrated with a combination of current thrust fault models, are used to interpret the D3b fold-to-fault progression. ?? 2006 Elsevier Ltd. All rights reserved.

NRL Plasma Formulary

DTIC Science & Technology

2006-01-01

1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no...Description SI Gaussian Faraday’s law ∇ × E = −∂B ∂t ∇ × E = − 1 c ∂B ∂t Ampere’s law ∇ × H = ∂D ∂t + J ∇ × H = 1 c ∂D ∂t + 4π c J Poisson equation ∇ · D = ρ...gravitational or V/NL buoyancy force)1/2 Gay– Lussac Ga 1/β∆T Inverse of relative change in volume during heating Grashof Gr gL3β∆T/ν2 Buoyancy force/viscous

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.

Wireless Rover Meets 3D Design and Product Development

ERIC Educational Resources Information Center

Deal, Walter F., III; Hsiung, Steve C.

2016-01-01

Today there are a number of 3D printing technologies that are low cost and within the budgets of middle and high school programs. Educational technology companies offer a variety of 3D printing technologies and parallel curriculum materials to enable technology and engineering teachers to easily add 3D learning activities to their programs.…

Clinical characterization of 2D pressure field in human left ventricles

NASA Astrophysics Data System (ADS)

Borja, Maria; Rossini, Lorenzo; Martinez-Legazpi, Pablo; Benito, Yolanda; Alhama, Marta; Yotti, Raquel; Perez Del Villar, Candelas; Gonzalez-Mansilla, Ana; Barrio, Alicia; Fernandez-Aviles, Francisco; Bermejo, Javier; Khan, Andrew; Del Alamo, Juan Carlos

2014-11-01

The evaluation of left ventricle (LV) function in the clinical setting remains a challenge. Pressure gradient is a reliable and reproducible indicator of the LV function. We obtain 2D relative pressure field in the LV using in-vivo measurements obtained by processing Doppler-echocardiography images of healthy and dilated hearts. Exploiting mass conservation, we solve the Poisson pressure equation (PPE) dropping the time derivatives and viscous terms. The flow acceleration appears only in the boundary conditions, making our method weakly sensible to the time resolution of in-vivo acquisitions. To ensure continuity with respect to the discrete operator and grid used, a potential flow correction is applied beforehand, which gives another Poisson equation. The new incompressible velocity field ensures that the compatibility equation for the PPE is satisfied. Both Poisson equations are efficiently solved on a Cartesian grid using a multi-grid method and immersed boundary for the LV wall. The whole process is computationally inexpensive and could play a diagnostic role in the clinical assessment of LV function.

Semi-Lagrangian particle methods for high-dimensional Vlasov-Poisson systems

NASA Astrophysics Data System (ADS)

Cottet, Georges-Henri

2018-07-01

This paper deals with the implementation of high order semi-Lagrangian particle methods to handle high dimensional Vlasov-Poisson systems. It is based on recent developments in the numerical analysis of particle methods and the paper focuses on specific algorithmic features to handle large dimensions. The methods are tested with uniform particle distributions in particular against a recent multi-resolution wavelet based method on a 4D plasma instability case and a 6D gravitational case. Conservation properties, accuracy and computational costs are monitored. The excellent accuracy/cost trade-off shown by the method opens new perspective for accurate simulations of high dimensional kinetic equations by particle methods.

Poisson equation for the Mercedes diagram in string theory at genus one

NASA Astrophysics Data System (ADS)

Basu, Anirban

2016-03-01

The Mercedes diagram has four trivalent vertices which are connected by six links such that they form the edges of a tetrahedron. This three-loop Feynman diagram contributes to the {D}12{{ R }}4 amplitude at genus one in type II string theory, where the vertices are the points of insertion of the graviton vertex operators, and the links are the scalar propagators on the toroidal worldsheet. We obtain a modular invariant Poisson equation satisfied by the Mercedes diagram, where the source terms involve one- and two-loop Feynman diagrams. We calculate its contribution to the {D}12{{ R }}4 amplitude.

First principle study of structural, elastic and electronic properties of APt3 (A=Mg, Sc, Y and Zr)

NASA Astrophysics Data System (ADS)

Benamer, A.; Roumili, A.; Medkour, Y.; Charifi, Z.

2018-02-01

We report results obtained from first principle calculations on APt3 compounds with A=Mg, Sc, Y and Zr. Our results of the lattice parameter a are in good agreement with experimental data, with deviations less than 0.8%. Single crystal elastic constants are calculated, then polycrystalline elastic moduli (bulk, shear and Young moduli, Poisson ration, anisotropy factor) are presented. Based on Debye model, Debye temperature ϴD is calculated from the sound velocities Vl, Vt and Vm. Band structure results show that the studied compounds are electrical conductors, the conduction mechanism is assured by Pt-d electrons. Different hybridisation states are observed between Pt-d and A-d orbitals. The study of the charge density distribution and the population analysis shows the coexistence of ionic, covalent and metallic bonds.

Recognizing human activities using appearance metric feature and kinematics feature

NASA Astrophysics Data System (ADS)

Qian, Huimin; Zhou, Jun; Lu, Xinbiao; Wu, Xinye

2017-05-01

The problem of automatically recognizing human activities from videos through the fusion of the two most important cues, appearance metric feature and kinematics feature, is considered. And a system of two-dimensional (2-D) Poisson equations is introduced to extract the more discriminative appearance metric feature. Specifically, the moving human blobs are first detected out from the video by background subtraction technique to form a binary image sequence, from which the appearance feature designated as the motion accumulation image and the kinematics feature termed as centroid instantaneous velocity are extracted. Second, 2-D discrete Poisson equations are employed to reinterpret the motion accumulation image to produce a more differentiated Poisson silhouette image, from which the appearance feature vector is created through the dimension reduction technique called bidirectional 2-D principal component analysis, considering the balance between classification accuracy and time consumption. Finally, a cascaded classifier based on the nearest neighbor classifier and two directed acyclic graph support vector machine classifiers, integrated with the fusion of the appearance feature vector and centroid instantaneous velocity vector, is applied to recognize the human activities. Experimental results on the open databases and a homemade one confirm the recognition performance of the proposed algorithm.

Wavelet Transforms in Parallel Image Processing

DTIC Science & Technology

1994-01-27

NUMBER OF PAGES Object Segmentation, Texture Segmentation, Image Compression, Image 137 Halftoning , Neural Network, Parallel Algorithms, 2D and 3D...Vector Quantization of Wavelet Transform Coefficients ........ ............................. 57 B.1.f Adaptive Image Halftoning based on Wavelet...application has been directed to the adaptive image halftoning . The gray information at a pixel, including its gray value and gradient, is represented by

76 FR 20750 - Self-Regulatory Organizations; EDGX Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-13

... on the Exchange's Internet Web site at http://www.directedge.com . \\3\\ A Member is any registered... strategy to the ROUD/ROUE routing strategies is Parallel D or Parallel 2D with the DRT (Dark routing... one method. The Commission will post all comments on the Commission's Internet Web site ( http://www...

Functional Integration

NASA Astrophysics Data System (ADS)

Cartier, Pierre; DeWitt-Morette, Cecile

2006-11-01

Acknowledgements; List symbols, conventions, and formulary; Part I. The Physical and Mathematical Environment: 1. The physical and mathematical environment; Part II. Quantum Mechanics: 2. First lesson: gaussian integrals; 3. Selected examples; 4. Semiclassical expansion: WKB; 5. Semiclassical expansion: beyond WKB; 6. Quantum dynamics: path integrals and operator formalism; Part III. Methods from Differential Geometry: 7. Symmetries; 8. Homotopy; 9. Grassmann analysis: basics; 10. Grassmann analysis: applications; 11. Volume elements, divergences, gradients; Part IV. Non-Gaussian Applications: 12. Poisson processes in physics; 13. A mathematical theory of Poisson processes; 14. First exit time: energy problems; Part V. Problems in Quantum Field Theory: 15. Renormalization 1: an introduction; 16. Renormalization 2: scaling; 17. Renormalization 3: combinatorics; 18. Volume elements in quantum field theory Bryce DeWitt; Part VI. Projects: 19. Projects; Appendix A. Forward and backward integrals: spaces of pointed paths; Appendix B. Product integrals; Appendix C. A compendium of gaussian integrals; Appendix D. Wick calculus Alexander Wurm; Appendix E. The Jacobi operator; Appendix F. Change of variables of integration; Appendix G. Analytic properties of covariances; Appendix H. Feynman's checkerboard; Bibliography; Index.

Functional Integration

NASA Astrophysics Data System (ADS)

Cartier, Pierre; DeWitt-Morette, Cecile

2010-06-01

Acknowledgements; List symbols, conventions, and formulary; Part I. The Physical and Mathematical Environment: 1. The physical and mathematical environment; Part II. Quantum Mechanics: 2. First lesson: gaussian integrals; 3. Selected examples; 4. Semiclassical expansion: WKB; 5. Semiclassical expansion: beyond WKB; 6. Quantum dynamics: path integrals and operator formalism; Part III. Methods from Differential Geometry: 7. Symmetries; 8. Homotopy; 9. Grassmann analysis: basics; 10. Grassmann analysis: applications; 11. Volume elements, divergences, gradients; Part IV. Non-Gaussian Applications: 12. Poisson processes in physics; 13. A mathematical theory of Poisson processes; 14. First exit time: energy problems; Part V. Problems in Quantum Field Theory: 15. Renormalization 1: an introduction; 16. Renormalization 2: scaling; 17. Renormalization 3: combinatorics; 18. Volume elements in quantum field theory Bryce DeWitt; Part VI. Projects: 19. Projects; Appendix A. Forward and backward integrals: spaces of pointed paths; Appendix B. Product integrals; Appendix C. A compendium of gaussian integrals; Appendix D. Wick calculus Alexander Wurm; Appendix E. The Jacobi operator; Appendix F. Change of variables of integration; Appendix G. Analytic properties of covariances; Appendix H. Feynman's checkerboard; Bibliography; Index.

A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

DOE PAGES

Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; ...

2013-01-01

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in amore » 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.« less

Single atom visibility in STEM optical depth sectioning

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

Ishikawa, Ryo; Pennycook, Stephen J.; Lupini, Andrew R.

The continuing development of aberration correctors for the scanning transmission electron microscope (STEM) offers the possibility of locating single atoms in crystals in 3D via optical depth sectioning. The main factors that determine the feasibility of such an approach are visibility and dose requirements. In this paper, we show how Poisson's statistics can be quantitatively incorporated into STEM image simulations and demonstrate that the 3D location of single cerium atoms in wurtzite-type aluminum nitride is indeed feasible under large-angle illumination conditions with a relatively low dose. We also show that chromatic aberration does not presently represent a limitation provided amore » cold field emission source is used. Finally, these results suggest efforts into improved aberration corrector designs for larger illumination angles that offer significant potential for 3D structure determination of materials.« less

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

NASA Astrophysics Data System (ADS)

Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

2018-03-01

The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

Single atom visibility in STEM optical depth sectioning

DOE PAGES

Ishikawa, Ryo; Pennycook, Stephen J.; Lupini, Andrew R.; ...

2016-10-19

The continuing development of aberration correctors for the scanning transmission electron microscope (STEM) offers the possibility of locating single atoms in crystals in 3D via optical depth sectioning. The main factors that determine the feasibility of such an approach are visibility and dose requirements. In this paper, we show how Poisson's statistics can be quantitatively incorporated into STEM image simulations and demonstrate that the 3D location of single cerium atoms in wurtzite-type aluminum nitride is indeed feasible under large-angle illumination conditions with a relatively low dose. We also show that chromatic aberration does not presently represent a limitation provided amore » cold field emission source is used. Finally, these results suggest efforts into improved aberration corrector designs for larger illumination angles that offer significant potential for 3D structure determination of materials.« less

3D 14N/1H Double Quantum/1H Single Quantum Correlation Solid-State NMR for Probing Parallel and Anti-Parallel Beta-Sheet Arrangement of Oligo-Peptides at Natural Abundance.

PubMed

Hong, You-Lee; Asakura, Tetsuo; Nishiyama, Yusuke

2018-05-08

β-sheet structure of oligo- and poly-peptides can be formed in anti-parallel (AP)- and parallel (P)-structure, which is the important feature to understand the structures. In principle, P- and AP-β-sheet structures can be identified by the presence (AP) and absence (P) of the interstrand 1HNH/1HNH correlations on a diagonal in 2D 1H double quantum (DQ)/1H single quantum (SQ) spectrum due to the different interstrand 1HNH/1HNH distances between these two arrangements. However, the 1HNH/1HNH peaks overlap to the 1HNH3+/1HNH3+ peaks, which always give cross peaks regardless of the β-sheet arrangement. The 1HNH3+/1HNH3+ peaks disturb the observation of the presence/absence of 1HNH/1HNH correlations and the assignment of 1HNH and 1HNH3+ is not always available. Here, 3D 14N/1H DQ/1H SQ correlation solid-state NMR experiments at fast magic angle spinning (70 kHz) are introduced to distinguish AP and P β-sheet structure. The 14N dimension allows the separate observation of 1HNH/1HNH peaks from 1HNH3+/1HNH3+ peaks with clear assignment of 1HNH and 1HNH3+. In addition, the high natural abundance of 1H and 14N enables 3D 14N/1H DQ/1H SQ experiments of oligo-alanines (Ala3-6) in four hours without any isotope labelling. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3-D Electromagnetic field analysis of wireless power transfer system using K computer

NASA Astrophysics Data System (ADS)

Kawase, Yoshihiro; Yamaguchi, Tadashi; Murashita, Masaya; Tsukada, Shota; Ota, Tomohiro; Yamamoto, Takeshi

2018-05-01

We analyze the electromagnetic field of a wireless power transfer system using the 3-D parallel finite element method on K computer, which is a super computer in Japan. It is clarified that the electromagnetic field of the wireless power transfer system can be analyzed in a practical time using the parallel computation on K computer, moreover, the accuracy of the loss calculation becomes better as the mesh division of the shield becomes fine.

Parallelized multi–graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy

PubMed Central

Tankam, Patrice; Santhanam, Anand P.; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P.

2014-01-01

Abstract. Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing. PMID:24695868

Parallelized multi-graphics processing unit framework for high-speed Gabor-domain optical coherence microscopy.

PubMed

Tankam, Patrice; Santhanam, Anand P; Lee, Kye-Sung; Won, Jungeun; Canavesi, Cristina; Rolland, Jannick P

2014-07-01

Gabor-domain optical coherence microscopy (GD-OCM) is a volumetric high-resolution technique capable of acquiring three-dimensional (3-D) skin images with histological resolution. Real-time image processing is needed to enable GD-OCM imaging in a clinical setting. We present a parallelized and scalable multi-graphics processing unit (GPU) computing framework for real-time GD-OCM image processing. A parallelized control mechanism was developed to individually assign computation tasks to each of the GPUs. For each GPU, the optimal number of amplitude-scans (A-scans) to be processed in parallel was selected to maximize GPU memory usage and core throughput. We investigated five computing architectures for computational speed-up in processing 1000×1000 A-scans. The proposed parallelized multi-GPU computing framework enables processing at a computational speed faster than the GD-OCM image acquisition, thereby facilitating high-speed GD-OCM imaging in a clinical setting. Using two parallelized GPUs, the image processing of a 1×1×0.6  mm3 skin sample was performed in about 13 s, and the performance was benchmarked at 6.5 s with four GPUs. This work thus demonstrates that 3-D GD-OCM data may be displayed in real-time to the examiner using parallelized GPU processing.

The Casimir effect for parallel plates revisited

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

Kawakami, N. A.; Nemes, M. C.; Wreszinski, Walter F.

2007-10-15

The Casimir effect for a massless scalar field with Dirichlet and periodic boundary conditions (bc's) on infinite parallel plates is revisited in the local quantum field theory (lqft) framework introduced by Kay [Phys. Rev. D 20, 3052 (1979)]. The model displays a number of more realistic features than the ones he treated. In addition to local observables, as the energy density, we propose to consider intensive variables, such as the energy per unit area {epsilon}, as fundamental observables. Adopting this view, lqft rejects Dirichlet (the same result may be proved for Neumann or mixed) bc, and accepts periodic bc: inmore » the former case {epsilon} diverges, in the latter it is finite, as is shown by an expression for the local energy density obtained from lqft through the use of the Poisson summation formula. Another way to see this uses methods from the Euler summation formula: in the proof of regularization independence of the energy per unit area, a regularization-dependent surface term arises upon use of Dirichlet bc, but not periodic bc. For the conformally invariant scalar quantum field, this surface term is absent due to the condition of zero trace of the energy momentum tensor, as remarked by De Witt [Phys. Rep. 19, 295 (1975)]. The latter property does not hold in the application to the dark energy problem in cosmology, in which we argue that periodic bc might play a distinguished role.« less

The stress analysis method for three-dimensional composite materials

NASA Astrophysics Data System (ADS)

Nagai, Kanehiro; Yokoyama, Atsushi; Maekawa, Zen'ichiro; Hamada, Hiroyuki

1994-05-01

This study proposes a stress analysis method for three-dimensionally fiber reinforced composite materials. In this method, the rule-of mixture for composites is successfully applied to 3-D space in which material properties would change 3-dimensionally. The fundamental formulas for Young's modulus, shear modulus, and Poisson's ratio are derived. Also, we discuss a strength estimation and an optimum material design technique for 3-D composite materials. The analysis is executed for a triaxial orthogonally woven fabric, and their results are compared to the experimental data in order to verify the accuracy of this method. The present methodology can be easily understood with basic material mechanics and elementary mathematics, so it enables us to write a computer program of this theory without difficulty. Furthermore, this method can be applied to various types of 3-D composites because of its general-purpose characteristics.

A novel method for the accurate evaluation of Poisson's ratio of soft polymer materials.

PubMed

Lee, Jae-Hoon; Lee, Sang-Soo; Chang, Jun-Dong; Thompson, Mark S; Kang, Dong-Joong; Park, Sungchan; Park, Seonghun

2013-01-01

A new method with a simple algorithm was developed to accurately measure Poisson's ratio of soft materials such as polyvinyl alcohol hydrogel (PVA-H) with a custom experimental apparatus consisting of a tension device, a micro X-Y stage, an optical microscope, and a charge-coupled device camera. In the proposed method, the initial positions of the four vertices of an arbitrarily selected quadrilateral from the sample surface were first measured to generate a 2D 1st-order 4-node quadrilateral element for finite element numerical analysis. Next, minimum and maximum principal strains were calculated from differences between the initial and deformed shapes of the quadrilateral under tension. Finally, Poisson's ratio of PVA-H was determined by the ratio of minimum principal strain to maximum principal strain. This novel method has an advantage in the accurate evaluation of Poisson's ratio despite misalignment between specimens and experimental devices. In this study, Poisson's ratio of PVA-H was 0.44 ± 0.025 (n = 6) for 2.6-47.0% elongations with a tendency to decrease with increasing elongation. The current evaluation method of Poisson's ratio with a simple measurement system can be employed to a real-time automated vision-tracking system which is used to accurately evaluate the material properties of various soft materials.

Determination of Poisson Ratio of Bovine Extraocular Muscle by Computed X-Ray Tomography

PubMed Central

Kim, Hansang; Yoo, Lawrence; Shin, Andrew; Demer, Joseph L.

2013-01-01

The Poisson ratio (PR) is a fundamental mechanical parameter that approximates the ratio of relative change in cross sectional area to tensile elongation. However, the PR of extraocular muscle (EOM) is almost never measured because of experimental constraints. The problem was overcome by determining changes in EOM dimensions using computed X-ray tomography (CT) at microscopic resolution during tensile elongation to determine transverse strain indicated by the change in cross-section. Fresh bovine EOM specimens were prepared. Specimens were clamped in a tensile fixture within a CT scanner (SkyScan, Belgium) with temperature and humidity control and stretched up to 35% of initial length. Sets of 500–800 contiguous CT images were obtained at 10-micron resolution before and after tensile loading. Digital 3D models were then built and discretized into 6–8-micron-thick elements. Changes in longitudinal thickness of each microscopic element were determined to calculate strain. Green's theorem was used to calculate areal strain in transverse directions orthogonal to the stretching direction. The mean PR from discretized 3D models for every microscopic element in 14 EOM specimens averaged 0.457 ± 0.004 (SD). The measured PR of bovine EOM is thus near the limit of incompressibility. PMID:23484091

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

Effect of 3D magnetic perturbations on divertor conditions and detachment in tokamak and stellarator

DOE PAGES

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.; ...

2017-06-22

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

Effect of 3D magnetic perturbations on divertor conditions and detachment in tokamak and stellarator

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

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

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.

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

Investigation of Dynamic Crack Coalescence Using a Gypsum-Like 3D Printing Material

NASA Astrophysics Data System (ADS)

Jiang, Chao; Zhao, Gao-Feng; Zhu, Jianbo; Zhao, Yi-Xin; Shen, Luming

2016-10-01

Dynamic crack coalescence attracts great attention in rock mechanics. However, specimen preparation in experimental study is a time-consuming and difficult procedure. In this work, a gypsum-like material by powder bed and inkjet 3D printing technique was applied to produce specimens with preset cracks for split Hopkinson pressure bar (SHPB) test. From micro X-ray CT test, it was found that the 3D printing technique could successfully prepare specimens that contain preset cracks with width of 0.2 mm. Basic mechanical properties of the 3D printing material, i.e., the elastic modulus, the Poisson's ratio, the density, the compressive strength, the indirect tensile strength, and the fracture toughness, were obtained and reported. Unlike 3D printed specimens using polylactic acid, these gypsum-like specimens can produce failure patterns much closer to those observed in classical rock mechanical tests. Finally, the dynamic crack coalescence of the 3D printed specimens with preset cracks were captured using a high-speed camera during SHPB tests. Failure patterns of these 3D printed specimens are similar to the specimens made by Portland cement concrete. Our results indicate that sample preparation by 3D printing is highly competitive due to its quickness in prototyping, precision and flexibility on the geometry, and high material homogeneity.

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.

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

Haghighat, A.; Sjoden, G.E.; Wagner, J.C.

In the past 10 yr, the Penn State Transport Theory Group (PSTTG) has concentrated its efforts on developing accurate and efficient particle transport codes to address increasing needs for efficient and accurate simulation of nuclear systems. The PSTTG's efforts have primarily focused on shielding applications that are generally treated using multigroup, multidimensional, discrete ordinates (S{sub n}) deterministic and/or statistical Monte Carlo methods. The difficulty with the existing public codes is that they require significant (impractical) computation time for simulation of complex three-dimensional (3-D) problems. For the S{sub n} codes, the large memory requirements are handled through the use of scratchmore » files (i.e., read-from and write-to-disk) that significantly increases the necessary execution time. Further, the lack of flexible features and/or utilities for preparing input and processing output makes these codes difficult to use. The Monte Carlo method becomes impractical because variance reduction (VR) methods have to be used, and normally determination of the necessary parameters for the VR methods is very difficult and time consuming for a complex 3-D problem. For the deterministic method, the authors have developed the 3-D parallel PENTRAN (Parallel Environment Neutral-particle TRANsport) code system that, in addition to a parallel 3-D S{sub n} solver, includes pre- and postprocessing utilities. PENTRAN provides for full phase-space decomposition, memory partitioning, and parallel input/output to provide the capability of solving large problems in a relatively short time. Besides having a modular parallel structure, PENTRAN has several unique new formulations and features that are necessary for achieving high parallel performance. For the Monte Carlo method, the major difficulty currently facing most users is the selection of an effective VR method and its associated parameters. For complex problems, generally, this process is very time consuming and may be complicated due to the possibility of biasing the results. In an attempt to eliminate this problem, the authors have developed the A{sup 3}MCNP (automated adjoint accelerated MCNP) code that automatically prepares parameters for source and transport biasing within a weight-window VR approach based on the S{sub n} adjoint function. A{sup 3}MCNP prepares the necessary input files for performing multigroup, 3-D adjoint S{sub n} calculations using TORT.« less

76 FR 21076 - Self-Regulatory Organizations; EDGA Exchange, Inc.; Notice of Filing and Immediate Effectiveness...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-14

... on the Exchange's Internet Web site at http://www.directedge.com . \\3\\ A Member is any registered... Parallel D or Parallel 2D with the DRT (Dark routing technique) option on BZX. BZX charges $0.0020 per... the DRT (Dark routing technique) option on BZX or SCAN/STGY on Nasdaq OMX Exchange (``Nasdaq.'') BATS...

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.

Anomalous elasticity, fluctuations and disorder in elastic membranes

NASA Astrophysics Data System (ADS)

Le Doussal, Pierre; Radzihovsky, Leo

2018-05-01

Motivated by freely suspended graphene and polymerized membranes in soft and biological matter we present a detailed study of a tensionless elastic sheet in the presence of thermal fluctuations and quenched disorder. The manuscript is based on an extensive draft dating back to 1993, that was circulated privately. It presents the general theoretical framework and calculational details of numerous results, partial forms of which have been published in brief Letters (Le Doussal and Radzihovsky, 1992; 1993). The experimental realization atom-thin graphene sheets (Novoselov et al., 2004) have driven a resurgence in this fascinating subject, making our dated predictions and their detailed derivations timely. To this end we analyze the statistical mechanics of a generalized D-dimensional elastic "membrane" embedded in d dimensions using a self-consistent screening approximation (SCSA), that has proved to be unprecedentedly accurate in this system, exact in three complementary limits: (i) d → ∞, (ii) D → 4, and (iii) D = d. Focusing on the critical "flat" phase, for a homogeneous two-dimensional (D = 2) membrane embedded in three dimensions (d = 3), we predict its universal roughness exponent ζ = 0 . 590, length-scale dependent elastic moduli exponents η = 0 . 821 and ηu = 0 . 358, and an anomalous Poisson ratio, σ = - 1 / 3. In the presence of random uncorrelated heterogeneity the membrane exhibits a glassy wrinkled ground state, characterized by ζ‧ = 0 . 775 ,η‧ = 0 . 449, ηu‧ = 1 . 101 and a Poisson ratio σ‧ = - 1 / 3. Motivated by a number of physical realizations (charged impurities, disclinations and dislocations) we also study power-law correlated quenched disorder that leads to a variety of distinct glassy wrinkled phases. Finally, neglecting self-avoiding interaction we demonstrate that at high temperature a "phantom" sheet undergoes a continuous crumpling transition, characterized by a radius of gyration exponent, ν = 0 . 732 and η = 0 . 535. Many of these universal predictions have received considerable support from simulations. We hope that this detailed presentation of the SCSA theory will be useful to further theoretical developments and corresponding experimental investigations on freely suspended graphene.

Dynamically accumulated dose and 4D accumulated dose for moving tumors

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

Li Heng; Li Yupeng; Zhang Xiaodong

2012-12-15

Purpose: The purpose of this work was to investigate the relationship between dynamically accumulated dose (dynamic dose) and 4D accumulated dose (4D dose) for irradiation of moving tumors, and to quantify the dose uncertainty induced by tumor motion. Methods: The authors established that regardless of treatment modality and delivery properties, the dynamic dose will converge to the 4D dose, instead of the 3D static dose, after multiple deliveries. The bounds of dynamic dose, or the maximum estimation error using 4D or static dose, were established for the 4D and static doses, respectively. Numerical simulations were performed (1) to prove themore » principle that for each phase, after multiple deliveries, the average number of deliveries for any given time converges to the total number of fractions (K) over the number of phases (N); (2) to investigate the dose difference between the 4D and dynamic doses as a function of the number of deliveries for deliveries of a 'pulsed beam'; and (3) to investigate the dose difference between 4D dose and dynamic doses as a function of delivery time for deliveries of a 'continuous beam.' A Poisson model was developed to estimate the mean dose error as a function of number of deliveries or delivered time for both pulsed beam and continuous beam. Results: The numerical simulations confirmed that the number of deliveries for each phase converges to K/N, assuming a random starting phase. Simulations for the pulsed beam and continuous beam also suggested that the dose error is a strong function of the number of deliveries and/or total deliver time and could be a function of the breathing cycle, depending on the mode of delivery. The Poisson model agrees well with the simulation. Conclusions: Dynamically accumulated dose will converge to the 4D accumulated dose after multiple deliveries, regardless of treatment modality. Bounds of the dynamic dose could be determined using quantities derived from 4D doses, and the mean dose difference between the dynamic dose and 4D dose as a function of number of deliveries and/or total deliver time was also established.« less

Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver

NASA Astrophysics Data System (ADS)

Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre

2014-06-01

This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.

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.

Extremely high resolution 3D electrical resistivity tomography to depict archaeological subsurface structures

NASA Astrophysics Data System (ADS)

Al-Saadi, Osamah; Schmidt, Volkmar; Becken, Michael; Fritsch, Thomas

2017-04-01

Electrical resistivity tomography (ERT) methods have been increasingly used in various shallow depth archaeological prospections in the last few decades. These non-invasive techniques are very useful in saving time, costs, and efforts. Both 2D and 3D ERT techniques are used to obtain detailed images of subsurface anomalies. In two surveyed areas near Nonnweiler (Germany), we present the results of the full 3D setup with a roll-along technique and of the quasi-3D setup (parallel and orthogonal profiles in dipole-dipole configuration). In area A, a dipole-dipole array with 96 electrodes in a uniform rectangular survey grid has been used in full 3D to investigate a presumed Roman building. A roll-along technique has been utilized to cover a large part of the archaeological site with an electrode spacing of 1 meter and with 0.5 meter for a more detailed image. Additional dense parallel 2D profiles have been carried out in dipole-dipole array with 0.25 meter electrode spacing and 0.25 meter between adjacent profiles in both direction for higher- resolution subsurface images. We have designed a new field procedure, which used an electrode array fixed in a frame. This facilitates efficient field operation, which comprised 2376 electrode positions. With the quasi 3D imaging, we confirmed the full 3D inversion model but at a much better resolution. In area B, dense parallel 2D profiles were directly used to survey the second target with also 0.25 meter electrode spacing and profiles separation respectively. The same field measurement design has been utilized and comprised 9648 electrode positions in total. The quasi-3D inversion results clearly revealed the main structures of the Roman construction. These ERT inversion results coincided well with the archaeological excavation, which has been done in some parts of this area. The ERT result successfully images parts from the walls and also smaller internal structures of the Roman building.

MPACT Standard Input User s Manual, Version 2.2.0

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

Collins, Benjamin S.; Downar, Thomas; Fitzgerald, Andrew

The MPACT (Michigan PArallel Charactistics based Transport) code is designed to perform high-fidelity light water reactor (LWR) analysis using whole-core pin-resolved neutron transport calculations on modern parallel-computing hardware. The code consists of several libraries which provide the functionality necessary to solve steady-state eigenvalue problems. Several transport capabilities are available within MPACT including both 2-D and 3-D Method of Characteristics (MOC). A three-dimensional whole core solution based on the 2D-1D solution method provides the capability for full core depletion calculations.

Robust Parallel Motion Estimation and Mapping with Stereo Cameras in Underground Infrastructure

NASA Astrophysics Data System (ADS)

Liu, Chun; Li, Zhengning; Zhou, Yuan

2016-06-01

Presently, we developed a novel robust motion estimation method for localization and mapping in underground infrastructure using a pre-calibrated rigid stereo camera rig. Localization and mapping in underground infrastructure is important to safety. Yet it's also nontrivial since most underground infrastructures have poor lighting condition and featureless structure. Overcoming these difficulties, we discovered that parallel system is more efficient than the EKF-based SLAM approach since parallel system divides motion estimation and 3D mapping tasks into separate threads, eliminating data-association problem which is quite an issue in SLAM. Moreover, the motion estimation thread takes the advantage of state-of-art robust visual odometry algorithm which is highly functional under low illumination and provides accurate pose information. We designed and built an unmanned vehicle and used the vehicle to collect a dataset in an underground garage. The parallel system was evaluated by the actual dataset. Motion estimation results indicated a relative position error of 0.3%, and 3D mapping results showed a mean position error of 13cm. Off-line process reduced position error to 2cm. Performance evaluation by actual dataset showed that our system is capable of robust motion estimation and accurate 3D mapping in poor illumination and featureless underground environment.

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

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

Parallel computing of a digital hologram and particle searching for microdigital-holographic particle-tracking velocimetry

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

Satake, Shin-ichi; Kanamori, Hiroyuki; Kunugi, Tomoaki

2007-02-01

We have developed a parallel algorithm for microdigital-holographic particle-tracking velocimetry. The algorithm is used in (1) numerical reconstruction of a particle image computer using a digital hologram, and (2) searching for particles. The numerical reconstruction from the digital hologram makes use of the Fresnel diffraction equation and the FFT (fast Fourier transform),whereas the particle search algorithm looks for local maximum graduation in a reconstruction field represented by a 3D matrix. To achieve high performance computing for both calculations (reconstruction and particle search), two memory partitions are allocated to the 3D matrix. In this matrix, the reconstruction part consists of horizontallymore » placed 2D memory partitions on the x-y plane for the FFT, whereas, the particle search part consists of vertically placed 2D memory partitions set along the z axes.Consequently, the scalability can be obtained for the proportion of processor elements,where the benchmarks are carried out for parallel computation by a SGI Altix machine.« less

Feasibility Study on 3-D Printing of Metallic Structural Materials with Robotized Laser-Based Metal Additive Manufacturing

NASA Astrophysics Data System (ADS)

Ding, Yaoyu; Kovacevic, Radovan

2016-07-01

Metallic structural materials continue to open new avenues in achieving exotic mechanical properties that are naturally unavailable. They hold great potential in developing novel products in diverse industries such as the automotive, aerospace, biomedical, oil and gas, and defense. Currently, the use of metallic structural materials in industry is still limited because of difficulties in their manufacturing. This article studied the feasibility of printing metallic structural materials with robotized laser-based metal additive manufacturing (RLMAM). In this study, two metallic structural materials characterized by an enlarged positive Poisson's ratio and a negative Poisson's ratio were designed and simulated, respectively. An RLMAM system developed at the Research Center for Advanced Manufacturing of Southern Methodist University was used to print them. The results of the tensile tests indicated that the printed samples successfully achieved the corresponding mechanical properties.

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

Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

NASA Astrophysics Data System (ADS)

Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

2016-08-01

This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

Exploiting Multiple Levels of Parallelism in Sparse Matrix-Matrix Multiplication

DOE PAGES

Azad, Ariful; Ballard, Grey; Buluc, Aydin; ...

2016-11-08

Sparse matrix-matrix multiplication (or SpGEMM) is a key primitive for many high-performance graph algorithms as well as for some linear solvers, such as algebraic multigrid. The scaling of existing parallel implementations of SpGEMM is heavily bound by communication. Even though 3D (or 2.5D) algorithms have been proposed and theoretically analyzed in the flat MPI model on Erdös-Rényi matrices, those algorithms had not been implemented in practice and their complexities had not been analyzed for the general case. In this work, we present the first implementation of the 3D SpGEMM formulation that exploits multiple (intranode and internode) levels of parallelism, achievingmore » significant speedups over the state-of-the-art publicly available codes at all levels of concurrencies. We extensively evaluate our implementation and identify bottlenecks that should be subject to further research.« less

Moderately nonlinear diffuse-charge dynamics under an ac voltage.

PubMed

Stout, Robert F; Khair, Aditya S

2015-09-01

The response of a symmetric binary electrolyte between two parallel, blocking electrodes to a moderate amplitude ac voltage is quantified. The diffuse charge dynamics are modeled via the Poisson-Nernst-Planck equations for a dilute solution of point-like ions. The solution to these equations is expressed as a Fourier series with a voltage perturbation expansion for arbitrary Debye layer thickness and ac frequency. Here, the perturbation expansion in voltage proceeds in powers of V_{o}/(k_{B}T/e), where V_{o} is the amplitude of the driving voltage and k_{B}T/e is the thermal voltage with k_{B} as Boltzmann's constant, T as the temperature, and e as the fundamental charge. We show that the response of the electrolyte remains essentially linear in voltage amplitude at frequencies greater than the RC frequency of Debye layer charging, D/λ_{D}L, where D is the ion diffusivity, λ_{D} is the Debye layer thickness, and L is half the cell width. In contrast, nonlinear response is predicted at frequencies below the RC frequency. We find that the ion densities exhibit symmetric deviations from the (uniform) equilibrium density at even orders of the voltage amplitude. This leads to the voltage dependence of the current in the external circuit arising from the odd orders of voltage. For instance, the first nonlinear contribution to the current is O(V_{o}^{3}) which contains the expected third harmonic but also a component oscillating at the applied frequency. We use this to compute a generalized impedance for moderate voltages, the first nonlinear contribution to which is quadratic in V_{o}. This contribution predicts a decrease in the imaginary part of the impedance at low frequency, which is due to the increase in Debye layer capacitance with increasing V_{o}. In contrast, the real part of the impedance increases at low frequency, due to adsorption of neutral salt from the bulk to the Debye layer.

Impact of physical confinement on nuclei geometry and cell division dynamics in 3D spheroids.

PubMed

Desmaison, Annaïck; Guillaume, Ludivine; Triclin, Sarah; Weiss, Pierre; Ducommun, Bernard; Lobjois, Valérie

2018-06-08

Multicellular tumour spheroids are used as a culture model to reproduce the 3D architecture, proliferation gradient and cell interactions of a tumour micro-domain. However, their 3D characterization at the cell scale remains challenging due to size and cell density issues. In this study, we developed a methodology based on 3D light sheet fluorescence microscopy (LSFM) image analysis and convex hull calculation that allows characterizing the 3D shape and orientation of cell nuclei relative to the spheroid surface. By using this technique and optically cleared spheroids, we found that in freely growing spheroids, nuclei display an elongated shape and are preferentially oriented parallel to the spheroid surface. This geometry is lost when spheroids are grown in conditions of physical confinement. Live 3D LSFM analysis of cell division revealed that confined growth also altered the preferential cell division axis orientation parallel to the spheroid surface and induced prometaphase delay. These results provide key information and parameters that help understanding the impact of physical confinement on cell proliferation within tumour micro-domains.

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.

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

Parallel transjugular intrahepatic portosystemic shunt for controlling portal hypertension complications in cirrhotic patients.

PubMed

He, Fu-Liang; Wang, Lei; Yue, Zhen-Dong; Zhao, Hong-Wei; Liu, Fu-Quan

2014-09-07

To evaluate the feasibility of a second parallel transjugular intrahepatic portosystemic shunt (TIPS) to reduce portal venous pressure and control complications of portal hypertension. From January 2011 to December 2012, 10 cirrhotic patients were treated for complications of portal hypertension. The demographic data, operative data, postoperative recovery data, hemodynamic data, and complications were analyzed. Ten patients underwent a primary and parallel TIPS. Technical success rate was 100% with no technical complications. The mean duration of the first operation was 89.20 ± 29.46 min and the second operation was 57.0 ± 12.99 min. The mean portal system pressure decreased from 54.80 ± 4.16 mmHg to 39.0 ± 3.20 mmHg after the primary TIPS and from 44.40 ± 3.95 mmHg to 26.10 ± 4.07 mmHg after the parallel TIPS creation. The mean portosystemic pressure gradient decreased from 43.80 ± 6.18 mmHg to 31.90 ± 2.85 mmHg after the primary TIPS and from 35.60 ± 2.72 mmHg to 15.30 ± 3.27 mmHg after the parallel TIPS creation. Clinical improvement was seen in all patients after the parallel TIPS creation. One patient suffered from transient grade I hepatic encephalopathy (HE) after the primary TIPS and four patients experienced transient grade I-II after the parallel TIPS procedure. Mean hospital stay after the first and second operations were 15.0 ± 3.71 d and 16.90 ± 5.11 d (P = 0.014), respectively. After a mean 14.0 ± 3.13 mo follow-up, ascites and bleeding were well controlled and no stenosis of the stents was found. Parallel TIPS is an effective approach for controlling portal hypertension complications.

Implementation of parallel transmit beamforming using orthogonal frequency division multiplexing--achievable resolution and interbeam interference.

PubMed

Demi, Libertario; Viti, Jacopo; Kusters, Lieneke; Guidi, Francesco; Tortoli, Piero; Mischi, Massimo

2013-11-01

The speed of sound in the human body limits the achievable data acquisition rate of pulsed ultrasound scanners. To overcome this limitation, parallel beamforming techniques are used in ultrasound 2-D and 3-D imaging systems. Different parallel beamforming approaches have been proposed. They may be grouped into two major categories: parallel beamforming in reception and parallel beamforming in transmission. The first category is not optimal for harmonic imaging; the second category may be more easily applied to harmonic imaging. However, inter-beam interference represents an issue. To overcome these shortcomings and exploit the benefit of combining harmonic imaging and high data acquisition rate, a new approach has been recently presented which relies on orthogonal frequency division multiplexing (OFDM) to perform parallel beamforming in transmission. In this paper, parallel transmit beamforming using OFDM is implemented for the first time on an ultrasound scanner. An advanced open platform for ultrasound research is used to investigate the axial resolution and interbeam interference achievable with parallel transmit beamforming using OFDM. Both fundamental and second-harmonic imaging modalities have been considered. Results show that, for fundamental imaging, axial resolution in the order of 2 mm can be achieved in combination with interbeam interference in the order of -30 dB. For second-harmonic imaging, axial resolution in the order of 1 mm can be achieved in combination with interbeam interference in the order of -35 dB.

Laplace-domain waveform modeling and inversion for the 3D acoustic-elastic coupled media

NASA Astrophysics Data System (ADS)

Shin, Jungkyun; Shin, Changsoo; Calandra, Henri

2016-06-01

Laplace-domain waveform inversion reconstructs long-wavelength subsurface models by using the zero-frequency component of damped seismic signals. Despite the computational advantages of Laplace-domain waveform inversion over conventional frequency-domain waveform inversion, an acoustic assumption and an iterative matrix solver have been used to invert 3D marine datasets to mitigate the intensive computing cost. In this study, we develop a Laplace-domain waveform modeling and inversion algorithm for 3D acoustic-elastic coupled media by using a parallel sparse direct solver library (MUltifrontal Massively Parallel Solver, MUMPS). We precisely simulate a real marine environment by coupling the 3D acoustic and elastic wave equations with the proper boundary condition at the fluid-solid interface. In addition, we can extract the elastic properties of the Earth below the sea bottom from the recorded acoustic pressure datasets. As a matrix solver, the parallel sparse direct solver is used to factorize the non-symmetric impedance matrix in a distributed memory architecture and rapidly solve the wave field for a number of shots by using the lower and upper matrix factors. Using both synthetic datasets and real datasets obtained by a 3D wide azimuth survey, the long-wavelength component of the P-wave and S-wave velocity models is reconstructed and the proposed modeling and inversion algorithm are verified. A cluster of 80 CPU cores is used for this study.

Unique Zigzag-Shaped Buckling Zn2C Monolayer with Strain-Tunable Band Gap and Negative Poisson Ratio.

PubMed

Meng, Lingbiao; Zhang, Yingjuan; Zhou, Minjie; Zhang, Jicheng; Zhou, Xiuwen; Ni, Shuang; Wu, Weidong

2018-02-19

Designing new materials with reduced dimensionality and distinguished properties has continuously attracted intense interest for materials innovation. Here we report a novel two-dimensional (2D) Zn 2 C monolayer nanomaterial with exceptional structure and properties by means of first-principles calculations. This new Zn 2 C monolayer is composed of quasi-tetrahedral tetracoordinate carbon and quasi-linear bicoordinate zinc, featuring a peculiar zigzag-shaped buckling configuration. The unique coordinate topology endows this natural 2D semiconducting monolayer with strongly strain tunable band gap and unusual negative Poisson ratios. The monolayer has good dynamic and thermal stabilities and is also the lowest-energy structure of 2D space indicated by the particle-swarm optimization (PSO) method, implying its synthetic feasibility. With these intriguing properties the material may find applications in nanoelectronics and micromechanics.

Raytracing and Direct-Drive Targets

NASA Astrophysics Data System (ADS)

Schmitt, Andrew J.; Bates, Jason; Fyfe, David; Eimerl, David

2013-10-01

Accurate simulation of the effects of laser imprinting and drive asymmetries in directly driven targets requires the ability to distinguish between raytrace noise and the intensity structure produced by the spatial and temporal incoherence of optical smoothing. We have developed and implemented a smoother raytrace algorithm for our mpi-parallel radiation hydrodynamics code, FAST3D. The underlying approach is to connect the rays into either sheets (in 2D) or volume-enclosing chunks (in 3D) so that the absorbed energy distribution continuously covers the propagation area illuminated by the laser. We will describe the status and show the different scalings encountered in 2D and 3D problems as the computational size, parallelization strategy, and number of rays is varied. Finally, we show results using the method in current NIKE experimental target simulations and in proposed symmetric and polar direct-drive target designs. Supported by US DoE/NNSA.

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

MHD Code Optimizations and Jets in Dense Gaseous Halos

NASA Astrophysics Data System (ADS)

Gaibler, Volker; Vigelius, Matthias; Krause, Martin; Camenzind, Max

We have further optimized and extended the 3D-MHD-code NIRVANA. The magnetized part runs in parallel, reaching 19 Gflops per SX-6 node, and has a passively advected particle population. In addition, the code is MPI-parallel now - on top of the shared memory parallelization. On a 512^3 grid, we reach 561 Gflops with 32 nodes on the SX-8. Also, we have successfully used FLASH on the Opteron cluster. Scientific results are preliminary so far. We report one computation of highly resolved cocoon turbulence. While we find some similarities to earlier 2D work by us and others, we note a strange reluctancy of cold material to enter the low density cocoon, which has to be investigated further.

Compound Poisson Law for Hitting Times to Periodic Orbits in Two-Dimensional Hyperbolic Systems

NASA Astrophysics Data System (ADS)

Carney, Meagan; Nicol, Matthew; Zhang, Hong-Kun

2017-11-01

We show that a compound Poisson distribution holds for scaled exceedances of observables φ uniquely maximized at a periodic point ζ in a variety of two-dimensional hyperbolic dynamical systems with singularities (M,T,μ ), including the billiard maps of Sinai dispersing billiards in both the finite and infinite horizon case. The observable we consider is of form φ (z)=-ln d(z,ζ ) where d is a metric defined in terms of the stable and unstable foliation. The compound Poisson process we obtain is a Pólya-Aeppli distibution of index θ . We calculate θ in terms of the derivative of the map T. Furthermore if we define M_n=\\max {φ ,\\ldots ,φ circ T^n} and u_n (τ ) by \\lim _{n→ ∞} nμ (φ >u_n (τ ) )=τ the maximal process satisfies an extreme value law of form μ (M_n ≤ u_n)=e^{-θ τ }. These results generalize to a broader class of functions maximized at ζ , though the formulas regarding the parameters in the distribution need to be modified.

Specialized Computer Systems for Environment Visualization

NASA Astrophysics Data System (ADS)

Al-Oraiqat, Anas M.; Bashkov, Evgeniy A.; Zori, Sergii A.

2018-06-01

The need for real time image generation of landscapes arises in various fields as part of tasks solved by virtual and augmented reality systems, as well as geographic information systems. Such systems provide opportunities for collecting, storing, analyzing and graphically visualizing geographic data. Algorithmic and hardware software tools for increasing the realism and efficiency of the environment visualization in 3D visualization systems are proposed. This paper discusses a modified path tracing algorithm with a two-level hierarchy of bounding volumes and finding intersections with Axis-Aligned Bounding Box. The proposed algorithm eliminates the branching and hence makes the algorithm more suitable to be implemented on the multi-threaded CPU and GPU. A modified ROAM algorithm is used to solve the qualitative visualization of reliefs' problems and landscapes. The algorithm is implemented on parallel systems—cluster and Compute Unified Device Architecture-networks. Results show that the implementation on MPI clusters is more efficient than Graphics Processing Unit/Graphics Processing Clusters and allows real-time synthesis. The organization and algorithms of the parallel GPU system for the 3D pseudo stereo image/video synthesis are proposed. With realizing possibility analysis on a parallel GPU-architecture of each stage, 3D pseudo stereo synthesis is performed. An experimental prototype of a specialized hardware-software system 3D pseudo stereo imaging and video was developed on the CPU/GPU. The experimental results show that the proposed adaptation of 3D pseudo stereo imaging to the architecture of GPU-systems is efficient. Also it accelerates the computational procedures of 3D pseudo-stereo synthesis for the anaglyph and anamorphic formats of the 3D stereo frame without performing optimization procedures. The acceleration is on average 11 and 54 times for test GPUs.

A parallel algorithm for the two-dimensional time fractional diffusion equation with implicit difference method.

PubMed

Gong, Chunye; Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie

2014-01-01

It is very time consuming to solve fractional differential equations. The computational complexity of two-dimensional fractional differential equation (2D-TFDE) with iterative implicit finite difference method is O(M(x)M(y)N(2)). In this paper, we present a parallel algorithm for 2D-TFDE and give an in-depth discussion about this algorithm. A task distribution model and data layout with virtual boundary are designed for this parallel algorithm. The experimental results show that the parallel algorithm compares well with the exact solution. The parallel algorithm on single Intel Xeon X5540 CPU runs 3.16-4.17 times faster than the serial algorithm on single CPU core. The parallel efficiency of 81 processes is up to 88.24% compared with 9 processes on a distributed memory cluster system. We do think that the parallel computing technology will become a very basic method for the computational intensive fractional applications in the near future.

Relationship among physical activity, smoking, drinking and clustering of the metabolic syndrome diagnostic components.

PubMed

Katano, Sayuri; Nakamura, Yasuyuki; Nakamura, Aki; Murakami, Yoshitaka; Tanaka, Taichiro; Nakagawa, Hideaki; Takebayashi, Toru; Yamato, Hiroshi; Okayama, Akira; Miura, Katsuyuki; Okamura, Tomonori; Ueshima, Hirotsugu

2010-06-30

To examine the relation between lifestyle and the number of metabolic syndrome (MetS) diagnostic components in a general population, and to find a means of preventing the development of MetS components. We examined baseline data from 3,365 participants (2,714 men and 651 women) aged 19 to 69 years who underwent a physical examination, lifestyle survey, and blood chemical examination. The physical activity of each participant was classified according to the International Physical Activity Questionnaire (IPAQ). We defined four components for MetS in this study as follows: 1) high BP: systolic BP > or = 130 mmHg or diastolic BP > or = 85 mmHg, or the use of antihypertensive drugs; 2) dyslipidemia: high-density lipoprotein-cholesterol concentration < 40 mg/dL, triglycerides concentration > or = 150 mg/dL, or on medication for dyslipidemia; 3) Impaired glucose tolerance: fasting blood sugar level > or = 110 mg/d, or if less than 8 hours after meals > or = 140 mg/dL), or on medication for diabetes mellitus; 4) obesity: body mass index > or = 25 kg/m(2). Those who had 0 to 4 MetS diagnostic components accounted for 1,726, 949, 484, 190, and 16 participants, respectively, in the Poisson distribution. Poisson regression analysis revealed that independent factors contributing to the number of MetS diagnostic components were being male (regression coefficient b=0.600, p < 0.01), age (b=0.027, p < 0.01), IPAQ class (b=-0.272, p= 0.03), and alcohol consumption (b=0.020, p=0.01). The contribution of current smoking was not statistically significant (b=-0.067, p=0.76). Moderate physical activity was inversely associated with the number of MetS diagnostic components, whereas smoking was not associated.

Methodes iteratives paralleles: Applications en neutronique et en mecanique des fluides

NASA Astrophysics Data System (ADS)

Qaddouri, Abdessamad

Dans cette these, le calcul parallele est applique successivement a la neutronique et a la mecanique des fluides. Dans chacune de ces deux applications, des methodes iteratives sont utilisees pour resoudre le systeme d'equations algebriques resultant de la discretisation des equations du probleme physique. Dans le probleme de neutronique, le calcul des matrices des probabilites de collision (PC) ainsi qu'un schema iteratif multigroupe utilisant une methode inverse de puissance sont parallelises. Dans le probleme de mecanique des fluides, un code d'elements finis utilisant un algorithme iteratif du type GMRES preconditionne est parallelise. Cette these est presentee sous forme de six articles suivis d'une conclusion. Les cinq premiers articles traitent des applications en neutronique, articles qui representent l'evolution de notre travail dans ce domaine. Cette evolution passe par un calcul parallele des matrices des PC et un algorithme multigroupe parallele teste sur un probleme unidimensionnel (article 1), puis par deux algorithmes paralleles l'un mutiregion l'autre multigroupe, testes sur des problemes bidimensionnels (articles 2--3). Ces deux premieres etapes sont suivies par l'application de deux techniques d'acceleration, le rebalancement neutronique et la minimisation du residu aux deux algorithmes paralleles (article 4). Finalement, on a mis en oeuvre l'algorithme multigroupe et le calcul parallele des matrices des PC sur un code de production DRAGON ou les tests sont plus realistes et peuvent etre tridimensionnels (article 5). Le sixieme article (article 6), consacre a l'application a la mecanique des fluides, traite la parallelisation d'un code d'elements finis FES ou le partitionneur de graphe METIS et la librairie PSPARSLIB sont utilises.

Parallel PAB3D: Experiences with a Prototype in MPI

NASA Technical Reports Server (NTRS)

Guerinoni, Fabio; Abdol-Hamid, Khaled S.; Pao, S. Paul

1998-01-01

PAB3D is a three-dimensional Navier Stokes solver that has gained acceptance in the research and industrial communities. It takes as computational domain, a set disjoint blocks covering the physical domain. This is the first report on the implementation of PAB3D using the Message Passing Interface (MPI), a standard for parallel processing. We discuss briefly the characteristics of tile code and define a prototype for testing. The principal data structure used for communication is derived from preprocessing "patching". We describe a simple interface (COMMSYS) for MPI communication, and some general techniques likely to be encountered when working on problems of this nature. Last, we identify levels of improvement from the current version and outline future work.

Fast precalculated triangular mesh algorithm for 3D binary computer-generated holograms.

PubMed

Yang, Fan; Kaczorowski, Andrzej; Wilkinson, Tim D

2014-12-10

A new method for constructing computer-generated holograms using a precalculated triangular mesh is presented. The speed of calculation can be increased dramatically by exploiting both the precalculated base triangle and GPU parallel computing. Unlike algorithms using point-based sources, this method can reconstruct a more vivid 3D object instead of a "hollow image." In addition, there is no need to do a fast Fourier transform for each 3D element every time. A ferroelectric liquid crystal spatial light modulator is used to display the binary hologram within our experiment and the hologram of a base right triangle is produced by utilizing just a one-step Fourier transform in the 2D case, which can be expanded to the 3D case by multiplying by a suitable Fresnel phase plane. All 3D holograms generated in this paper are based on Fresnel propagation; thus, the Fresnel plane is treated as a vital element in producing the hologram. A GeForce GTX 770 graphics card with 2 GB memory is used to achieve parallel computing.

Parallelized Three-Dimensional Resistivity Inversion Using Finite Elements And Adjoint State Methods

NASA Astrophysics Data System (ADS)

Schaa, Ralf; Gross, Lutz; Du Plessis, Jaco

2015-04-01

The resistivity method is one of the oldest geophysical exploration methods, which employs one pair of electrodes to inject current into the ground and one or more pairs of electrodes to measure the electrical potential difference. The potential difference is a non-linear function of the subsurface resistivity distribution described by an elliptic partial differential equation (PDE) of the Poisson type. Inversion of measured potentials solves for the subsurface resistivity represented by PDE coefficients. With increasing advances in multichannel resistivity acquisition systems (systems with more than 60 channels and full waveform recording are now emerging), inversion software require efficient storage and solver algorithms. We developed the finite element solver Escript, which provides a user-friendly programming environment in Python to solve large-scale PDE-based problems (see https://launchpad.net/escript-finley). Using finite elements, highly irregular shaped geology and topography can readily be taken into account. For the 3D resistivity problem, we have implemented the secondary potential approach, where the PDE is decomposed into a primary potential caused by the source current and the secondary potential caused by changes in subsurface resistivity. The primary potential is calculated analytically, and the boundary value problem for the secondary potential is solved using nodal finite elements. This approach removes the singularity caused by the source currents and provides more accurate 3D resistivity models. To solve the inversion problem we apply a 'first optimize then discretize' approach using the quasi-Newton scheme in form of the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) method (see Gross & Kemp 2013). The evaluation of the cost function requires the solution of the secondary potential PDE for each source current and the solution of the corresponding adjoint-state PDE for the cost function gradients with respect to the subsurface resistivity. The Hessian of the regularization term is used as preconditioner which requires an additional PDE solution in each iteration step. As it turns out, the relevant PDEs are naturally formulated in the finite element framework. Using the domain decomposition method provided in Escript, the inversion scheme has been parallelized for distributed memory computers with multi-core shared memory nodes. We show numerical examples from simple layered models to complex 3D models and compare with the results from other methods. The inversion scheme is furthermore tested on a field data example to characterise localised freshwater discharge in a coastal environment.. References: L. Gross and C. Kemp (2013) Large Scale Joint Inversion of Geophysical Data using the Finite Element Method in escript. ASEG Extended Abstracts 2013, http://dx.doi.org/10.1071/ASEG2013ab306

Poisson's ratio model derived from P- and S-wave reflection seismic data at the CO2CRC Otway Project pilot site, Australia

NASA Astrophysics Data System (ADS)

Beilecke, Thies; Krawczyk, Charlotte M.; Tanner, David C.; Ziesch, Jennifer; Research Group Protect

2014-05-01

Compressional wave (P-wave) reflection seismic field measurements are a standard tool for subsurface exploration. 2-D seismic measurements are often used for overview measurements, but also as near-surface supplement to fill gaps that often exist in 3-D seismic data sets. Such supplementing 2-D measurements are typically simple with respect to field layout. This is an opportunity for the use of shear waves (S-waves). Within the last years, S-waves have become more and more important. One reason is that P- and S-waves are differently sensitive to fluids and pore fill so that the additional S-wave information can be used to enhance lithological studies. Another reason is that S-waves have the advantage of higher spatial resolution. Within the same signal bandwidth they typically have about half the wavelength of P-waves. In near-surface unconsolidated sediments they can even enhance the structural resolution by one order of magnitude. We make use of these capabilities within the PROTECT project. In addition to already existing 2-D P-wave data, we carried out a near surface 2-D S-wave field survey at the CO2CRC Otway Project pilot site, close to Warrnambool, Australia in November 2013. The combined analysis of P-wave and S-wave data is used to construct a Poisson's Ratio 2-D model down to roughly 600 m depth. The Poisson's ratio values along a 1 km long profile at the site are surprisingly high, ranging from 0.47 in the carbonate-dominated near surface to 0.4 at depth. In the literature, average lab measurements of 0.22 for unfissured carbonates and 0.37 for fissured examples have been reported. The high values that we found may indicate areas of rather unconsolidated or fractured material, or enhanced fluid contents, and will be subject of further studies. This work is integrated in a larger workflow towards prediction of CO2 leakage and monitoring strategies for subsurface storage in general. Acknowledgement: This work was sponsored in part by the Australian Commonwealth Government through the Cooperative Research Centre for Greenhouse Gas Technologies (CO2CRC). PROTECT is funded through the Geotechnologien research programme in Germany (grant 03G0797).

Time domain topology optimization of 3D nanophotonic devices

NASA Astrophysics Data System (ADS)

Elesin, Y.; Lazarov, B. S.; Jensen, J. S.; Sigmund, O.

2014-02-01

We present an efficient parallel topology optimization framework for design of large scale 3D nanophotonic devices. The code shows excellent scalability and is demonstrated for optimization of broadband frequency splitter, waveguide intersection, photonic crystal-based waveguide and nanowire-based waveguide. The obtained results are compared to simplified 2D studies and we demonstrate that 3D topology optimization may lead to significant performance improvements.

3-D modeling of ductile tearing using finite elements: Computational aspects and techniques

NASA Astrophysics Data System (ADS)

Gullerud, Arne Stewart

This research focuses on the development and application of computational tools to perform large-scale, 3-D modeling of ductile tearing in engineering components under quasi-static to mild loading rates. Two standard models for ductile tearing---the computational cell methodology and crack growth controlled by the crack tip opening angle (CTOA)---are described and their 3-D implementations are explored. For the computational cell methodology, quantification of the effects of several numerical issues---computational load step size, procedures for force release after cell deletion, and the porosity for cell deletion---enables construction of computational algorithms to remove the dependence of predicted crack growth on these issues. This work also describes two extensions of the CTOA approach into 3-D: a general 3-D method and a constant front technique. Analyses compare the characteristics of the extensions, and a validation study explores the ability of the constant front extension to predict crack growth in thin aluminum test specimens over a range of specimen geometries, absolutes sizes, and levels of out-of-plane constraint. To provide a computational framework suitable for the solution of these problems, this work also describes the parallel implementation of a nonlinear, implicit finite element code. The implementation employs an explicit message-passing approach using the MPI standard to maintain portability, a domain decomposition of element data to provide parallel execution, and a master-worker organization of the computational processes to enhance future extensibility. A linear preconditioned conjugate gradient (LPCG) solver serves as the core of the solution process. The parallel LPCG solver utilizes an element-by-element (EBE) structure of the computations to permit a dual-level decomposition of the element data: domain decomposition of the mesh provides efficient coarse-grain parallel execution, while decomposition of the domains into blocks of similar elements (same type, constitutive model, etc.) provides fine-grain parallel computation on each processor. A major focus of the LPCG solver is a new implementation of the Hughes-Winget element-by-element (HW) preconditioner. The implementation employs a weighted dependency graph combined with a new coloring algorithm to provide load-balanced scheduling for the preconditioner and overlapped communication/computation. This approach enables efficient parallel application of the HW preconditioner for arbitrary unstructured meshes.

Three-dimensional ionic conduction in the strained electrolytes of solid oxide fuel cells

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

Han, Yupei; Zou, Minda; Lv, Weiqiang

2016-05-07

Flexible power sources including fuel cells and batteries are the key to realizing flexible electronic devices with pronounced foldability. To understand the bending effects in these devices, theoretical analysis on three-dimensional (3-D) lattice bending is necessary. In this report, we derive a 3-D analytical model to analyze the effects of electrolyte crystal bending on ionic conductivity in flexible solid-state batteries/fuel cells. By employing solid oxide fuel cells as a materials' platform, the intrinsic parameters of bent electrolyte materials, including lattice constant, Young's modulus, and Poisson ratio, are evaluated. Our work facilitates the rational design of highly efficient flexible electrolytes formore » high-performance flexible device applications.« less

A fully parallel in time and space algorithm for simulating the electrical activity of a neural tissue.

PubMed

Bedez, Mathieu; Belhachmi, Zakaria; Haeberlé, Olivier; Greget, Renaud; Moussaoui, Saliha; Bouteiller, Jean-Marie; Bischoff, Serge

2016-01-15

The resolution of a model describing the electrical activity of neural tissue and its propagation within this tissue is highly consuming in term of computing time and requires strong computing power to achieve good results. In this study, we present a method to solve a model describing the electrical propagation in neuronal tissue, using parareal algorithm, coupling with parallelization space using CUDA in graphical processing unit (GPU). We applied the method of resolution to different dimensions of the geometry of our model (1-D, 2-D and 3-D). The GPU results are compared with simulations from a multi-core processor cluster, using message-passing interface (MPI), where the spatial scale was parallelized in order to reach a comparable calculation time than that of the presented method using GPU. A gain of a factor 100 in term of computational time between sequential results and those obtained using the GPU has been obtained, in the case of 3-D geometry. Given the structure of the GPU, this factor increases according to the fineness of the geometry used in the computation. To the best of our knowledge, it is the first time such a method is used, even in the case of neuroscience. Parallelization time coupled with GPU parallelization space allows for drastically reducing computational time with a fine resolution of the model describing the propagation of the electrical signal in a neuronal tissue. Copyright © 2015 Elsevier B.V. All rights reserved.

Transport Equation Based Wall Distance Computations Aimed at Flows With Time-Dependent Geometry

NASA Technical Reports Server (NTRS)

Tucker, Paul G.; Rumsey, Christopher L.; Bartels, Robert E.; Biedron, Robert T.

2003-01-01

Eikonal, Hamilton-Jacobi and Poisson equations can be used for economical nearest wall distance computation and modification. Economical computations may be especially useful for aeroelastic and adaptive grid problems for which the grid deforms, and the nearest wall distance needs to be repeatedly computed. Modifications are directed at remedying turbulence model defects. For complex grid structures, implementation of the Eikonal and Hamilton-Jacobi approaches is not straightforward. This prohibits their use in industrial CFD solvers. However, both the Eikonal and Hamilton-Jacobi equations can be written in advection and advection-diffusion forms, respectively. These, like the Poisson s Laplacian, are commonly occurring industrial CFD solver elements. Use of the NASA CFL3D code to solve the Eikonal and Hamilton-Jacobi equations in advective-based forms is explored. The advection-based distance equations are found to have robust convergence. Geometries studied include single and two element airfoils, wing body and double delta configurations along with a complex electronics system. It is shown that for Eikonal accuracy, upwind metric differences are required. The Poisson approach is found effective and, since it does not require offset metric evaluations, easiest to implement. The sensitivity of flow solutions to wall distance assumptions is explored. Generally, results are not greatly affected by wall distance traits.

Transport Equation Based Wall Distance Computations Aimed at Flows With Time-Dependent Geometry

NASA Technical Reports Server (NTRS)

Tucker, Paul G.; Rumsey, Christopher L.; Bartels, Robert E.; Biedron, Robert T.

2003-01-01

Eikonal, Hamilton-Jacobi and Poisson equations can be used for economical nearest wall distance computation and modification. Economical computations may be especially useful for aeroelastic and adaptive grid problems for which the grid deforms, and the nearest wall distance needs to be repeatedly computed. Modifications are directed at remedying turbulence model defects. For complex grid structures, implementation of the Eikonal and Hamilton-Jacobi approaches is not straightforward. This prohibits their use in industrial CFD solvers. However, both the Eikonal and Hamilton-Jacobi equations can be written in advection and advection-diffusion forms, respectively. These, like the Poisson's Laplacian, are commonly occurring industrial CFD solver elements. Use of the NASA CFL3D code to solve the Eikonal and Hamilton-Jacobi equations in advective-based forms is explored. The advection-based distance equations are found to have robust convergence. Geometries studied include single and two element airfoils, wing body and double delta configurations along with a complex electronics system. It is shown that for Eikonal accuracy, upwind metric differences are required. The Poisson approach is found effective and, since it does not require offset metric evaluations, easiest to implement. The sensitivity of flow solutions to wall distance assumptions is explored. Generally, results are not greatly affected by wall distance traits.

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 CARLOS-3D code development

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

Putnam, J.M.; Kotulski, J.D.

1996-02-01

CARLOS-3D is a three-dimensional scattering code which was developed under the sponsorship of the Electromagnetic Code Consortium, and is currently used by over 80 aerospace companies and government agencies. The code has been extensively validated and runs on both serial workstations and parallel super computers such as the Intel Paragon. CARLOS-3D is a three-dimensional surface integral equation scattering code based on a Galerkin method of moments formulation employing Rao- Wilton-Glisson roof-top basis for triangular faceted surfaces. Fully arbitrary 3D geometries composed of multiple conducting and homogeneous bulk dielectric materials can be modeled. This presentation describes some of the extensions tomore » the CARLOS-3D code, and how the operator structure of the code facilitated these improvements. Body of revolution (BOR) and two-dimensional geometries were incorporated by simply including new input routines, and the appropriate Galerkin matrix operator routines. Some additional modifications were required in the combined field integral equation matrix generation routine due to the symmetric nature of the BOR and 2D operators. Quadrilateral patched surfaces with linear roof-top basis functions were also implemented in the same manner. Quadrilateral facets and triangular facets can be used in combination to more efficiently model geometries with both large smooth surfaces and surfaces with fine detail such as gaps and cracks. Since the parallel implementation in CARLOS-3D is at high level, these changes were independent of the computer platform being used. This approach minimizes code maintenance, while providing capabilities with little additional effort. Results are presented showing the performance and accuracy of the code for some large scattering problems. Comparisons between triangular faceted and quadrilateral faceted geometry representations will be shown for some complex scatterers.« less

Methods for analyzing matched designs with double controls: excess risk is easily estimated and misinterpreted when evaluating traffic deaths.

PubMed

Redelmeier, Donald A; Tibshirani, Robert J

2018-06-01

To demonstrate analytic approaches for matched studies where two controls are linked to each case and events are accumulating counts rather than binary outcomes. A secondary intent is to clarify the distinction between total risk and excess risk (unmatched vs. matched perspectives). We review past research testing whether elections can lead to increased traffic risks. The results are reinterpreted by analyzing both the total count of individuals in fatal crashes and the excess count of individuals in fatal crashes, each time accounting for the matched double controls. Overall, 1,546 individuals were in fatal crashes on the 10 election days (average = 155/d), and 2,593 individuals were in fatal crashes on the 20 control days (average = 130/d). Poisson regression of total counts yielded a relative risk of 1.19 (95% confidence interval: 1.12-1.27). Poisson regression of excess counts yielded a relative risk of 3.22 (95% confidence interval: 2.72-3.80). The discrepancy between analyses of total counts and excess counts replicated with alternative statistical models and was visualized in graphical displays. Available approaches provide methods for analyzing count data in matched designs with double controls and help clarify the distinction between increases in total risk and increases in excess risk. Copyright © 2018 Elsevier Inc. All rights reserved.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

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.

Progress on the Multiphysics Capabilities of the Parallel Electromagnetic ACE3P Simulation Suite

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

Kononenko, Oleksiy

2015-03-26

ACE3P is a 3D parallel simulation suite that is being developed at SLAC National Accelerator Laboratory. Effectively utilizing supercomputer resources, ACE3P has become a key tool for the coupled electromagnetic, thermal and mechanical research and design of particle accelerators. Based on the existing finite-element infrastructure, a massively parallel eigensolver is developed for modal analysis of mechanical structures. It complements a set of the multiphysics tools in ACE3P and, in particular, can be used for the comprehensive study of microphonics in accelerating cavities ensuring the operational reliability of a particle accelerator.

Parallel Directionally Split Solver Based on Reformulation of Pipelined Thomas Algorithm

NASA Technical Reports Server (NTRS)

Povitsky, A.

1998-01-01

In this research an efficient parallel algorithm for 3-D directionally split problems is developed. The proposed algorithm is based on a reformulated version of the pipelined Thomas algorithm that starts the backward step computations immediately after the completion of the forward step computations for the first portion of lines This algorithm has data available for other computational tasks while processors are idle from the Thomas algorithm. The proposed 3-D directionally split solver is based on the static scheduling of processors where local and non-local, data-dependent and data-independent computations are scheduled while processors are idle. A theoretical model of parallelization efficiency is used to define optimal parameters of the algorithm, to show an asymptotic parallelization penalty and to obtain an optimal cover of a global domain with subdomains. It is shown by computational experiments and by the theoretical model that the proposed algorithm reduces the parallelization penalty about two times over the basic algorithm for the range of the number of processors (subdomains) considered and the number of grid nodes per subdomain.

F3D Image Processing and Analysis for Many - and Multi-core Platforms

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

F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expeditesmore » any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element. This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.« less

Interpretation of deep directional resistivity measurements acquired in high-angle and horizontal wells using 3-D inversion

NASA Astrophysics Data System (ADS)

Puzyrev, Vladimir; Torres-Verdín, Carlos; Calo, Victor

2018-05-01

The interpretation of resistivity measurements acquired in high-angle and horizontal wells is a critical technical problem in formation evaluation. We develop an efficient parallel 3-D inversion method to estimate the spatial distribution of electrical resistivity in the neighbourhood of a well from deep directional electromagnetic induction measurements. The methodology places no restriction on the spatial distribution of the electrical resistivity around arbitrary well trajectories. The fast forward modelling of triaxial induction measurements performed with multiple transmitter-receiver configurations employs a parallel direct solver. The inversion uses a pre-conditioned gradient-based method whose accuracy is improved using the Wolfe conditions to estimate optimal step lengths at each iteration. The large transmitter-receiver offsets, used in the latest generation of commercial directional resistivity tools, improve the depth of investigation to over 30 m from the wellbore. Several challenging synthetic examples confirm the feasibility of the full 3-D inversion-based interpretations for these distances, hence enabling the integration of resistivity measurements with seismic amplitude data to improve the forecast of the petrophysical and fluid properties. Employing parallel direct solvers for the triaxial induction problems allows for large reductions in computational effort, thereby opening the possibility to invert multiposition 3-D data in practical CPU times.

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.

Application of Parallel Time-Implicit Discontinuous Galerkin Finite Element Methods to Hypersonic Nonequilibrium Flow Problems

DTIC Science & Technology

2014-05-01

heating prediction to grid alignment along the shock . . . . . . . . 36 1-12 Large variation in heating predictions for 3D hypersonic flow over cylinder...100 4-12 Taylor Vortex problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 4-13 Taylor Vortex problem: 3D ...149 6-16 3D contours for temperature, T for MIG and US3D for only O2 test case . . . . 150 6-17 Stagnation line plots for only

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin.

PubMed

Ghanta, Sindhu; Jordan, Michael I; Kose, Kivanc; Brooks, Dana H; Rajadhyaksha, Milind; Dy, Jennifer G

2017-01-01

Segmenting objects of interest from 3D data sets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution, and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, the shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance, and unknown locations. The driving application that inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear, and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease, and cancer usually start. Detecting the DEJ is challenging, because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped "peaks and valleys." In addition, RCM imaging resolution, contrast, and intensity vary with depth. Thus, a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10- 20 μm .

A Marked Poisson Process Driven Latent Shape Model for 3D Segmentation of Reflectance Confocal Microscopy Image Stacks of Human Skin

PubMed Central

Ghanta, Sindhu; Jordan, Michael I.; Kose, Kivanc; Brooks, Dana H.; Rajadhyaksha, Milind; Dy, Jennifer G.

2016-01-01

Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging. To address such complex segmentation problems, we propose a unified probabilistic framework that can incorporate the uncertainty associated with complex shapes, variable appearance and unknown locations. The driving application which inspired the development of this framework is a biologically important segmentation problem: the task of automatically detecting and segmenting the dermal-epidermal junction (DEJ) in 3D reflectance confocal microscopy (RCM) images of human skin. RCM imaging allows noninvasive observation of cellular, nuclear and morphological detail. The DEJ is an important morphological feature as it is where disorder, disease and cancer usually start. Detecting the DEJ is challenging because it is a 2D surface in a 3D volume which has strong but highly variable number of irregularly spaced and variably shaped “peaks and valleys”. In addition, RCM imaging resolution, contrast and intensity vary with depth. Thus a prior model needs to incorporate the intrinsic structure while allowing variability in essentially all its parameters. We propose a model which can incorporate objects of interest with complex shapes and variable appearance in an unsupervised setting by utilizing domain knowledge to build appropriate priors of the model. Our novel strategy to model this structure combines a spatial Poisson process with shape priors and performs inference using Gibbs sampling. Experimental results show that the proposed unsupervised model is able to automatically detect the DEJ with physiologically relevant accuracy in the range 10 – 20µm. PMID:27723590

The limits of hamiltonian structures in three-dimensional elasticity, shells, and rods

NASA Astrophysics Data System (ADS)

Ge, Z.; Kruse, H. P.; Marsden, J. E.

1996-01-01

This paper uses Hamiltonian structures to study the problem of the limit of three-dimensional (3D) elastic models to shell and rod models. In the case of shells, we show that the Hamiltonian structure for a three-dimensional elastic body converges, in a sense made precise, to that for a shell model described by a one-director Cosserat surface as the thickness goes to zero. We study limiting procedures that give rise to unconstrained as well as constrained Cosserat director models. The case of a rod is also considered and similar convergence results are established, with the limiting model being a geometrically exact director rod model (in the framework developed by Antman, Simo, and coworkers). The resulting model may or may not have constraints, depending on the nature of the constitutive relations and their behavior under the limiting procedure. The closeness of Hamiltonian structures is measured by the closeness of Poisson brackets on certain classes of functions, as well as the Hamiltonians. This provides one way of justifying the dynamic one-director model for shells. Another way of stating the convergence result is that there is an almost-Poisson embedding from the phase space of the shell to the phase space of the 3D elastic body, which implies that, in the sense of Hamiltonian structures, the dynamics of the elastic body is close to that of the shell. The constitutive equations of the 3D model and their behavior as the thickness tends to zero dictates whether the limiting 2D model is a constrained or an unconstrained director model. We apply our theory in the specific case of a 3D Saint Venant-Kirchhoff material and derive the corresponding limiting shell and rod theories. The limiting shell model is an interesting Kirchhoff-like shell model in which the stored energy function is explicitly derived in terms of the shell curvature. For rods, one gets (with an additional inextensibility constraint) a one-director Kirchhoff elastic rod model, which reduces to the well-known Euler elastica if one adds an additional single constraint that the director lines up with the Frenet frame.

Three-dimensional vectorial multifocal arrays created by pseudo-period encoding

NASA Astrophysics Data System (ADS)

Zeng, Tingting; Chang, Chenliang; Chen, Zhaozhong; Wang, Hui-Tian; Ding, Jianping

2018-06-01

Multifocal arrays have been attracting considerable attention recently owing to their potential applications in parallel optical tweezers, parallel single-molecule orientation determination, parallel recording and multifocal multiphoton microscopy. However, the generation of vectorial multifocal arrays with a tailorable structure and polarization state remains a great challenge, and reports on multifocal arrays have hitherto been restricted either to scalar focal spots without polarization versatility or to regular arrays with fixed spacing. In this work, we propose a specific pseudo-period encoding technique to create three-dimensional (3D) vectorial multifocal arrays with the ability to manipulate the position, polarization state and intensity of each focal spot. We experimentally validated the flexibility of our approach in the generation of 3D vectorial multiple spots with polarization multiplicity and position tunability.

Correlation of generation interval and scale of large-scale submarine landslides using 3D seismic data off Shimokita Peninsula, Northeast Japan

NASA Astrophysics Data System (ADS)

Nakamura, Yuki; Ashi, Juichiro; Morita, Sumito

2016-04-01

To clarify timing and scale of past submarine landslides is important to understand formation processes of the landslides. The study area is in a part of continental slope of the Japan Trench, where a number of large-scale submarine landslide (slump) deposits have been identified in Pliocene and Quaternary formations by analysing METI's 3D seismic data "Sanrikuoki 3D" off Shimokita Peninsula (Morita et al., 2011). As structural features, swarm of parallel dikes which are likely dewatering paths formed accompanying the slumping deformation, and slip directions are basically perpendicular to the parallel dikes. Therefore, parallel dikes are good indicator for estimation of slip directions. Slip direction of each slide was determined one kilometre grid in the survey area of 40 km x 20 km. The remarkable slip direction varies from Pliocene to Quaternary in the survey area. Parallel dike structure is also available for the distinguishment of the slump deposit and normal deposit on time slice images. By tracing outline of slump deposits at each depth, we identified general morphology of the overall slump deposits, and calculated the volume of the extracted slump deposits so as to estimate the scale of each event. We investigated temporal and spatial variation of depositional pattern of the slump deposits. Calculating the generation interval of the slumps, some periodicity is likely recognized, especially large slump do not occur in succession. Additionally, examining the relationship of the cumulative volume and the generation interval, certain correlation is observed in Pliocene and Quaternary. Key words: submarine landslides, 3D seismic data, Shimokita Peninsula

Subaru HDS transmission spectroscopy of the transiting extrasolar planet HD209458b

NASA Astrophysics Data System (ADS)

Narita, N.; Suto, Y.; Winn, J. N.; Turner, E. L.; Aoki, W.; Leigh, C. J.; Sato, B.; Tamura, M.; Yamada, T.

2006-02-01

We have searched for absorption in several common atomic species due to the atmosphere or exosphere of the transiting extrasolar planet HD 209458b, using high precision optical spectra obtained with the Subaru High Dispersion Spectrograph (HDS). Previously we reported an upper limit on Hα absorption of 0.1% (3σ) within a 5.1Å band. Using the same procedure, we now report upper limits on absorption due to the optical transitions of Na D, Li, Hα, Hβ, Hγ, Fe, and Ca. The 3σ upper limit for each transition is approximately 1% within a 0.3Å band (the core of the line), and a few tenths of a per cent within a 2Å band (the full line width). The wide-band results are close to the expected limit due to photon-counting (Poisson) statistics, although in the narrow-band case we have encountered unexplained systematic errors at a few times the Poisson level. These results are consistent with all previously reported detections (Charbonneau et al. 2002, ApJ, 568, 377) and upper limits (Bundy & Marcy 2000, PASP, 112, 1421; Moutou et al. 2001, A&A, 371, 260), but are significantly more sensitive yet achieved from ground based observations.

5D Tempest simulations of kinetic edge turbulence

NASA Astrophysics Data System (ADS)

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

2006-10-01

Results are presented from the development and application of TEMPEST, a nonlinear five dimensional (3d2v) gyrokinetic continuum code. The simulation results and theoretical analysis include studies of H-mode edge plasma neoclassical transport and turbulence in real divertor geometry and its relationship to plasma flow generation with zero external momentum input, including the important orbit-squeezing effect due to the large electric field flow-shear in the edge. In order to extend the code to 5D, we have formulated a set of fully nonlinear electrostatic gyrokinetic equations and a fully nonlinear gyrokinetic Poisson's equation which is valid for both neoclassical and turbulence simulations. Our 5D gyrokinetic code is built on 4D version of Tempest neoclassical code with extension to a fifth dimension in binormal direction. The code is able to simulate either a full torus or a toroidal segment. Progress on performing 5D turbulence simulations will be reported.

Truncated Painlevé expansion: Tanh-traveling wave solutions and reduction of sine-Poisson equation to a quadrature for stationary and nonstationary three-dimensional collisionless cold plasma

NASA Astrophysics Data System (ADS)

Ibrahim, R. S.; El-Kalaawy, O. H.

2006-10-01

The relativistic nonlinear self-consistent equations for a collisionless cold plasma with stationary ions [R. S. Ibrahim, IMA J. Appl. Math. 68, 523 (2003)] are extended to 3 and 3+1 dimensions. The resulting system of equations is reduced to the sine-Poisson equation. The truncated Painlevé expansion and reduction of the partial differential equation to a quadrature problem (RQ method) are described and applied to obtain the traveling wave solutions of the sine-Poisson equation for stationary and nonstationary equations in 3 and 3+1 dimensions describing the charge-density equilibrium configuration model.

Performance of a parallel thermal-hydraulics code TEMPEST

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

Fann, G.I.; Trent, D.S.

The authors describe the parallelization of the Tempest thermal-hydraulics code. The serial version of this code is used for production quality 3-D thermal-hydraulics simulations. Good speedup was obtained with a parallel diagonally preconditioned BiCGStab non-symmetric linear solver, using a spatial domain decomposition approach for the semi-iterative pressure-based and mass-conserved algorithm. The test case used here to illustrate the performance of the BiCGStab solver is a 3-D natural convection problem modeled using finite volume discretization in cylindrical coordinates. The BiCGStab solver replaced the LSOR-ADI method for solving the pressure equation in TEMPEST. BiCGStab also solves the coupled thermal energy equation. Scalingmore » performance of 3 problem sizes (221220 nodes, 358120 nodes, and 701220 nodes) are presented. These problems were run on 2 different parallel machines: IBM-SP and SGI PowerChallenge. The largest problem attains a speedup of 68 on an 128 processor IBM-SP. In real terms, this is over 34 times faster than the fastest serial production time using the LSOR-ADI solver.« less

High-speed parallel implementation of a modified PBR algorithm on DSP-based EH topology

NASA Astrophysics Data System (ADS)

Rajan, K.; Patnaik, L. M.; Ramakrishna, J.

1997-08-01

Algebraic Reconstruction Technique (ART) is an age-old method used for solving the problem of three-dimensional (3-D) reconstruction from projections in electron microscopy and radiology. In medical applications, direct 3-D reconstruction is at the forefront of investigation. The simultaneous iterative reconstruction technique (SIRT) is an ART-type algorithm with the potential of generating in a few iterations tomographic images of a quality comparable to that of convolution backprojection (CBP) methods. Pixel-based reconstruction (PBR) is similar to SIRT reconstruction, and it has been shown that PBR algorithms give better quality pictures compared to those produced by SIRT algorithms. In this work, we propose a few modifications to the PBR algorithms. The modified algorithms are shown to give better quality pictures compared to PBR algorithms. The PBR algorithm and the modified PBR algorithms are highly compute intensive, Not many attempts have been made to reconstruct objects in the true 3-D sense because of the high computational overhead. In this study, we have developed parallel two-dimensional (2-D) and 3-D reconstruction algorithms based on modified PBR. We attempt to solve the two problems encountered by the PBR and modified PBR algorithms, i.e., the long computational time and the large memory requirements, by parallelizing the algorithm on a multiprocessor system. We investigate the possible task and data partitioning schemes by exploiting the potential parallelism in the PBR algorithm subject to minimizing the memory requirement. We have implemented an extended hypercube (EH) architecture for the high-speed execution of the 3-D reconstruction algorithm using the commercially available fast floating point digital signal processor (DSP) chips as the processing elements (PEs) and dual-port random access memories (DPR) as channels between the PEs. We discuss and compare the performances of the PBR algorithm on an IBM 6000 RISC workstation, on a Silicon Graphics Indigo 2 workstation, and on an EH system. The results show that an EH(3,1) using DSP chips as PEs executes the modified PBR algorithm about 100 times faster than an LBM 6000 RISC workstation. We have executed the algorithms on a 4-node IBM SP2 parallel computer. The results show that execution time of the algorithm on an EH(3,1) is better than that of a 4-node IBM SP2 system. The speed-up of an EH(3,1) system with eight PEs and one network controller is approximately 7.85.

Master-slave interferometry for parallel spectral domain interferometry sensing and versatile 3D optical coherence tomography.

PubMed

Podoleanu, Adrian Gh; Bradu, Adrian

2013-08-12

Conventional spectral domain interferometry (SDI) methods suffer from the need of data linearization. When applied to optical coherence tomography (OCT), conventional SDI methods are limited in their 3D capability, as they cannot deliver direct en-face cuts. Here we introduce a novel SDI method, which eliminates these disadvantages. We denote this method as Master - Slave Interferometry (MSI), because a signal is acquired by a slave interferometer for an optical path difference (OPD) value determined by a master interferometer. The MSI method radically changes the main building block of an SDI sensor and of a spectral domain OCT set-up. The serially provided signal in conventional technology is replaced by multiple signals, a signal for each OPD point in the object investigated. This opens novel avenues in parallel sensing and in parallelization of signal processing in 3D-OCT, with applications in high- resolution medical imaging and microscopy investigation of biosamples. Eliminating the need of linearization leads to lower cost OCT systems and opens potential avenues in increasing the speed of production of en-face OCT images in comparison with conventional SDI.

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.

Poisson's ratio of collagen fibrils measured by small angle X-ray scattering of strained bovine pericardium

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

Wells, Hannah C.; Sizeland, Katie H.; Kayed, Hanan R.

Type I collagen is the main structural component of skin, tendons, and skin products, such as leather. Understanding the mechanical performance of collagen fibrils is important for understanding the mechanical performance of the tissues that they make up, while the mechanical properties of bulk tissue are well characterized, less is known about the mechanical behavior of individual collagen fibrils. In this study, bovine pericardium is subjected to strain while small angle X-ray scattering (SAXS) patterns are recorded using synchrotron radiation. The change in d-spacing, which is a measure of fibril extension, and the change in fibril diameter are determined frommore » SAXS. The tissue is strained 0.25 (25%) with a corresponding strain in the collagen fibrils of 0.045 observed. The ratio of collagen fibril width contraction to length extension, or the Poisson's ratio, is 2.1 ± 0.7 for a tissue strain from 0 to 0.25. This Poisson's ratio indicates that the volume of individual collagen fibrils decreases with increasing strain, which is quite unlike most engineering materials. This high Poisson's ratio of individual fibrils may contribute to high Poisson's ratio observed for tissues, contributing to some of the remarkable properties of collagen-based materials.« less

Recent Progress on the Parallel Implementation of Moving-Body Overset Grid Schemes

NASA Technical Reports Server (NTRS)

Wissink, Andrew; Allen, Edwin (Technical Monitor)

1998-01-01

Viscous calculations about geometrically complex bodies in which there is relative motion between component parts is one of the most computationally demanding problems facing CFD researchers today. This presentation documents results from the first two years of a CHSSI-funded effort within the U.S. Army AFDD to develop scalable dynamic overset grid methods for unsteady viscous calculations with moving-body problems. The first pan of the presentation will focus on results from OVERFLOW-D1, a parallelized moving-body overset grid scheme that employs traditional Chimera methodology. The two processes that dominate the cost of such problems are the flow solution on each component and the intergrid connectivity solution. Parallel implementations of the OVERFLOW flow solver and DCF3D connectivity software are coupled with a proposed two-part static-dynamic load balancing scheme and tested on the IBM SP and Cray T3E multi-processors. The second part of the presentation will cover some recent results from OVERFLOW-D2, a new flow solver that employs Cartesian grids with various levels of refinement, facilitating solution adaption. A study of the parallel performance of the scheme on large distributed- memory multiprocessor computer architectures will be reported.

Parallel 3D-TLM algorithm for simulation of the Earth-ionosphere cavity

NASA Astrophysics Data System (ADS)

Toledo-Redondo, Sergio; Salinas, Alfonso; Morente-Molinera, Juan Antonio; Méndez, Antonio; Fornieles, Jesús; Portí, Jorge; Morente, Juan Antonio

2013-03-01

A parallel 3D algorithm for solving time-domain electromagnetic problems with arbitrary geometries is presented. The technique employed is the Transmission Line Modeling (TLM) method implemented in Shared Memory (SM) environments. The benchmarking performed reveals that the maximum speedup depends on the memory size of the problem as well as multiple hardware factors, like the disposition of CPUs, cache, or memory. A maximum speedup of 15 has been measured for the largest problem. In certain circumstances of low memory requirements, superlinear speedup is achieved using our algorithm. The model is employed to model the Earth-ionosphere cavity, thus enabling a study of the natural electromagnetic phenomena that occur in it. The algorithm allows complete 3D simulations of the cavity with a resolution of 10 km, within a reasonable timescale.

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

Wrinkle and roughness measurement by the Antera 3D and its application for evaluation of cosmetic products.

PubMed

Messaraa, C; Metois, A; Walsh, M; Hurley, S; Doyle, L; Mansfield, A; O'Connor, C; Mavon, A

2018-01-24

Skin topographic measurements are of paramount importance in the field of dermo-cosmetic evaluation. The aim of this study was to investigate how the Antera 3D, a multi-purpose handheld camera, correlates with other topographic techniques and changes in skin topography following the use of a cosmetic product. Skin topographic measurements were collected on 26 female volunteers aged 45-70 years with the Antera 3D, the DermaTOP and image analysis on parallel-polarized pictures. Different filters for analysis from the Antera 3D were investigated for repeatability, correlations with other imaging techniques and ability to detect improvements of skin topography following application of a serum. Most of Antera 3D parameters were found to be strongly correlated with the DermaTOP parameters. No association was found between the Antera 3D parameters and measurements on parallel-polarized photographs. The measurements repeatability was comparable among the different filters for analysis, with the exception of wrinkle max depth and roughness Rt. Following a single application of a tightening serum, both Antera 3D wrinkles and texture parameters were able to record significant improvements, with the best improvements observed with the large filter. The Antera 3D demonstrated its relevance for cosmetic product evaluation. We also provide recommendations for the analysis based on our findings. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

NIF Ignition Target 3D Point Design

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

Jones, O; Marinak, M; Milovich, J

2008-11-05

We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Syntheticmore » diagnostics.« less

Analytical and numerical techniques for predicting the interfacial stresses of wavy carbon nanotube/polymer composites

NASA Astrophysics Data System (ADS)

Yazdchi, K.; Salehi, M.; Shokrieh, M. M.

2009-03-01

By introducing a new simplified 3D representative volume element for wavy carbon nanotubes, an analytical model is developed to study the stress transfer in single-walled carbon nanotube-reinforced polymer composites. Based on the pull-out modeling technique, the effects of waviness, aspect ratio, and Poisson ratio on the axial and interfacial shear stresses are analyzed in detail. The results of the present analytical model are in a good agreement with corresponding results for straight nanotubes.

Repairable-conditionally repairable damage model based on dual Poisson processes.

PubMed

Lind, B K; Persson, L M; Edgren, M R; Hedlöf, I; Brahme, A

2003-09-01

The advent of intensity-modulated radiation therapy makes it increasingly important to model the response accurately when large volumes of normal tissues are irradiated by controlled graded dose distributions aimed at maximizing tumor cure and minimizing normal tissue toxicity. The cell survival model proposed here is very useful and flexible for accurate description of the response of healthy tissues as well as tumors in classical and truly radiobiologically optimized radiation therapy. The repairable-conditionally repairable (RCR) model distinguishes between two different types of damage, namely the potentially repairable, which may also be lethal, i.e. if unrepaired or misrepaired, and the conditionally repairable, which may be repaired or may lead to apoptosis if it has not been repaired correctly. When potentially repairable damage is being repaired, for example by nonhomologous end joining, conditionally repairable damage may require in addition a high-fidelity correction by homologous repair. The induction of both types of damage is assumed to be described by Poisson statistics. The resultant cell survival expression has the unique ability to fit most experimental data well at low doses (the initial hypersensitive range), intermediate doses (on the shoulder of the survival curve), and high doses (on the quasi-exponential region of the survival curve). The complete Poisson expression can be approximated well by a simple bi-exponential cell survival expression, S(D) = e(-aD) + bDe(-cD), where the first term describes the survival of undamaged cells and the last term represents survival after complete repair of sublethal damage. The bi-exponential expression makes it easy to derive D(0), D(q), n and alpha, beta values to facilitate comparison with classical cell survival models.

High efficiency integration of three-dimensional functional microdevices inside a microfluidic chip by using femtosecond laser multifoci parallel microfabrication

NASA Astrophysics Data System (ADS)

Xu, Bing; Du, Wen-Qiang; Li, Jia-Wen; Hu, Yan-Lei; Yang, Liang; Zhang, Chen-Chu; Li, Guo-Qiang; Lao, Zhao-Xin; Ni, Jin-Cheng; Chu, Jia-Ru; Wu, Dong; Liu, Su-Ling; Sugioka, Koji

2016-01-01

High efficiency fabrication and integration of three-dimension (3D) functional devices in Lab-on-a-chip systems are crucial for microfluidic applications. Here, a spatial light modulator (SLM)-based multifoci parallel femtosecond laser scanning technology was proposed to integrate microstructures inside a given ‘Y’ shape microchannel. The key novelty of our approach lies on rapidly integrating 3D microdevices inside a microchip for the first time, which significantly reduces the fabrication time. The high quality integration of various 2D-3D microstructures was ensured by quantitatively optimizing the experimental conditions including prebaking time, laser power and developing time. To verify the designable and versatile capability of this method for integrating functional 3D microdevices in microchannel, a series of microfilters with adjustable pore sizes from 12.2 μm to 6.7 μm were fabricated to demonstrate selective filtering of the polystyrene (PS) particles and cancer cells with different sizes. The filter can be cleaned by reversing the flow and reused for many times. This technology will advance the fabrication technique of 3D integrated microfluidic and optofluidic chips.

Convergence of Spectral Discretizations of the Vlasov--Poisson System

DOE PAGES

Manzini, G.; Funaro, D.; Delzanno, G. L.

2017-09-26

Here we prove the convergence of a spectral discretization of the Vlasov-Poisson system. The velocity term of the Vlasov equation is discretized using either Hermite functions on the infinite domain or Legendre polynomials on a bounded domain. The spatial term of the Vlasov and Poisson equations is discretized using periodic Fourier expansions. Boundary conditions are treated in weak form through a penalty type term that can be applied also in the Hermite case. As a matter of fact, stability properties of the approximated scheme descend from this added term. The convergence analysis is carried out in detail for the 1D-1Vmore » case, but results can be generalized to multidimensional domains, obtained as Cartesian product, in both space and velocity. The error estimates show the spectral convergence under suitable regularity assumptions on the exact solution.« less

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.

Noncommutative spherically symmetric spacetimes at semiclassical order

NASA Astrophysics Data System (ADS)

Fritz, Christopher; Majid, Shahn

2017-07-01

Working within the recent formalism of Poisson-Riemannian geometry, we completely solve the case of generic spherically symmetric metric and spherically symmetric Poisson-bracket to find a unique answer for the quantum differential calculus, quantum metric and quantum Levi-Civita connection at semiclassical order O(λ) . Here λ is the deformation parameter, plausibly the Planck scale. We find that r, t, d r, d t are all forced to be central, i.e. undeformed at order λ, while for each value of r, t we are forced to have a fuzzy sphere of radius r with a unique differential calculus which is necessarily nonassociative at order λ2 . We give the spherically symmetric quantisation of the FLRW cosmology in detail and also recover a previous analysis for the Schwarzschild black hole, now showing that the quantum Ricci tensor for the latter vanishes at order λ. The quantum Laplace-Beltrami operator for spherically symmetric models turns out to be undeformed at order λ while more generally in Poisson-Riemannian geometry we show that it deforms to □f+λ2ωαβ(Ricγα-Sγα)(∇^βdf)γ+O(λ2) in terms of the classical Levi-Civita connection \\widehat\

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

On Subset Selection Procedures for Poisson Processes and Some Applications to the Binomial and Multinomial Problems

DTIC Science & Technology

1976-07-01

PURDUE UNIVERSITY DEPARTMENT OF STATISTICS DIVISION OF MATHEMATICAL SCIENCES ON SUBSET SELECTION PROCEDURES FOR POISSON PROCESSES AND SOME...Mathematical Sciences Mimeograph Series #457, July 1976 This research was supported by the Office of Naval Research under Contract NOOO14-75-C-0455 at Purdue...11 CON PC-111 riFIC-F ,A.F ANO ADDPFS Office of INaval ResearchJu#07 Washington, DC07 36AE 14~~~ rjCr; NF A ’ , A FAA D F 6 - I S it 9 i 1, - ,1 I

Acceleration techniques and their impact on arterial input function sampling: Non-accelerated versus view-sharing and compressed sensing sequences.

PubMed

Benz, Matthias R; Bongartz, Georg; Froehlich, Johannes M; Winkel, David; Boll, Daniel T; Heye, Tobias

2018-07-01

The aim was to investigate the variation of the arterial input function (AIF) within and between various DCE MRI sequences. A dynamic flow-phantom and steady signal reference were scanned on a 3T MRI using fast low angle shot (FLASH) 2d, FLASH3d (parallel imaging factor (P) = P0, P2, P4), volumetric interpolated breath-hold examination (VIBE) (P = P0, P3, P2 × 2, P2 × 3, P3 × 2), golden-angle radial sparse parallel imaging (GRASP), and time-resolved imaging with stochastic trajectories (TWIST). Signal over time curves were normalized and quantitatively analyzed by full width half maximum (FWHM) measurements to assess variation within and between sequences. The coefficient of variation (CV) for the steady signal reference ranged from 0.07-0.8%. The non-accelerated gradient echo FLASH2d, FLASH3d, and VIBE sequences showed low within sequence variation with 2.1%, 1.0%, and 1.6%. The maximum FWHM CV was 3.2% for parallel imaging acceleration (VIBE P2 × 3), 2.7% for GRASP and 9.1% for TWIST. The FWHM CV between sequences ranged from 8.5-14.4% for most non-accelerated/accelerated gradient echo sequences except 6.2% for FLASH3d P0 and 0.3% for FLASH3d P2; GRASP FWHM CV was 9.9% versus 28% for TWIST. MRI acceleration techniques vary in reproducibility and quantification of the AIF. Incomplete coverage of the k-space with TWIST as a representative of view-sharing techniques showed the highest variation within sequences and might be less suited for reproducible quantification of the AIF. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Performance assessment of KORAT-3D on the ANL IBM-SP computer

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

Alexeyev, A.V.; Zvenigorodskaya, O.A.; Shagaliev, R.M.

1999-09-01

The TENAR code is currently being developed at the Russian Federal Nuclear Center (VNIIEF) as a coupled dynamics code for the simulation of transients in VVER and RBMK systems and other nuclear systems. The neutronic module in this code system is KORAT-3D. This module is also one of the most computationally intensive components of the code system. A parallel version of KORAT-3D has been implemented to achieve the goal of obtaining transient solutions in reasonable computational time, particularly for RBMK calculations that involve the application of >100,000 nodes. An evaluation of the KORAT-3D code performance was recently undertaken on themore » Argonne National Laboratory (ANL) IBM ScalablePower (SP) parallel computer located in the Mathematics and Computer Science Division of ANL. At the time of the study, the ANL IBM-SP computer had 80 processors. This study was conducted under the auspices of a technical staff exchange program sponsored by the International Nuclear Safety Center (INSC).« less

Three d10 coordination polymers assembled from 3,5-bis(imidazole-1-yl)pyridine and different polycarboxylates: Syntheses, structures and luminescence properties

NASA Astrophysics Data System (ADS)

Pan, Jie; Zhang, Di; Xue, Zhen-Zhen; Wei, Li; Han, Song-De; Wang, Guo-Ming

2017-11-01

Three novel Zn(II)/Cd(II) coordination polymers, [Cd2(bip)2(m-bdc)2(H2O)2·3H2O]n (1), [Zn2(bip)2(p-bdc)2·2.5H2O]n (2) and [Zn(bip) (p-bdc)·3H2O]n (3), where bip = 3,5-bis(imidazole-1-yl)pyridine, m-H2bdc = 1,3-benzenedicarboxylic acid, p-H2bdc = 1,4-benzenedicarboxylic acid, have been successfully synthesized under solvothermal conditions. The linkage of different ligands with Cd(II) ions in compound 1 affords a (3,5)-connected layer. Furthermore, 2D→3D parallel polycatenation occurs wherein the layers are polycatenated with the adjacent two parallel layers to form a 3D framework. In 2 and 3, the polycarboxylates act as pillars to combine the metal-bip chains, yielding the layered structures. These 2D networks are extended to the final 3D supramolecular architectures by π-π stacking interactions. The results show that bip can act as a versatile building block for the construction of various coordination polymers. Moreover, the fluorescent properties of 1-3 in the solid state at room temperature have been investigated.

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

NASA Technical Reports Server (NTRS)

Morano, Eric; Mavriplis, D. J.

1995-01-01

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

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.

An Advanced simulation Code for Modeling Inductive Output Tubes

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

Thuc Bui; R. Lawrence Ives

2012-04-27

During the Phase I program, CCR completed several major building blocks for a 3D large signal, inductive output tube (IOT) code using modern computer language and programming techniques. These included a 3D, Helmholtz, time-harmonic, field solver with a fully functional graphical user interface (GUI), automeshing and adaptivity. Other building blocks included the improved electrostatic Poisson solver with temporal boundary conditions to provide temporal fields for the time-stepping particle pusher as well as the self electric field caused by time-varying space charge. The magnetostatic field solver was also updated to solve for the self magnetic field caused by time changing currentmore » density in the output cavity gap. The goal function to optimize an IOT cavity was also formulated, and the optimization methodologies were investigated.« 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.

Use Computer-Aided Tools to Parallelize Large CFD Applications

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Yan, J.

2000-01-01

Porting applications to high performance parallel computers is always a challenging task. It is time consuming and costly. With rapid progressing in hardware architectures and increasing complexity of real applications in recent years, the problem becomes even more sever. Today, scalability and high performance are mostly involving handwritten parallel programs using message-passing libraries (e.g. MPI). However, this process is very difficult and often error-prone. The recent reemergence of shared memory parallel (SMP) architectures, such as the cache coherent Non-Uniform Memory Access (ccNUMA) architecture used in the SGI Origin 2000, show good prospects for scaling beyond hundreds of processors. Programming on an SMP is simplified by working in a globally accessible address space. The user can supply compiler directives, such as OpenMP, to parallelize the code. As an industry standard for portable implementation of parallel programs for SMPs, OpenMP is a set of compiler directives and callable runtime library routines that extend Fortran, C and C++ to express shared memory parallelism. It promises an incremental path for parallel conversion of existing software, as well as scalability and performance for a complete rewrite or an entirely new development. Perhaps the main disadvantage of programming with directives is that inserted directives may not necessarily enhance performance. In the worst cases, it can create erroneous results. While vendors have provided tools to perform error-checking and profiling, automation in directive insertion is very limited and often failed on large programs, primarily due to the lack of a thorough enough data dependence analysis. To overcome the deficiency, we have developed a toolkit, CAPO, to automatically insert OpenMP directives in Fortran programs and apply certain degrees of optimization. CAPO is aimed at taking advantage of detailed inter-procedural dependence analysis provided by CAPTools, developed by the University of Greenwich, to reduce potential errors made by users. Earlier tests on NAS Benchmarks and ARC3D have demonstrated good success of this tool. In this study, we have applied CAPO to parallelize three large applications in the area of computational fluid dynamics (CFD): OVERFLOW, TLNS3D and INS3D. These codes are widely used for solving Navier-Stokes equations with complicated boundary conditions and turbulence model in multiple zones. Each one comprises of from 50K to 1,00k lines of FORTRAN77. As an example, CAPO took 77 hours to complete the data dependence analysis of OVERFLOW on a workstation (SGI, 175MHz, R10K processor). A fair amount of effort was spent on correcting false dependencies due to lack of necessary knowledge during the analysis. Even so, CAPO provides an easy way for user to interact with the parallelization process. The OpenMP version was generated within a day after the analysis was completed. Due to sequential algorithms involved, code sections in TLNS3D and INS3D need to be restructured by hand to produce more efficient parallel codes. An included figure shows preliminary test results of the generated OVERFLOW with several test cases in single zone. The MPI data points for the small test case were taken from a handcoded MPI version. As we can see, CAPO's version has achieved 18 fold speed up on 32 nodes of the SGI O2K. For the small test case, it outperformed the MPI version. These results are very encouraging, but further work is needed. For example, although CAPO attempts to place directives on the outer- most parallel loops in an interprocedural framework, it does not insert directives based on the best manual strategy. In particular, it lacks the support of parallelization at the multi-zone level. Future work will emphasize on the development of methodology to work in a multi-zone level and with a hybrid approach. Development of tools to perform more complicated code transformation is also needed.

A parallel 3-D discrete wavelet transform architecture using pipelined lifting scheme approach for video coding

NASA Astrophysics Data System (ADS)

Hegde, Ganapathi; Vaya, Pukhraj

2013-10-01

This article presents a parallel architecture for 3-D discrete wavelet transform (3-DDWT). The proposed design is based on the 1-D pipelined lifting scheme. The architecture is fully scalable beyond the present coherent Daubechies filter bank (9, 7). This 3-DDWT architecture has advantages such as no group of pictures restriction and reduced memory referencing. It offers low power consumption, low latency and high throughput. The computing technique is based on the concept that lifting scheme minimises the storage requirement. The application specific integrated circuit implementation of the proposed architecture is done by synthesising it using 65 nm Taiwan Semiconductor Manufacturing Company standard cell library. It offers a speed of 486 MHz with a power consumption of 2.56 mW. This architecture is suitable for real-time video compression even with large frame dimensions.

A Smart Cage With Uniform Wireless Power Distribution in 3D for Enabling Long-Term Experiments With Freely Moving Animals.

PubMed

Mirbozorgi, S Abdollah; Bahrami, Hadi; Sawan, Mohamad; Gosselin, Benoit

2016-04-01

This paper presents a novel experimental chamber with uniform wireless power distribution in 3D for enabling long-term biomedical experiments with small freely moving animal subjects. The implemented power transmission chamber prototype is based on arrays of parallel resonators and multicoil inductive links, to form a novel and highly efficient wireless power transmission system. The power transmitter unit includes several identical resonators enclosed in a scalable array of overlapping square coils which are connected in parallel to provide uniform power distribution along x and y. Moreover, the proposed chamber uses two arrays of primary resonators, facing each other, and connected in parallel to achieve uniform power distribution along the z axis. Each surface includes 9 overlapped coils connected in parallel and implemented into two layers of FR4 printed circuit board. The chamber features a natural power localization mechanism, which simplifies its implementation and ease its operation by avoiding the need for active detection and control mechanisms. A single power surface based on the proposed approach can provide a power transfer efficiency (PTE) of 69% and a power delivered to the load (PDL) of 120 mW, for a separation distance of 4 cm, whereas the complete chamber prototype provides a uniform PTE of 59% and a PDL of 100 mW in 3D, everywhere inside the chamber with a size of 27×27×16 cm(3).

Single-breath-hold abdominal [Formula: see text]  mapping using 3D Cartesian Look-Locker with spatiotemporal sparsity constraints.

PubMed

Lugauer, Felix; Wetzl, Jens; Forman, Christoph; Schneider, Manuel; Kiefer, Berthold; Hornegger, Joachim; Nickel, Dominik; Maier, Andreas

2018-06-01

Our aim was to develop and validate a 3D Cartesian Look-Locker [Formula: see text] mapping technique that achieves high accuracy and whole-liver coverage within a single breath-hold. The proposed method combines sparse Cartesian sampling based on a spatiotemporally incoherent Poisson pattern and k-space segmentation, dedicated for high-temporal-resolution imaging. This combination allows capturing tissue with short relaxation times with volumetric coverage. A joint reconstruction of the 3D + inversion time (TI) data via compressed sensing exploits the spatiotemporal sparsity and ensures consistent quality for the subsequent multistep [Formula: see text] mapping. Data from the National Institute of Standards and Technology (NIST) phantom and 11 volunteers, along with reference 2D Look-Locker acquisitions, are used for validation. 2D and 3D methods are compared based on [Formula: see text] values in different abdominal tissues at 1.5 and 3 T. [Formula: see text] maps obtained from the proposed 3D method compare favorably with those from the 2D reference and additionally allow for reformatting or volumetric analysis. Excellent agreement is shown in phantom [bias[Formula: see text] < 2%, bias[Formula: see text] < 5% for (120; 2000) ms] and volunteer data (3D and 2D deviation < 4% for liver, muscle, and spleen) for clinically acceptable scan (20 s) and reconstruction times (< 4 min). Whole-liver [Formula: see text] mapping with high accuracy and precision is feasible in one breath-hold using spatiotemporally incoherent, sparse 3D Cartesian sampling.

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

Towards circuit optogenetics.

PubMed

Chen, I-Wen; Papagiakoumou, Eirini; Emiliani, Valentina

2018-06-01

Optogenetics neuronal targeting combined with single-photon wide-field illumination has already proved its enormous potential in neuroscience, enabling the optical control of entire neuronal networks and disentangling their role in the control of specific behaviors. However, establishing how a single or a sub-set of neurons controls a specific behavior, or how functionally identical neurons are connected in a particular task, or yet how behaviors can be modified in real-time by the complex wiring diagram of neuronal connections requires more sophisticated approaches enabling to drive neuronal circuits activity with single-cell precision and millisecond temporal resolution. This has motivated on one side the development of flexible optical methods for two-photon (2P) optogenetic activation using either, or a hybrid of two approaches: scanning and parallel illumination. On the other side, it has stimulated the engineering of new opsins with modified spectral characteristics, channel kinetics and spatial distribution of expression, offering the necessary flexibility of choosing the appropriate opsin for each application. The need for optical manipulation of multiple targets with millisecond temporal resolution has imposed three-dimension (3D) parallel holographic illumination as the technique of choice for optical control of neuronal circuits organized in 3D. Today 3D parallel illumination exists in several complementary variants, each with a different degree of simplicity, light uniformity, temporal precision and axial resolution. In parallel, the possibility to reach hundreds of targets in 3D volumes has prompted the development of low-repetition rate amplified laser sources enabling high peak power, while keeping low average power for stimulating each cell. All together those progresses open the way for a precise optical manipulation of neuronal circuits with unprecedented precision and flexibility. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impact of local diffusion on macroscopic dispersion in three-dimensional porous media

NASA Astrophysics Data System (ADS)

Dartois, Arthur; Beaudoin, Anthony; Huberson, Serge

2018-02-01

While macroscopic longitudinal and transverse dispersion in three-dimensional porous media has been simulated previously mostly under purely advective conditions, the impact of diffusion on macroscopic dispersion in 3D remains an open question. Furthermore, both in 2D and 3D, recurring difficulties have been encountered due to computer limitation or analytical approximation. In this work, we use the Lagrangian velocity covariance function and the temporal derivative of second-order moments to study the influence of diffusion on dispersion in highly heterogeneous 2D and 3D porous media. The first approach characterizes the correlation between the values of Eulerian velocity components sampled by particles undergoing diffusion at two times. The second approach allows the estimation of dispersion coefficients and the analysis of their behaviours as functions of diffusion. These two approaches allowed us to reach new results. The influence of diffusion on dispersion seems to be globally similar between highly heterogeneous 2D and 3D porous media. Diffusion induces a decrease in the dispersion in the direction parallel to the flow direction and an increase in the dispersion in the direction perpendicular to the flow direction. However, the amplification of these two effects with the permeability variance is clearly different between 2D and 3D. For the direction parallel to the flow direction, the amplification is more important in 3D than in 2D. It is reversed in the direction perpendicular to the flow direction.

Reconstruction of 3D Shapes of Opaque Cumulus Clouds from Airborne Multiangle Imaging: A Proof-of-Concept

NASA Astrophysics Data System (ADS)

Davis, A. B.; Bal, G.; Chen, J.

2015-12-01

Operational remote sensing of microphysical and optical cloud properties is invariably predicated on the assumption of plane-parallel slab geometry for the targeted cloud. The sole benefit of this often-questionable assumption about the cloud is that it leads to one-dimensional (1D) radiative transfer (RT)---a textbook, computationally tractable model. We present new results as evidence that, thanks to converging advances in 3D RT, inverse problem theory, algorithm implementation, and computer hardware, we are at the dawn of a new era in cloud remote sensing where we can finally go beyond the plane-parallel paradigm. Granted, the plane-parallel/1D RT assumption is reasonable for spatially extended stratiform cloud layers, as well as the smoothly distributed background aerosol layers. However, these 1D RT-friendly scenarios exclude cases that are critically important for climate physics. 1D RT---whence operational cloud remote sensing---fails catastrophically for cumuliform clouds that have fully 3D outer shapes and internal structures driven by shallow or deep convection. For these situations, the first order of business in a robust characterization by remote sensing is to abandon the slab geometry framework and determine the 3D geometry of the cloud, as a first step toward bone fide 3D cloud tomography. With this specific goal in mind, we deliver a proof-of-concept for an entirely new kind of remote sensing applicable to 3D clouds. It is based on highly simplified 3D RT and exploits multi-angular suites of cloud images at high spatial resolution. Airborne sensors like AirMSPI readily acquire such data. The key element of the reconstruction algorithm is a sophisticated solution of the nonlinear inverse problem via linearization of the forward model and an iteration scheme supported, where necessary, by adaptive regularization. Currently, the demo uses a 2D setting to show how either vertical profiles or horizontal slices of the cloud can be accurately reconstructed. Extension to 3D volumes is straightforward but the next challenge is to accommodate images at lower spatial resolution, e.g., from MISR/Terra. G. Bal, J. Chen, and A.B. Davis (2015). Reconstruction of cloud geometry from multi-angle images, Inverse Problems in Imaging (submitted).

Detecting Planar Surfaces in Outdoor Urban Environments

DTIC Science & Technology

2008-09-01

coplanar or parallel scene points and lines. Sturm and Maybank (18) perform 3D reconstruction given user-provided coplanarity, perpendicularity, and... Maybank , S. J. A method for intactive 3d reconstruction of piercewise planar objects from single images. in BMVC, 1999, 265–274 [19] Schaffalitzky, F

Parallel Tetrahedral Mesh Adaptation with Dynamic Load Balancing

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.

1999-01-01

The ability to dynamically adapt an unstructured grid is a powerful tool for efficiently solving computational problems with evolving physical features. In this paper, we report on our experience parallelizing an edge-based adaptation scheme, called 3D_TAG. using message passing. Results show excellent speedup when a realistic helicopter rotor mesh is randomly refined. However. performance deteriorates when the mesh is refined using a solution-based error indicator since mesh adaptation for practical problems occurs in a localized region., creating a severe load imbalance. To address this problem, we have developed PLUM, a global dynamic load balancing framework for adaptive numerical computations. Even though PLUM primarily balances processor workloads for the solution phase, it reduces the load imbalance problem within mesh adaptation by repartitioning the mesh after targeting edges for refinement but before the actual subdivision. This dramatically improves the performance of parallel 3D_TAG since refinement occurs in a more load balanced fashion. We also present optimal and heuristic algorithms that, when applied to the default mapping of a parallel repartitioner, significantly reduce the data redistribution overhead. Finally, portability is examined by comparing performance on three state-of-the-art parallel machines.

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.

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

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions

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

Lu Benzhuo; Holst, Michael J.; Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA 92093

2010-09-20

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for simulating electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised formore » time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.« less

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions

PubMed Central

Lu, Benzhuo; Holst, Michael J.; McCammon, J. Andrew; Zhou, Y. C.

2010-01-01

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems. PMID:21709855

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.

PubMed

Lu, Benzhuo; Holst, Michael J; McCammon, J Andrew; Zhou, Y C

2010-09-20

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.

Demonstration of an optoelectronic interconnect architecture for a parallel modified signed-digit adder and subtracter

NASA Astrophysics Data System (ADS)

Sun, Degui; Wang, Na-Xin; He, Li-Ming; Weng, Zhao-Heng; Wang, Daheng; Chen, Ray T.

1996-06-01

A space-position-logic-encoding scheme is proposed and demonstrated. This encoding scheme not only makes the best use of the convenience of binary logic operation, but is also suitable for the trinary property of modified signed- digit (MSD) numbers. Based on the space-position-logic-encoding scheme, a fully parallel modified signed-digit adder and subtractor is built using optoelectronic switch technologies in conjunction with fiber-multistage 3D optoelectronic interconnects. Thus an effective combination of a parallel algorithm and a parallel architecture is implemented. In addition, the performance of the optoelectronic switches used in this system is experimentally studied and verified. Both the 3-bit experimental model and the experimental results of a parallel addition and a parallel subtraction are provided and discussed. Finally, the speed ratio between the MSD adder and binary adders is discussed and the advantage of the MSD in operating speed is demonstrated.

Analysis of the Poisson-Nernst-Planck equation in a ball for modeling the Voltage-Current relation in neurobiological microdomains

NASA Astrophysics Data System (ADS)

Cartailler, J.; Schuss, Z.; Holcman, D.

2017-01-01

The electro-diffusion of ions is often described by the Poisson-Nernst-Planck (PNP) equations, which couple nonlinearly the charge concentration and the electric potential. This model is used, among others, to describe the motion of ions in neuronal micro-compartments. It remains at this time an open question how to determine the relaxation and the steady state distribution of voltage when an initial charge of ions is injected into a domain bounded by an impermeable dielectric membrane. The purpose of this paper is to construct an asymptotic approximation to the solution of the stationary PNP equations in a d-dimensional ball (d = 1 , 2 , 3) in the limit of large total charge. In this geometry the PNP system reduces to the Liouville-Gelfand-Bratú (LGB) equation, with the difference that the boundary condition is Neumann, not Dirichlet, and there is a minus sign in the exponent of the exponential term. The entire boundary is impermeable to ions and the electric field satisfies the compatibility condition of Poisson's equation. These differences replace attraction by repulsion in the LGB equation, thus completely changing the solution. We find that the voltage is maximal in the center and decreases toward the boundary. We also find that the potential drop between the center and the surface increases logarithmically in the total number of charges and not linearly, as in classical capacitance theory. This logarithmic singularity is obtained for d = 3 from an asymptotic argument and cannot be derived from the analysis of the phase portrait. These results are used to derive the relation between the outward current and the voltage in a dendritic spine, which is idealized as a dielectric sphere connected smoothly to the nerve axon by a narrow neck. This is a fundamental microdomain involved in neuronal communication. We compute the escape rate of an ion from the steady density in a ball, which models a neuronal spine head, to a small absorbing window in the sphere. We predict that the current is defined by the narrow neck that is connected to the sphere by a small absorbing window, as suggested by the narrow escape theory, while voltage is controlled by the PNP equations independently of the neck.

High-order Spatio-temporal Schemes for Coupled, Multi-physics Reactor Simulations

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

Mr. Vijay S. Mahadevan; Dr. Jean C. Ragusa

2008-09-01

This report summarizes the work done in the summer of 08 by the Ph.D. student Vijay Mahadevan. The main focus of the work was to coupled 3-D neutron difusion to 3-D heat conduction in parallel with accuracy greater than or equal to 2nd order in space and time. Results show that the goal was attained.

Evaluation of Holographic Technology in Close Air Support Mission Planning and Execution

DTIC Science & Technology

2008-03-18

Figures Figure 1: 2D representation of 3D hologram of Baghdad area using 1-meter resolution LIDAR data...Alias Maya Software................................................................................................. 11 Figure 3: Suburban...and light detection and ranging ( LIDAR ) sensors for several geographic areas was performed in parallel with formulation of the approach

Introduction to 3D Graphics through Excel

ERIC Educational Resources Information Center

Benacka, Jan

2013-01-01

The article presents a method of explaining the principles of 3D graphics through making a revolvable and sizable orthographic parallel projection of cuboid in Excel. No programming is used. The method was tried in fourteen 90 minute lessons with 181 participants, which were Informatics teachers, undergraduates of Applied Informatics and gymnasium…

Determination of orthotropic mechanical properties of 3D printed parts for structural health monitoring

NASA Astrophysics Data System (ADS)

Poissenot-Arrigoni, Bastien; Scheyer, Austin; Anton, Steven R.

2017-04-01

The evolution of additive manufacturing has allowed engineers to use 3D printing for many purposes. As a natural consequence of the 3D printing process, the printed object is anisotropic. As part of an ongoing project to embed piezoelectric devices in 3D printed structures for structural health monitoring (SHM), this study aims to find the mechanical properties of the 3D printed material and the influence of different external factors on those properties. The orthotropic mechanical properties of a 3D printed structure are dependent on the printing parameters used to create the structure. In order to develop an orthotropic material model, mechanical properties will be found experimentally from additively manufactured samples created from polylactic acid (PLA) using a consumer-level fused deposition modeling (FDM) printer; the Lulzbot TAZ 6. Nine mechanical constants including three Young's moduli, three Poisson's ratios, and three shear moduli are needed to fully describe the 3D elastic behavior of the material. Printed specimens with different raster orientations and print orientations allow calculation of the different material constants. In this work, seven of the nine mechanical constants were found. Two shear moduli were unable to be measured due to difficulties in printing two of the sample orientations. These mechanical properties are needed in order to develop orthotropic material models of systems employing 3D printed PLA. The results from this paper will be used to create a model of a piezoelectric transducer embedded in a 3D printed structure for structural health monitoring.

Image reconstruction from cone-beam projections with attenuation correction

NASA Astrophysics Data System (ADS)

Weng, Yi

1997-07-01

In single photon emission computered tomography (SPECT) imaging, photon attenuation within the body is a major factor contributing to the quantitative inaccuracy in measuring the distribution of radioactivity. Cone-beam SPECT provides improved sensitivity for imaging small organs. This thesis extends the results for 2D parallel- beam and fan-beam geometry to 3D parallel-beam and cone- beam geometries in order to derive filtered backprojection reconstruction algorithms for the 3D exponential parallel-beam transform and for the exponential cone-beam transform with sampling on a sphere. An exact inversion formula for the 3D exponential parallel-beam transform is obtained and is extended to the 3D exponential cone-beam transform. Sampling on a sphere is not useful clinically and current cone-beam tomography, with the focal point traversing a planar orbit, does not acquire sufficient data to give an accurate reconstruction. Thus a data acquisition method that obtains complete data for cone-beam SPECT by simultaneously rotating the gamma camera and translating the patient bed, so that cone-beam projections can be obtained with the focal point traversing a helix that surrounds the patient was developed. First, an implementation of Grangeat's algorithm for helical cone- beam projections was developed without attenuation correction. A fast new rebinning scheme was developed that uses all of the detected data to reconstruct the image and properly normalizes any multiply scanned data. In the case of attenuation no theorem analogous to Tuy's has been proven. We hypothesized that an artifact-free reconstruction could be obtained even if the cone-beam data are attenuated, provided the imaging orbit satisfies Tuy's condition and the exact attenuation map is known. Cone-beam emission data were acquired by using a circle- and-line and a helix orbit on a clinical SPECT system. An iterative conjugate gradient reconstruction algorithm was used to reconstruct projection data with a known attenuation map. The quantitative accuracy of the attenuation-corrected emission reconstruction was significantly improved.

3D Parallel Multigrid Methods for Real-Time Fluid Simulation

NASA Astrophysics Data System (ADS)

Wan, Feifei; Yin, Yong; Zhang, Suiyu

2018-03-01

The multigrid method is widely used in fluid simulation because of its strong convergence. In addition to operating accuracy, operational efficiency is also an important factor to consider in order to enable real-time fluid simulation in computer graphics. For this problem, we compared the performance of the Algebraic Multigrid and the Geometric Multigrid in the V-Cycle and Full-Cycle schemes respectively, and analyze the convergence and speed of different methods. All the calculations are done on the parallel computing of GPU in this paper. Finally, we experiment with the 3D-grid for each scale, and give the exact experimental results.

Hypoxic stellate cells of pancreatic cancer stroma regulate extracellular matrix fiber organization and cancer cell motility.

PubMed

Sada, Masafumi; Ohuchida, Kenoki; Horioka, Kohei; Okumura, Takashi; Moriyama, Taiki; Miyasaka, Yoshihiro; Ohtsuka, Takao; Mizumoto, Kazuhiro; Oda, Yoshinao; Nakamura, Masafumi

2016-03-28

Desmoplasia and hypoxia in pancreatic cancer mutually affect each other and create a tumor-supportive microenvironment. Here, we show that microenvironment remodeling by hypoxic pancreatic stellate cells (PSCs) promotes cancer cell motility through alteration of extracellular matrix (ECM) fiber architecture. Three-dimensional (3-D) matrices derived from PSCs under hypoxia exhibited highly organized parallel-patterned matrix fibers compared with 3-D matrices derived from PSCs under normoxia, and promoted cancer cell motility by inducing directional migration of cancer cells due to the parallel fiber architecture. Microarray analysis revealed that procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) in PSCs was the gene that potentially regulates ECM fiber architecture under hypoxia. Stromal PLOD2 expression in surgical specimens of pancreatic cancer was confirmed by immunohistochemistry. RNA interference-mediated knockdown of PLOD2 in PSCs blocked parallel fiber architecture of 3-D matrices, leading to decreased directional migration of cancer cells within the matrices. In conclusion, these findings indicate that hypoxia-induced PLOD2 expression in PSCs creates a permissive microenvironment for migration of cancer cells through architectural regulation of stromal ECM in pancreatic cancer. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Massive parallel 3D PIC simulation of negative ion extraction

NASA Astrophysics Data System (ADS)

Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu

2017-09-01

The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.

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

PubMed Central

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

2016-01-01

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

Poisson equation for the three-loop ladder diagram in string theory at genus one

NASA Astrophysics Data System (ADS)

Basu, Anirban

2016-11-01

The three-loop ladder diagram is a graph with six links and four cubic vertices that contributes to the D12ℛ4 amplitude at genus one in type II string theory. The vertices represent the insertion points of vertex operators on the toroidal worldsheet and the links represent scalar Green functions connecting them. By using the properties of the Green function and manipulating the various expressions, we obtain a modular invariant Poisson equation satisfied by this diagram, with source terms involving one-, two- and three-loop diagrams. Unlike the source terms in the Poisson equations for diagrams at lower orders in the momentum expansion or the Mercedes diagram, a particular source term involves a five-point function containing a holomorphic and a antiholomorphic worldsheet derivative acting on different Green functions. We also obtain simple equalities between topologically distinct diagrams, and consider some elementary examples.

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

Unweighted least squares phase unwrapping by means of multigrid techniques

NASA Astrophysics Data System (ADS)

Pritt, Mark D.

1995-11-01

We present a multigrid algorithm for unweighted least squares phase unwrapping. This algorithm applies Gauss-Seidel relaxation schemes to solve the Poisson equation on smaller, coarser grids and transfers the intermediate results to the finer grids. This approach forms the basis of our multigrid algorithm for weighted least squares phase unwrapping, which is described in a separate paper. The key idea of our multigrid approach is to maintain the partial derivatives of the phase data in separate arrays and to correct these derivatives at the boundaries of the coarser grids. This maintains the boundary conditions necessary for rapid convergence to the correct solution. Although the multigrid algorithm is an iterative algorithm, we demonstrate that it is nearly as fast as the direct Fourier-based method. We also describe how to parallelize the algorithm for execution on a distributed-memory parallel processor computer or a network-cluster of workstations.

3D Cloud Radiative Effects on Aerosol Optical Thickness Retrievals in Cumulus Cloud Fields in the Biomass Burning Region in Brazil

NASA Technical Reports Server (NTRS)

Wen, Guo-Yong; Marshak, Alexander; Cahalan, Robert F.

2004-01-01

Aerosol amount in clear regions of a cloudy atmosphere is a critical parameter in studying the interaction between aerosols and clouds. Since the global cloud cover is about 50%, cloudy scenes are often encountered in any satellite images. Aerosols are more or less transparent, while clouds are extremely reflective in the visible spectrum of solar radiation. The radiative transfer in clear-cloudy condition is highly three- dimensional (3D). This paper focuses on estimating the 3D effects on aerosol optical thickness retrievals using Monte Carlo simulations. An ASTER image of cumulus cloud fields in the biomass burning region in Brazil is simulated in this study. The MODIS products (i-e., cloud optical thickness, particle effective radius, cloud top pressure, surface reflectance, etc.) are used to construct the cloud property and surface reflectance fields. To estimate the cloud 3-D effects, we assume a plane-parallel stratification of aerosol properties in the 60 km x 60 km ASTER image. The simulated solar radiation at the top of the atmosphere is compared with plane-parallel calculations. Furthermore, the 3D cloud radiative effects on aerosol optical thickness retrieval are estimated.

Particle-in-cell simulations with charge-conserving current deposition on graphic processing units

NASA Astrophysics Data System (ADS)

Ren, Chuang; Kong, Xianglong; Huang, Michael; Decyk, Viktor; Mori, Warren

2011-10-01

Recently using CUDA, we have developed an electromagnetic Particle-in-Cell (PIC) code with charge-conserving current deposition for Nvidia graphic processing units (GPU's) (Kong et al., Journal of Computational Physics 230, 1676 (2011). On a Tesla M2050 (Fermi) card, the GPU PIC code can achieve a one-particle-step process time of 1.2 - 3.2 ns in 2D and 2.3 - 7.2 ns in 3D, depending on plasma temperatures. In this talk we will discuss novel algorithms for GPU-PIC including charge-conserving current deposition scheme with few branching and parallel particle sorting. These algorithms have made efficient use of the GPU shared memory. We will also discuss how to replace the computation kernels of existing parallel CPU codes while keeping their parallel structures. This work was supported by U.S. Department of Energy under Grant Nos. DE-FG02-06ER54879 and DE-FC02-04ER54789 and by NSF under Grant Nos. PHY-0903797 and CCF-0747324.

Quantum Confinement at Polar Oxide Interfaces

NASA Astrophysics Data System (ADS)

Gariglio, Stefano; Li, Danfeng; Wu, Zhenping; Liu, Wei; Fete, Alexandre; Boselli, Margherita; Lemal, Sebastien; Bristowe, Nicholas; Ghosez, Philippe; Gabay, Marc; Triscone, Jean-Marc

The discovery of a two-dimensional electron liquid (2DEL), confined at the interface between the two band insulators LaAlO3 (LAO) and SrTiO3 (STO) has generated tremendous research interest. The 2DEL confinement lifts the degeneracy of Ti t2 g orbitals and promotes exotic physical properties. A previous study has demonstrated that a 2DEL is also observed when LAO is alloyed with STO (La,Al)1-x(Sr,Ti)xO3 (LASTO: x). The threshold thickness required for the onset of conductivity scales with x. We present here a study of superconductivity at the (LASTO:0.5)/STO interface. The thickness of the 2DEL, measured using perpendicular and parallel critical fields, is larger than the one at the LAO/STO interface. This change is due to a modification on the confining potential linked to a reduced charge transfer that is scaling as 1 / x . This scenario is also confirmed by a self-consistent Poisson-Schrödinger model and ab initio calculations. These compelling evidences support an intrinsic origin to the formation of the 2DEL in the LAO/STO system.

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

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

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

1997-06-01

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

Compact holographic optical neural network system for real-time pattern recognition

NASA Astrophysics Data System (ADS)

Lu, Taiwei; Mintzer, David T.; Kostrzewski, Andrew A.; Lin, Freddie S.

1996-08-01

One of the important characteristics of artificial neural networks is their capability for massive interconnection and parallel processing. Recently, specialized electronic neural network processors and VLSI neural chips have been introduced in the commercial market. The number of parallel channels they can handle is limited because of the limited parallel interconnections that can be implemented with 1D electronic wires. High-resolution pattern recognition problems can require a large number of neurons for parallel processing of an image. This paper describes a holographic optical neural network (HONN) that is based on high- resolution volume holographic materials and is capable of performing massive 3D parallel interconnection of tens of thousands of neurons. A HONN with more than 16,000 neurons packaged in an attache case has been developed. Rotation- shift-scale-invariant pattern recognition operations have been demonstrated with this system. System parameters such as the signal-to-noise ratio, dynamic range, and processing speed are discussed.

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.

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.

The Relation between Reconnected Flux, the Parallel Electric Field, and the Reconnection Rate in a Three-Dimensional Kinetic Simulation of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Wendel, D. E.; Olson, D. K.; Hesse, M.; Karimabadi, H.; Daughton, W. S.

2013-12-01

We investigate the distribution of parallel electric fields and their relationship to the location and rate of magnetic reconnection of a large particle-in-cell simulation of 3D turbulent magnetic reconnection with open boundary conditions. The simulation's guide field geometry inhibits the formation of topological features such as separators and null points. Therefore, we derive the location of potential changes in magnetic connectivity by finding the field lines that experience a large relative change between their endpoints, i.e., the quasi-separatrix layer. We find a correspondence between the locus of changes in magnetic connectivity, or the quasi-separatrix layer, and the map of large gradients in the integrated parallel electric field (or quasi-potential). Furthermore, we compare the distribution of parallel electric fields along field lines with the reconnection rate. We find the reconnection rate is controlled by only the low-amplitude, zeroth and first-order trends in the parallel electric field, while the contribution from high amplitude parallel fluctuations, such as electron holes, is negligible. The results impact the determination of reconnection sites within models of 3D turbulent reconnection as well as the inference of reconnection rates from in situ spacecraft measurements. It is difficult through direct observation to isolate the locus of the reconnection parallel electric field amidst the large amplitude fluctuations. However, we demonstrate that a positive slope of the partial sum of the parallel electric field along the field line as a function of field line length indicates where reconnection is occurring along the field line.

Concentric Parallel Combining Balun for Millimeter-Wave Power Amplifier in Low-Power CMOS with High-Power Density

NASA Astrophysics Data System (ADS)

Han, Jiang-An; Kong, Zhi-Hui; Ma, Kaixue; Yeo, Kiat Seng; Lim, Wei Meng

2016-11-01

This paper presents a novel balun for a millimeter-wave power amplifier (PA) design to achieve high-power density in a 65-nm low-power (LP) CMOS process. By using a concentric winding technique, the proposed parallel combining balun with compact size accomplishes power combining and unbalance-balance conversion concurrently. For calculating its power combination efficiency in the condition of various amplitude and phase wave components, a method basing on S-parameters is derived. Based on the proposed parallel combining balun, a fabricated 60-GHz industrial, scientific, and medical (ISM) band PA with single-ended I/O achieves an 18.9-dB gain and an 8.8-dBm output power at 1-dB compression and 14.3-dBm saturated output power ( P sat) at 62 GHz. This PA occupying only a 0.10-mm2 core area has demonstrated a high-power density of 269.15 mW/mm2 in 65 nm LP CMOS.

LB3D: A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids

NASA Astrophysics Data System (ADS)

Schmieschek, S.; Shamardin, L.; Frijters, S.; Krüger, T.; Schiller, U. D.; Harting, J.; Coveney, P. V.

2017-08-01

We introduce the lattice-Boltzmann code LB3D, version 7.1. Building on a parallel program and supporting tools which have enabled research utilising high performance computing resources for nearly two decades, LB3D version 7 provides a subset of the research code functionality as an open source project. Here, we describe the theoretical basis of the algorithm as well as computational aspects of the implementation. The software package is validated against simulations of meso-phases resulting from self-assembly in ternary fluid mixtures comprising immiscible and amphiphilic components such as water-oil-surfactant systems. The impact of the surfactant species on the dynamics of spinodal decomposition are tested and quantitative measurement of the permeability of a body centred cubic (BCC) model porous medium for a simple binary mixture is described. Single-core performance and scaling behaviour of the code are reported for simulations on current supercomputer architectures.

Nonlinear Finite Element Analysis of Metals and Metal Matrix Composites: A Local-Global Investigation

DTIC Science & Technology

1992-10-01

and SiC/Al [47] possess good chemical bonding and experience mechanical clamping due to the differences in thermal expansion coefficients between...Coefficient of Thermal 2.70 x 10.6 *F-1 4.09 x 10-6 *C-1 Expansion (ca) Poisson’s Ratio (v) 0.25 0.25 Fiber Diameter (d) 0.0056 in 0.014224 cm...Properties of the matrix (as fabricated) Coefficient of Thermal 5.4 x 10-6 "F1 9.72 x 10-6 "C-1 Expansion (a) Poisson’s Ratio (v) 0.351 0.351 Longitudinal

TOMO3D: 3-D joint refraction and reflection traveltime tomography parallel code for active-source seismic data—synthetic test

NASA Astrophysics Data System (ADS)

Meléndez, A.; Korenaga, J.; Sallarès, V.; Miniussi, A.; Ranero, C. R.

2015-10-01

We present a new 3-D traveltime tomography code (TOMO3D) for the modelling of active-source seismic data that uses the arrival times of both refracted and reflected seismic phases to derive the velocity distribution and the geometry of reflecting boundaries in the subsurface. This code is based on its popular 2-D version TOMO2D from which it inherited the methods to solve the forward and inverse problems. The traveltime calculations are done using a hybrid ray-tracing technique combining the graph and bending methods. The LSQR algorithm is used to perform the iterative regularized inversion to improve the initial velocity and depth models. In order to cope with an increased computational demand due to the incorporation of the third dimension, the forward problem solver, which takes most of the run time (˜90 per cent in the test presented here), has been parallelized with a combination of multi-processing and message passing interface standards. This parallelization distributes the ray-tracing and traveltime calculations among available computational resources. The code's performance is illustrated with a realistic synthetic example, including a checkerboard anomaly and two reflectors, which simulates the geometry of a subduction zone. The code is designed to invert for a single reflector at a time. A data-driven layer-stripping strategy is proposed for cases involving multiple reflectors, and it is tested for the successive inversion of the two reflectors. Layers are bound by consecutive reflectors, and an initial velocity model for each inversion step incorporates the results from previous steps. This strategy poses simpler inversion problems at each step, allowing the recovery of strong velocity discontinuities that would otherwise be smoothened.

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.

Numerical Analysis of 2-D and 3-D MHD Flows Relevant to Fusion Applications

DOE PAGES

Khodak, Andrei

2017-08-21

Here, the analysis of many fusion applications such as liquid-metal blankets requires application of computational fluid dynamics (CFD) methods for electrically conductive liquids in geometrically complex regions and in the presence of a strong magnetic field. A current state of the art general purpose CFD code allows modeling of the flow in complex geometric regions, with simultaneous conjugated heat transfer analysis in liquid and surrounding solid parts. Together with a magnetohydrodynamics (MHD) capability, the general purpose CFD code will be a valuable tool for the design and optimization of fusion devices. This paper describes an introduction of MHD capability intomore » the general purpose CFD code CFX, part of the ANSYS Workbench. The code was adapted for MHD problems using a magnetic induction approach. CFX allows introduction of user-defined variables using transport or Poisson equations. For MHD adaptation of the code three additional transport equations were introduced for the components of the magnetic field, in addition to the Poisson equation for electric potential. The Lorentz force is included in the momentum transport equation as a source term. Fusion applications usually involve very strong magnetic fields, with values of the Hartmann number of up to tens of thousands. In this situation a system of MHD equations become very rigid with very large source terms and very strong variable gradients. To increase system robustness, special measures were introduced during the iterative convergence process, such as linearization using source coefficient for momentum equations. The MHD implementation in general purpose CFD code was tested against benchmarks, specifically selected for liquid-metal blanket applications. Results of numerical simulations using present implementation closely match analytical solutions for a Hartmann number of up to 1500 for a 2-D laminar flow in the duct of square cross section, with conducting and nonconducting walls. Results for a 3-D test case are also included.« less

Numerical Analysis of 2-D and 3-D MHD Flows Relevant to Fusion Applications

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

Khodak, Andrei

Here, the analysis of many fusion applications such as liquid-metal blankets requires application of computational fluid dynamics (CFD) methods for electrically conductive liquids in geometrically complex regions and in the presence of a strong magnetic field. A current state of the art general purpose CFD code allows modeling of the flow in complex geometric regions, with simultaneous conjugated heat transfer analysis in liquid and surrounding solid parts. Together with a magnetohydrodynamics (MHD) capability, the general purpose CFD code will be a valuable tool for the design and optimization of fusion devices. This paper describes an introduction of MHD capability intomore » the general purpose CFD code CFX, part of the ANSYS Workbench. The code was adapted for MHD problems using a magnetic induction approach. CFX allows introduction of user-defined variables using transport or Poisson equations. For MHD adaptation of the code three additional transport equations were introduced for the components of the magnetic field, in addition to the Poisson equation for electric potential. The Lorentz force is included in the momentum transport equation as a source term. Fusion applications usually involve very strong magnetic fields, with values of the Hartmann number of up to tens of thousands. In this situation a system of MHD equations become very rigid with very large source terms and very strong variable gradients. To increase system robustness, special measures were introduced during the iterative convergence process, such as linearization using source coefficient for momentum equations. The MHD implementation in general purpose CFD code was tested against benchmarks, specifically selected for liquid-metal blanket applications. Results of numerical simulations using present implementation closely match analytical solutions for a Hartmann number of up to 1500 for a 2-D laminar flow in the duct of square cross section, with conducting and nonconducting walls. Results for a 3-D test case are also included.« less

Quantum Theory of Three-Dimensional Superresolution Using Rotating-PSF Imagery

NASA Astrophysics Data System (ADS)

Prasad, S.; Yu, Z.

The inverse of the quantum Fisher information (QFI) matrix (and extensions thereof) provides the ultimate lower bound on the variance of any unbiased estimation of a parameter from statistical data, whether of intrinsically quantum mechanical or classical character. We calculate the QFI for Poisson-shot-noise-limited imagery using the rotating PSF that can localize and resolve point sources fully in all three dimensions. We also propose an experimental approach based on the use of computer generated hologram and projective measurements to realize the QFI-limited variance for the problem of super-resolving a closely spaced pair of point sources at a highly reduced photon cost. The paper presents a preliminary analysis of quantum-limited three-dimensional (3D) pair optical super-resolution (OSR) problem with potential applications to astronomical imaging and 3D space-debris localization.

Automatic Generation of Directive-Based Parallel Programs for Shared Memory Parallel Systems

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Yan, Jerry; Frumkin, Michael

2000-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. Due to its ease of programming and its good performance, the technique has become very popular. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate directive-based, OpenMP, parallel programs. We outline techniques used in the implementation of the tool and present test results on the NAS parallel benchmarks and ARC3D, a CFD application. This work demonstrates the great potential of using computer-aided tools to quickly port parallel programs and also achieve good performance.

Real time 3D scanner: investigations and results

NASA Astrophysics Data System (ADS)

Nouri, Taoufik; Pflug, Leopold

1993-12-01

This article presents a concept of reconstruction of 3-D objects using non-invasive and touch loss techniques. The principle of this method is to display parallel interference optical fringes on an object and then to record the object under two angles of view. According to an appropriated treatment one reconstructs the 3-D object even when the object has no symmetrical plan. The 3-D surface data is available immediately in digital form for computer- visualization and for analysis software tools. The optical set-up for recording the 3-D object, the 3-D data extraction and treatment, as well as the reconstruction of the 3-D object are reported and commented on. This application is dedicated for reconstructive/cosmetic surgery, CAD, animation and research purposes.

Parallel Computer System for 3D Visualization Stereo on GPU

NASA Astrophysics Data System (ADS)

Al-Oraiqat, Anas M.; Zori, Sergii A.

2018-03-01

This paper proposes the organization of a parallel computer system based on Graphic Processors Unit (GPU) for 3D stereo image synthesis. The development is based on the modified ray tracing method developed by the authors for fast search of tracing rays intersections with scene objects. The system allows significant increase in the productivity for the 3D stereo synthesis of photorealistic quality. The generalized procedure of 3D stereo image synthesis on the Graphics Processing Unit/Graphics Processing Clusters (GPU/GPC) is proposed. The efficiency of the proposed solutions by GPU implementation is compared with single-threaded and multithreaded implementations on the CPU. The achieved average acceleration in multi-thread implementation on the test GPU and CPU is about 7.5 and 1.6 times, respectively. Studying the influence of choosing the size and configuration of the computational Compute Unified Device Archi-tecture (CUDA) network on the computational speed shows the importance of their correct selection. The obtained experimental estimations can be significantly improved by new GPUs with a large number of processing cores and multiprocessors, as well as optimized configuration of the computing CUDA network.

Demonstration of a full volume 3D pre-stack depth migration in the Garden Banks area using massively parallel processor (MPP) technology

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

Solano, M.; Chang, H.; VanDyke, J.

1996-12-31

This paper describes the implementation and results of portable, production-scale 3D Pre-stack Kirchhoff depth migration software. Full volume pre-stack imaging was applied to a six million trace (46.9 Gigabyte) data set from a subsalt play in the Garden Banks area in the Gulf of Mexico. The velocity model building and updating, were derived using image depth gathers and an image-driven strategy. After three velocity iterations, depth migrated sections revealed drilling targets that were not visible in the conventional 3D post-stack time migrated data set. As expected from the implementation of the migration algorithm, it was found that amplitudes are wellmore » preserved and anomalies associated with known reservoirs, conform to petrophysical predictions. Image gathers for velocity analysis and the final depth migrated volume, were generated on an 1824 node Intel Paragon at Sandia National Laboratories. The code has been successfully ported to a CRAY (T3D) and Unix workstation Parallel Virtual Machine environments (PVM).« less

Three-dimensional motion-picture imaging of dynamic object by parallel-phase-shifting digital holographic microscopy using an inverted magnification optical system

NASA Astrophysics Data System (ADS)

Fukuda, Takahito; Shinomura, Masato; Xia, Peng; Awatsuji, Yasuhiro; Nishio, Kenzo; Matoba, Osamu

2017-04-01

We constructed a parallel-phase-shifting digital holographic microscopy (PPSDHM) system using an inverted magnification optical system, and succeeded in three-dimensional (3D) motion-picture imaging for 3D displacement of a microscopic object. In the PPSDHM system, the inverted and afocal magnification optical system consisted of a microscope objective (16.56 mm focal length and 0.25 numerical aperture) and a convex lens (300 mm focal length and 82 mm aperture diameter). A polarization-imaging camera was used to record multiple phase-shifted holograms with a single-shot exposure. We recorded an alum crystal, sinking down in aqueous solution of alum, by the constructed PPSDHM system at 60 frames/s for about 20 s and reconstructed high-quality 3D motion-picture image of the crystal. Then, we calculated amounts of displacement of the crystal from the amounts in the focus plane and the magnifications of the magnification optical system, and obtained the 3D trajectory of the crystal by that amounts.

Three-dimensional charge coupled device

DOEpatents

Conder, Alan D.; Young, Bruce K. F.

1999-01-01

A monolithic three dimensional charged coupled device (3D-CCD) which utilizes the entire bulk of the semiconductor for charge generation, storage, and transfer. The 3D-CCD provides a vast improvement of current CCD architectures that use only the surface of the semiconductor substrate. The 3D-CCD is capable of developing a strong E-field throughout the depth of the semiconductor by using deep (buried) parallel (bulk) electrodes in the substrate material. Using backside illumination, the 3D-CCD architecture enables a single device to image photon energies from the visible, to the ultra-violet and soft x-ray, and out to higher energy x-rays of 30 keV and beyond. The buried or bulk electrodes are electrically connected to the surface electrodes, and an E-field parallel to the surface is established with the pixel in which the bulk electrodes are located. This E-field attracts charge to the bulk electrodes independent of depth and confines it within the pixel in which it is generated. Charge diffusion is greatly reduced because the E-field is strong due to the proximity of the bulk electrodes.

Process for fabricating a charge coupled device

DOEpatents

Conder, Alan D.; Young, Bruce K. F.

2002-01-01

A monolithic three dimensional charged coupled device (3D-CCD) which utilizes the entire bulk of the semiconductor for charge generation, storage, and transfer. The 3D-CCD provides a vast improvement of current CCD architectures that use only the surface of the semiconductor substrate. The 3D-CCD is capable of developing a strong E-field throughout the depth of the semiconductor by using deep (buried) parallel (bulk) electrodes in the substrate material. Using backside illumination, the 3D-CCD architecture enables a single device to image photon energies from the visible, to the ultra-violet and soft x-ray, and out to higher energy x-rays of 30 keV and beyond. The buried or bulk electrodes are electrically connected to the surface electrodes, and an E-field parallel to the surface is established with the pixel in which the bulk electrodes are located. This E-field attracts charge to the bulk electrodes independent of depth and confines it within the pixel in which it is generated. Charge diffusion is greatly reduced because the E-field is strong due to the proximity of the bulk electrodes.

External Theory for Stochastic Processes.

DTIC Science & Technology

1985-11-01

1.2 1.4 1.8 11111125 11.I6 MICROCOP RESOLUTION TEST CHART M.. MW’ PAPI ~ W W ’W IV AV a a W 4 * S6 _ ~.. r dV . Unclassif’ DA 7 4 9JT FILE COPY...intensity measure has the Laplace : <-f Transform L (f)=exp(-x (l-e - f ) whereas a Compound Poisson Process has Laplace Transform (2.3.1) L (f...see Example 2.2.4 as an illustration of this). The result is a clustering of exceedances, leading to a compounding of events in the limiting point

Bayer image parallel decoding based on GPU

NASA Astrophysics Data System (ADS)

Hu, Rihui; Xu, Zhiyong; Wei, Yuxing; Sun, Shaohua

2012-11-01

In the photoelectrical tracking system, Bayer image is decompressed in traditional method, which is CPU-based. However, it is too slow when the images become large, for example, 2K×2K×16bit. In order to accelerate the Bayer image decoding, this paper introduces a parallel speedup method for NVIDA's Graphics Processor Unit (GPU) which supports CUDA architecture. The decoding procedure can be divided into three parts: the first is serial part, the second is task-parallelism part, and the last is data-parallelism part including inverse quantization, inverse discrete wavelet transform (IDWT) as well as image post-processing part. For reducing the execution time, the task-parallelism part is optimized by OpenMP techniques. The data-parallelism part could advance its efficiency through executing on the GPU as CUDA parallel program. The optimization techniques include instruction optimization, shared memory access optimization, the access memory coalesced optimization and texture memory optimization. In particular, it can significantly speed up the IDWT by rewriting the 2D (Tow-dimensional) serial IDWT into 1D parallel IDWT. Through experimenting with 1K×1K×16bit Bayer image, data-parallelism part is 10 more times faster than CPU-based implementation. Finally, a CPU+GPU heterogeneous decompression system was designed. The experimental result shows that it could achieve 3 to 5 times speed increase compared to the CPU serial method.

Low-contrast lesion detection in tomosynthetic breast imaging using a realistic breast phantom

NASA Astrophysics Data System (ADS)

Zhou, Lili; Oldan, Jorge; Fisher, Paul; Gindi, Gene

2006-03-01

Tomosynthesis mammography is a potentially valuable technique for detection of breast cancer. In this simulation study, we investigate the efficacy of three different tomographic reconstruction methods, EM, SART and Backprojection, in the context of an especially difficult mammographic detection task. The task is the detection of a very low-contrast mass embedded in very dense fibro-glandular tissue - a clinically useful task for which tomosynthesis may be well suited. The project uses an anatomically realistic 3D digital breast phantom whose normal anatomic variability limits lesion conspicuity. In order to capture anatomical object variability, we generate an ensemble of phantoms, each of which comprises random instances of various breast structures. We construct medium-sized 3D breast phantoms which model random instances of ductal structures, fibrous connective tissue, Cooper's ligaments and power law structural noise for small scale object variability. Random instances of 7-8 mm irregular masses are generated by a 3D random walk algorithm and placed in very dense fibro-glandular tissue. Several other components of the breast phantom are held fixed, i.e. not randomly generated. These include the fixed breast shape and size, nipple structure, fixed lesion location, and a pectoralis muscle. We collect low-dose data using an isocentric tomosynthetic geometry at 11 angles over 50 degrees and add Poisson noise. The data is reconstructed using the three algorithms. Reconstructed slices through the center of the lesion are presented to human observers in a 2AFC (two-alternative-forced-choice) test that measures detectability by computing AUC (area under the ROC curve). The data collected in each simulation includes two sources of variability, that due to the anatomical variability of the phantom and that due to the Poisson data noise. We found that for this difficult task that the AUC value for EM (0.89) was greater than that for SART (0.83) and Backprojection (0.66).

Nigral dopamine type-1 receptors are reduced in Huntington's disease: A postmortem autoradiographic study using ( sup 3 H)SCH 23390 and correlation with ( sup 3 H)forskolin binding

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

Filloux, F.; Wagster, M.V.; Folstein, S.

1990-11-01

Intrastriatal injection of excitatory amino acids, particularly quinolinic acid, has been proposed as an animal model of Huntington's disease. Such neurotoxic lesions of caudate-putamen result in marked dopamine type-1 (D1) receptor losses in the injected nuclei as well as in the ipsilateral substantia nigra pars reticulata. Postmortem human substantia nigra from Huntington's disease brains and from control brains were examined using in vitro autoradiography. A marked reduction in ({sup 3}H)SCH 23390 binding (labeling D1 receptors) in the substantia nigra of postmortem brains of Huntington's patients was identified, thus paralleling the alterations seen in the animal models. A positive, statistically significantmore » correlation was also encountered between D1 receptor binding (labeled by ({sup 3}H)SCH 23390) and ({sup 3}H)forskolin binding (which identifies adenylate cyclase, a second messenger system linked to D1 receptor activation). The results suggest that in the human--as in lower vertebrates--D1 receptors are located on striatonigral terminals and that D1 receptor loss tends to be paralleled by a reduction in adenylate cyclase. Radioactive agents selective for the D1 receptor may prove useful in future studies of Huntington's disease using positron emission tomography scanning.« less

Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol.

PubMed

Sun, Bing; Shen, Feng; McCalla, Stephanie E; Kreutz, Jason E; Karymov, Mikhail A; Ismagilov, Rustem F

2013-02-05

Here we used a SlipChip microfluidic device to evaluate the performance of digital reverse transcription-loop-mediated isothermal amplification (dRT-LAMP) for quantification of HIV viral RNA. Tests are needed for monitoring HIV viral load to control the emergence of drug resistance and to diagnose acute HIV infections. In resource-limited settings, in vitro measurement of HIV viral load in a simple format is especially needed, and single-molecule counting using a digital format could provide a potential solution. We showed here that when one-step dRT-LAMP is used for quantification of HIV RNA, the digital count is lower than expected and is limited by the yield of desired cDNA. We were able to overcome the limitations by developing a microfluidic protocol to manipulate many single molecules in parallel through a two-step digital process. In the first step we compartmentalize the individual RNA molecules (based on Poisson statistics) and perform reverse transcription on each RNA molecule independently to produce DNA. In the second step, we perform the LAMP amplification on all individual DNA molecules in parallel. Using this new protocol, we increased the absolute efficiency (the ratio between the concentration calculated from the actual count and the expected concentration) of dRT-LAMP 10-fold, from ∼2% to ∼23%, by (i) using a more efficient reverse transcriptase, (ii) introducing RNase H to break up the DNA:RNA hybrid, and (iii) adding only the BIP primer during the RT step. We also used this two-step method to quantify HIV RNA purified from four patient samples and found that in some cases, the quantification results were highly sensitive to the sequence of the patient's HIV RNA. We learned the following three lessons from this work: (i) digital amplification technologies, including dLAMP and dPCR, may give adequate dilution curves and yet have low efficiency, thereby providing quantification values that underestimate the true concentration. Careful validation is essential before a method is considered to provide absolute quantification; (ii) the sensitivity of dLAMP to the sequence of the target nucleic acid necessitates additional validation with patient samples carrying the full spectrum of mutations; (iii) for multistep digital amplification chemistries, such as a combination of reverse transcription with amplification, microfluidic devices may be used to decouple these steps from one another and to perform them under different, individually optimized conditions for improved efficiency.

New 2D diffraction model and its applications to terahertz parallel-plate waveguide power splitters

PubMed Central

Zhang, Fan; Song, Kaijun; Fan, Yong

2017-01-01

A two-dimensional (2D) diffraction model for the calculation of the diffraction field in 2D space and its applications to terahertz parallel-plate waveguide power splitters are proposed in this paper. Compared with the Huygens-Fresnel principle in three-dimensional (3D) space, the proposed model provides an approximate analytical expression to calculate the diffraction field in 2D space. The diffraction filed is regarded as the superposition integral in 2D space. The calculated results obtained from the proposed diffraction model agree well with the ones by software HFSS based on the element method (FEM). Based on the proposed 2D diffraction model, two parallel-plate waveguide power splitters are presented. The splitters consist of a transmitting horn antenna, reflectors, and a receiving antenna array. The reflector is cylindrical parabolic with superimposed surface relief to efficiently couple the transmitted wave into the receiving antenna array. The reflector is applied as computer-generated holograms to match the transformed field to the receiving antenna aperture field. The power splitters were optimized by a modified real-coded genetic algorithm. The computed results of the splitters agreed well with the ones obtained by software HFSS verify the novel design method for power splitter, which shows good applied prospects of the proposed 2D diffraction model. PMID:28181514

An innovative hybrid 3D analytic-numerical model for air breathing parallel channel counter-flow PEM fuel cells.

PubMed

Tavčar, Gregor; Katrašnik, Tomaž

2014-01-01

The parallel straight channel PEM fuel cell model presented in this paper extends the innovative hybrid 3D analytic-numerical (HAN) approach previously published by the authors with capabilities to address ternary diffusion systems and counter-flow configurations. The model's core principle is modelling species transport by obtaining a 2D analytic solution for species concentration distribution in the plane perpendicular to the cannel gas-flow and coupling consecutive 2D solutions by means of a 1D numerical pipe-flow model. Electrochemical and other nonlinear phenomena are coupled to the species transport by a routine that uses derivative approximation with prediction-iteration. The latter is also the core of the counter-flow computation algorithm. A HAN model of a laboratory test fuel cell is presented and evaluated against a professional 3D CFD simulation tool showing very good agreement between results of the presented model and those of the CFD simulation. Furthermore, high accuracy results are achieved at moderate computational times, which is owed to the semi-analytic nature and to the efficient computational coupling of electrochemical kinetics and species transport.

Efficient sequential and parallel algorithms for finding edit distance based motifs.

PubMed

Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

2016-08-18

Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in this paper are also applicable to other motif search problems such as Planted Motif Search (PMS) and Simple Motif Search (SMS).

Generalized derivation extensions of 3-Lie algebras and corresponding Nambu-Poisson structures

NASA Astrophysics Data System (ADS)

Song, Lina; Jiang, Jun

2018-01-01

In this paper, we introduce the notion of a generalized derivation on a 3-Lie algebra. We construct a new 3-Lie algebra using a generalized derivation and call it the generalized derivation extension. We show that the corresponding Leibniz algebra on the space of fundamental objects is the double of a matched pair of Leibniz algebras. We also determine the corresponding Nambu-Poisson structures under some conditions.

3-D readout-electronics packaging for high-bandwidth massively paralleled imager

DOEpatents

Kwiatkowski, Kris; Lyke, James

2007-12-18

Dense, massively parallel signal processing electronics are co-packaged behind associated sensor pixels. Microchips containing a linear or bilinear arrangement of photo-sensors, together with associated complex electronics, are integrated into a simple 3-D structure (a "mirror cube"). An array of photo-sensitive cells are disposed on a stacked CMOS chip's surface at a 45.degree. angle from light reflecting mirror surfaces formed on a neighboring CMOS chip surface. Image processing electronics are held within the stacked CMOS chip layers. Electrical connections couple each of said stacked CMOS chip layers and a distribution grid, the connections for distributing power and signals to components associated with each stacked CSMO chip layer.

3D highly oriented nanoparticulate and microparticulate array ofmetal oxide materials

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

Vayssieres, Lionel; Guo, Jinghua; Nordgren, Joseph

2006-09-15

Advanced nano and micro particulate thin films of 3d transition and post-transition metal oxides consisting of nanorods and microrods with parallel and perpendicular orientation with respect to the substrate normal, have been successfully grown onto various substrates by heteronucleation, without template and/or surfactant, from the aqueous condensation of solution of metal salts or metal complexes (aqueous chemical growth). Three-dimensional arrays of iron oxide nanorods and zinc oxide nanorods with parallel and perpendicular orientation are presented as well as the oxygen K-edge polarization dependent x-ray absorption spectroscopy (XAS) study of anisotropic perpendicularly oriented microrod array of ZnO performed at synchrotron radiationmore » source facility.« less

Efficient simulation of pitch angle collisions in a 2+2-D Eulerian Vlasov code

NASA Astrophysics Data System (ADS)

Banks, Jeff; Berger, R.; Brunner, S.; Tran, T.

2014-10-01

Here we discuss pitch angle scattering collisions in the context of the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The collision operator is discretized using 4th order accurate conservative finite-differencing. The treatment of the Vlasov operator in phase-space uses an approach based on a minimally diffuse, fourth-order-accurate discretization (Banks and Hittinger, IEEE T. Plasma Sci. 39, 2198). The overall scheme is therefore discretely conservative and controls unphysical oscillations. Some details of the numerical scheme will be presented, and the implementation on modern highly concurrent parallel computers will be discussed. We will present results of collisional effects on linear and non-linear Landau damping of electron plasma waves (EPWs). In addition we will present initial results showing the effect of collisions on the evolution of EPWs in two space dimensions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and funded by the LDRD program at LLNL under project tracking code 12-ERD-061.

3D-radiative transfer in terrestrial atmosphere: An efficient parallel numerical procedure

NASA Astrophysics Data System (ADS)

Bass, L. P.; Germogenova, T. A.; Nikolaeva, O. V.; Kokhanovsky, A. A.; Kuznetsov, V. S.

2003-04-01

Light propagation and scattering in terrestrial atmosphere is usually studied in the framework of the 1D radiative transfer theory [1]. However, in reality particles (e.g., ice crystals, solid and liquid aerosols, cloud droplets) are randomly distributed in 3D space. In particular, their concentrations vary both in vertical and horizontal directions. Therefore, 3D effects influence modern cloud and aerosol retrieval procedures, which are currently based on the 1D radiative transfer theory. It should be pointed out that the standard radiative transfer equation allows to study these more complex situations as well [2]. In recent year the parallel version of the 2D and 3D RADUGA code has been developed. This version is successfully used in gammas and neutrons transport problems [3]. Applications of this code to radiative transfer in atmosphere problems are contained in [4]. Possibilities of code RADUGA are presented in [5]. The RADUGA code system is an universal solver of radiative transfer problems for complicated models, including 2D and 3D aerosol and cloud fields with arbitrary scattering anisotropy, light absorption, inhomogeneous underlying surface and topography. Both delta type and distributed light sources can be accounted for in the framework of the algorithm developed. The accurate numerical procedure is based on the new discrete ordinate SWDD scheme [6]. The algorithm is specifically designed for parallel supercomputers. The version RADUGA 5.1(P) can run on MBC1000M [7] (768 processors with 10 Gb of hard disc memory for each processor). The peak productivity is equal 1 Tfl. Corresponding scalar version RADUGA 5.1 is working on PC. As a first example of application of the algorithm developed, we have studied the shadowing effects of clouds on neighboring cloudless atmosphere, depending on the cloud optical thickness, surface albedo, and illumination conditions. This is of importance for modern satellite aerosol retrieval algorithms development. [1] Sobolev, V. V., 1972: Light scattering in planetary atmosphere, M.:Nauka. [2] Evans, K. F., 1998: The spherical harmonic discrete ordinate method for three dimensional atmospheric radiative transfer, J. Atmos. Sci., 55, 429 446. [3] L.P. Bass, T.A. Germogenova, V.S. Kuznetsov, O.V. Nikolaeva. RADUGA 5.1 and RADUGA 5.1(P) codes for stationary transport equation solution in 2D and 3D geometries on one and multiprocessors computers. Report on seminar “Algorithms and Codes for neutron physical of nuclear reactor calculations” (Neutronica 2001), Obninsk, Russia, 30 October 2 November 2001. [4] T.A. Germogenova, L.P. Bass, V.S. Kuznetsov, O.V. Nikolaeva. Mathematical modeling on parallel computers solar and laser radiation transport in 3D atmosphere. Report on International Symposium CIS countries “Atmosphere radiation”, 18 21 June 2002, St. Peterburg, Russia, p. 15 16. [5] L.P. Bass, T.A. Germogenova, O.V. Nikolaeva, V.S. Kuznetsov. Radiative Transfer Universal 2D 3D Code RADUGA 5.1(P) for Multiprocessor Computer. Abstract. Poster report on this Meeting. [6] L.P. Bass, O.V. Nikolaeva. Correct calculation of Angular Flux Distribution in Strongly Heterogeneous Media and Voids. Proc. of Joint International Conference on Mathematical Methods and Supercomputing for Nuclear Applications, Saratoga Springs, New York, October 5 9, 1997, p. 995 1004. [7] http://www/jscc.ru

Parallel Logic Programming and Parallel Systems Software and Hardware

DTIC Science & Technology

1989-07-29

Conference, Dallas TX. January 1985. (55) [Rous75] Roussel, P., "PROLOG: Manuel de Reference et d’Uilisation", Group d’ Intelligence Artificielle , Universite d...completed. Tools were provided for software development using artificial intelligence techniques. Al software for massively parallel architectures was...using artificial intelligence tech- niques. Al software for massively parallel architectures was started. 1. Introduction We describe research conducted

On-line range images registration with GPGPU

NASA Astrophysics Data System (ADS)

Będkowski, J.; Naruniec, J.

2013-03-01

This paper concerns implementation of algorithms in the two important aspects of modern 3D data processing: data registration and segmentation. Solution proposed for the first topic is based on the 3D space decomposition, while the latter on image processing and local neighbourhood search. Data processing is implemented by using NVIDIA compute unified device architecture (NIVIDIA CUDA) parallel computation. The result of the segmentation is a coloured map where different colours correspond to different objects, such as walls, floor and stairs. The research is related to the problem of collecting 3D data with a RGB-D camera mounted on a rotated head, to be used in mobile robot applications. Performance of the data registration algorithm is aimed for on-line processing. The iterative closest point (ICP) approach is chosen as a registration method. Computations are based on the parallel fast nearest neighbour search. This procedure decomposes 3D space into cubic buckets and, therefore, the time of the matching is deterministic. First technique of the data segmentation uses accele-rometers integrated with a RGB-D sensor to obtain rotation compensation and image processing method for defining pre-requisites of the known categories. The second technique uses the adapted nearest neighbour search procedure for obtaining normal vectors for each range point.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE PAGES

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.; ...

2016-09-18

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

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

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

An analytical drain current model for symmetric double-gate MOSFETs

NASA Astrophysics Data System (ADS)

Yu, Fei; Huang, Gongyi; Lin, Wei; Xu, Chuanzhong

2018-04-01

An analytical surface-potential-based drain current model of symmetric double-gate (sDG) MOSFETs is described as a SPICE compatible model in this paper. The continuous surface and central potentials from the accumulation to the strong inversion regions are solved from the 1-D Poisson's equation in sDG MOSFETs. Furthermore, the drain current is derived from the charge sheet model as a function of the surface potential. Over a wide range of terminal voltages, doping concentrations, and device geometries, the surface potential calculation scheme and drain current model are verified by solving the 1-D Poisson's equation based on the least square method and using the Silvaco Atlas simulation results and experimental data, respectively. Such a model can be adopted as a useful platform to develop the circuit simulator and provide the clear understanding of sDG MOSFET device physics.

Two dimensional analytical model for a reconfigurable field effect transistor

NASA Astrophysics Data System (ADS)

Ranjith, R.; Jayachandran, Remya; Suja, K. J.; Komaragiri, Rama S.

2018-02-01

This paper presents two-dimensional potential and current models for a reconfigurable field effect transistor (RFET). Two potential models which describe subthreshold and above-threshold channel potentials are developed by solving two-dimensional (2D) Poisson's equation. In the first potential model, 2D Poisson's equation is solved by considering constant/zero charge density in the channel region of the device to get the subthreshold potential characteristics. In the second model, accumulation charge density is considered to get above-threshold potential characteristics of the device. The proposed models are applicable for the device having lightly doped or intrinsic channel. While obtaining the mathematical model, whole body area is divided into two regions: gated region and un-gated region. The analytical models are compared with technology computer-aided design (TCAD) simulation results and are in complete agreement for different lengths of the gated regions as well as at various supply voltage levels.

From Wheatstone to Cameron and beyond: overview in 3-D and 4-D imaging technology

NASA Astrophysics Data System (ADS)

Gilbreath, G. Charmaine

2012-02-01

This paper reviews three-dimensional (3-D) and four-dimensional (4-D) imaging technology, from Wheatstone through today, with some prognostications for near future applications. This field is rich in variety, subject specialty, and applications. A major trend, multi-view stereoscopy, is moving the field forward to real-time wide-angle 3-D reconstruction as breakthroughs in parallel processing and multi-processor computers enable very fast processing. Real-time holography meets 4-D imaging reconstruction at the goal of achieving real-time, interactive, 3-D imaging. Applications to telesurgery and telemedicine as well as to the needs of the defense and intelligence communities are also discussed.

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

PubMed Central

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J.

2015-01-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes. PMID:25950438

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans.

PubMed

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J

2015-05-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3' UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.

Dendritic polyelectrolytes as seen by the Poisson-Boltzmann-Flory theory.

PubMed

Kłos, J S; Milewski, J

2018-06-20

G3-G9 dendritic polyelectrolytes accompanied by counterions are investigated using the Poisson-Boltzmann-Flory theory. Within this approach we solve numerically the Poisson-Boltzmann equation for the mean electrostatic potential and minimize the Poisson-Boltzmann-Flory free energy with respect to the size of the molecules. Such a scheme enables us to inspect the conformational and electrostatic properties of the dendrimers in equilibrium based on their response to varying the dendrimer generation. The calculations indicate that the G3-G6 dendrimers exist in the polyelectrolyte regime where absorption of counterions into the volume of the molecules is minor. Trapping of ions in the interior region becomes significant for the G7-G9 dendrimers and signals the emergence of the osmotic regime. We find that the behavior of the dendritic polyelectrolytes corresponds with the degree of ion trapping. In particular, in both regimes the polyelectrolytes are swollen as compared to their neutral counterparts and the expansion factor is maximal at the crossover generation G7.

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/.

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.

Interprétation cohérente du coefficient de Poisson négatif rapporté dans des multicouches métalliques : rôle du paramètre libre de contrainte

NASA Astrophysics Data System (ADS)

Badawi, K. F.; Goudeau, Ph.; Durand, N.

1998-04-01

Elastic properties of multilayers with low period thickness show in some cases anomalies which are generally correlated with structural modifications in individual layers. In the recent past, several studies have evidenced using X-ray diffraction in-plane and out-of-plane strains with the same sign. Some authors have then proposed in the case of W/Ni and Nb/Cu metallic superlattices to use a negative Poisson's ratio. This result is surprising because the value of this coefficient in metals is generally positive. In this article, we introduce a novel interpretation mainly based on the experimental determination by sin^2Psi method of the reference parameter (stress-free lattice parameter) used in strain calculations. Then, we show that the introduction of the bulk parameter instead of stress-free parameter for the reference parameter is an unrealistic assumption in the case of thin films and multilayers (W and Ag/Ni) and may thus lead to wrong results which are then in total disagreement with those obtained by other techniques. Therefore, the elastic anomaly concerning Poisson's ratio which has been reported by some authors in scientific literature do not result from real structure of multilayers but from experimental X-ray diffraction data analysis. Les propriétés élastiques dans certains systèmes multicouches de faible période présentent des anomalies qui sont généralement associées à des modifications des propriétés structurales de chacune des couches. Ainsi, plusieurs études ont mis en évidence par diffraction des rayons X des déformations de même signe dans le plan et selon la normale au plan des couches déposées. Certains auteurs ont alors proposé dans le cas de systèmes métalliques W/Ni et Nb/Cu l'utilisation d'un coefficient de Poisson négatif. Ce résultat est surprenant car la valeur de ce coefficient pour les métaux est généralement positive. Dans cet article, nous présentons une nouvelle interprétation reposant sur la détermination expérimentale par la méthode des sin^2Psi de la référence (paramètre libre de contrainte) servant de base au calcul des déformations. Nous montrons alors que l'introduction du paramètre du matériau massif comme référence est une hypothèse irréaliste dans le cas des films minces et multicouches (W et Ag/Ni) qui peut conduire à des résultats erronés et en total désaccord avec ceux obtenus par d'autres techniques. Ainsi, l'anomalie élastique au niveau du coefficient de Poisson soulevée par certains auteurs dans la littérature n'est pas imputable à la structure elle-même mais à l'analyse qui est faite des données expérimentales obtenues par diffraction des rayons X.

Parallelization of sequential Gaussian, indicator and direct simulation algorithms

NASA Astrophysics Data System (ADS)

Nunes, Ruben; Almeida, José A.

2010-08-01

Improving the performance and robustness of algorithms on new high-performance parallel computing architectures is a key issue in efficiently performing 2D and 3D studies with large amount of data. In geostatistics, sequential simulation algorithms are good candidates for parallelization. When compared with other computational applications in geosciences (such as fluid flow simulators), sequential simulation software is not extremely computationally intensive, but parallelization can make it more efficient and creates alternatives for its integration in inverse modelling approaches. This paper describes the implementation and benchmarking of a parallel version of the three classic sequential simulation algorithms: direct sequential simulation (DSS), sequential indicator simulation (SIS) and sequential Gaussian simulation (SGS). For this purpose, the source used was GSLIB, but the entire code was extensively modified to take into account the parallelization approach and was also rewritten in the C programming language. The paper also explains in detail the parallelization strategy and the main modifications. Regarding the integration of secondary information, the DSS algorithm is able to perform simple kriging with local means, kriging with an external drift and collocated cokriging with both local and global correlations. SIS includes a local correction of probabilities. Finally, a brief comparison is presented of simulation results using one, two and four processors. All performance tests were carried out on 2D soil data samples. The source code is completely open source and easy to read. It should be noted that the code is only fully compatible with Microsoft Visual C and should be adapted for other systems/compilers.

Parallel computation of fluid-structural interactions using high resolution upwind schemes

NASA Astrophysics Data System (ADS)

Hu, Zongjun

An efficient and accurate solver is developed to simulate the non-linear fluid-structural interactions in turbomachinery flutter flows. A new low diffusion E-CUSP scheme, Zha CUSP scheme, is developed to improve the efficiency and accuracy of the inviscid flux computation. The 3D unsteady Navier-Stokes equations with the Baldwin-Lomax turbulence model are solved using the finite volume method with the dual-time stepping scheme. The linearized equations are solved with Gauss-Seidel line iterations. The parallel computation is implemented using MPI protocol. The solver is validated with 2D cases for its turbulence modeling, parallel computation and unsteady calculation. The Zha CUSP scheme is validated with 2D cases, including a supersonic flat plate boundary layer, a transonic converging-diverging nozzle and a transonic inlet diffuser. The Zha CUSP2 scheme is tested with 3D cases, including a circular-to-rectangular nozzle, a subsonic compressor cascade and a transonic channel. The Zha CUSP schemes are proved to be accurate, robust and efficient in these tests. The steady and unsteady separation flows in a 3D stationary cascade under high incidence and three inlet Mach numbers are calculated to study the steady state separation flow patterns and their unsteady oscillation characteristics. The leading edge vortex shedding is the mechanism behind the unsteady characteristics of the high incidence separated flows. The separation flow characteristics is affected by the inlet Mach number. The blade aeroelasticity of a linear cascade with forced oscillating blades is studied using parallel computation. A simplified two-passage cascade with periodic boundary condition is first calculated under a medium frequency and a low incidence. The full scale cascade with 9 blades and two end walls is then studied more extensively under three oscillation frequencies and two incidence angles. The end wall influence and the blade stability are studied and compared under different frequencies and incidence angles. The Zha CUSP schemes are the first time to be applied in moving grid systems and 2D and 3D calculations. The implicit Gauss-Seidel iteration with dual time stepping is the first time to be used for moving grid systems. The NASA flutter cascade is the first time to be calculated in full scale.

Quantitative Imaging of Young's Modulus of Soft Tissues from Ultrasound Water Jet Indentation: A Finite Element Study

PubMed Central

Lu, Min-Hua; Mao, Rui; Lu, Yin; Liu, Zheng; Wang, Tian-Fu; Chen, Si-Ping

2012-01-01

Indentation testing is a widely used approach to evaluate mechanical characteristics of soft tissues quantitatively. Young's modulus of soft tissue can be calculated from the force-deformation data with known tissue thickness and Poisson's ratio using Hayes' equation. Our group previously developed a noncontact indentation system using a water jet as a soft indenter as well as the coupling medium for the propagation of high-frequency ultrasound. The novel system has shown its ability to detect the early degeneration of articular cartilage. However, there is still lack of a quantitative method to extract the intrinsic mechanical properties of soft tissue from water jet indentation. The purpose of this study is to investigate the relationship between the loading-unloading curves and the mechanical properties of soft tissues to provide an imaging technique of tissue mechanical properties. A 3D finite element model of water jet indentation was developed with consideration of finite deformation effect. An improved Hayes' equation has been derived by introducing a new scaling factor which is dependent on Poisson's ratios v, aspect ratio a/h (the radius of the indenter/the thickness of the test tissue), and deformation ratio d/h. With this model, the Young's modulus of soft tissue can be quantitatively evaluated and imaged with the error no more than 2%. PMID:22927890

Physically consistent data assimilation method based on feedback control for patient-specific blood flow analysis.

PubMed

Ii, Satoshi; Adib, Mohd Azrul Hisham Mohd; Watanabe, Yoshiyuki; Wada, Shigeo

2018-01-01

This paper presents a novel data assimilation method for patient-specific blood flow analysis based on feedback control theory called the physically consistent feedback control-based data assimilation (PFC-DA) method. In the PFC-DA method, the signal, which is the residual error term of the velocity when comparing the numerical and reference measurement data, is cast as a source term in a Poisson equation for the scalar potential field that induces flow in a closed system. The pressure values at the inlet and outlet boundaries are recursively calculated by this scalar potential field. Hence, the flow field is physically consistent because it is driven by the calculated inlet and outlet pressures, without any artificial body forces. As compared with existing variational approaches, although this PFC-DA method does not guarantee the optimal solution, only one additional Poisson equation for the scalar potential field is required, providing a remarkable improvement for such a small additional computational cost at every iteration. Through numerical examples for 2D and 3D exact flow fields, with both noise-free and noisy reference data as well as a blood flow analysis on a cerebral aneurysm using actual patient data, the robustness and accuracy of this approach is shown. Moreover, the feasibility of a patient-specific practical blood flow analysis is demonstrated. Copyright © 2017 John Wiley & Sons, Ltd.

Center of Excellence in Theoretical Geoplasma Research

DTIC Science & Technology

1989-11-10

iii) First results of closed-form solutions of the3 Balescu -Lenard-Poisson equations for collisional plasmas were reported I REPORT November 10, 1989...Basu, "Solutions of the Linearized Balescu -Lenard-Poisson Equations for a Weakly-Collisional Plasma: Some New Results". [511 American Geophysical Union

Three-Dimensional Effects of Crack Closure in Laminated Composite Plates Subjected to Bending Loads

DTIC Science & Technology

1994-06-01

Approved by: •UW. Kwon, Thesis Advisor wathe D.K~elleher, Chairman Department of Mechanical Engineering ii ABSTRACT Fracture is one of the dominant...5 A. OVERVIEW .......................................... 5 B. CONSTITUTIVE EQUATION .............................. 9 1. Isotropic...the elemental nodes. B. CONSTITUTIVE EQUATION The material property matrix [D] is a symmetric matrix which includes elasticity moduli and Poisson’s

3D-PDR: Three-dimensional photodissociation region code

NASA Astrophysics Data System (ADS)

Bisbas, T. G.; Bell, T. A.; Viti, S.; Yates, J.; Barlow, M. J.

2018-03-01

3D-PDR is a three-dimensional photodissociation region code written in Fortran. It uses the Sundials package (written in C) to solve the set of ordinary differential equations and it is the successor of the one-dimensional PDR code UCL_PDR (ascl:1303.004). Using the HEALpix ray-tracing scheme (ascl:1107.018), 3D-PDR solves a three-dimensional escape probability routine and evaluates the attenuation of the far-ultraviolet radiation in the PDR and the propagation of FIR/submm emission lines out of the PDR. The code is parallelized (OpenMP) and can be applied to 1D and 3D problems.

Design of materials with prescribed nonlinear properties

NASA Astrophysics Data System (ADS)

Wang, F.; Sigmund, O.; Jensen, J. S.

2014-09-01

We systematically design materials using topology optimization to achieve prescribed nonlinear properties under finite deformation. Instead of a formal homogenization procedure, a numerical experiment is proposed to evaluate the material performance in longitudinal and transverse tensile tests under finite deformation, i.e. stress-strain relations and Poissons ratio. By minimizing errors between actual and prescribed properties, materials are tailored to achieve the target. Both two dimensional (2D) truss-based and continuum materials are designed with various prescribed nonlinear properties. The numerical examples illustrate optimized materials with rubber-like behavior and also optimized materials with extreme strain-independent Poissons ratio for axial strain intervals of εi∈[0.00, 0.30].

A Hybrid Shared-Memory Parallel Max-Tree Algorithm for Extreme Dynamic-Range Images.

PubMed

Moschini, Ugo; Meijster, Arnold; Wilkinson, Michael H F

2018-03-01

Max-trees, or component trees, are graph structures that represent the connected components of an image in a hierarchical way. Nowadays, many application fields rely on images with high-dynamic range or floating point values. Efficient sequential algorithms exist to build trees and compute attributes for images of any bit depth. However, we show that the current parallel algorithms perform poorly already with integers at bit depths higher than 16 bits per pixel. We propose a parallel method combining the two worlds of flooding and merging max-tree algorithms. First, a pilot max-tree of a quantized version of the image is built in parallel using a flooding method. Later, this structure is used in a parallel leaf-to-root approach to compute efficiently the final max-tree and to drive the merging of the sub-trees computed by the threads. We present an analysis of the performance both on simulated and actual 2D images and 3D volumes. Execution times are about better than the fastest sequential algorithm and speed-up goes up to on 64 threads.

State of the art in electromagnetic modeling for the Compact Linear Collider

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

Candel, Arno; Kabel, Andreas; Lee, Lie-Quan

SLAC's Advanced Computations Department (ACD) has developed the parallel 3D electromagnetic time-domain code T3P for simulations of wakefields and transients in complex accelerator structures. T3P is based on state-of-the-art Finite Element methods on unstructured grids and features unconditional stability, quadratic surface approximation and up to 6th-order vector basis functions for unprecedented simulation accuracy. Optimized for large-scale parallel processing on leadership supercomputing facilities, T3P allows simulations of realistic 3D structures with fast turn-around times, aiding the design of the next generation of accelerator facilities. Applications include simulations of the proposed two-beam accelerator structures for the Compact Linear Collider (CLIC) - wakefieldmore » damping in the Power Extraction and Transfer Structure (PETS) and power transfer to the main beam accelerating structures are investigated.« less

Nanoscale lamellar photoconductor hybrids and methods of making same

DOEpatents

Stupp, Samuel I; Goldberger, Josh; Sofos, Marina

2013-02-05

An article of manufacture and methods of making same. In one embodiment, the article of manufacture has a plurality of zinc oxide layers substantially in parallel, wherein each zinc oxide layer has a thickness d.sub.1, and a plurality of organic molecule layers substantially in parallel, wherein each organic molecule layer has a thickness d.sub.2 and a plurality of molecules with a functional group that is bindable to zinc ions, wherein for every pair of neighboring zinc oxide layers, one of the plurality of organic molecule layers is positioned in between the pair of neighboring zinc oxide layers to allow the functional groups of the plurality of organic molecules to bind to zinc ions in the neighboring zinc oxide layers to form a lamellar hybrid structure with a geometric periodicity d.sub.1+d.sub.2, and wherein d.sub.1 and d.sub.2 satisfy the relationship of d.sub.1.ltoreq.d.sub.2.ltoreq.3d.sub.1.

Surface and 3D Quantum Hall Effects from Engineering of Exceptional Points in Nodal-Line Semimetals

NASA Astrophysics Data System (ADS)

Molina, Rafael A.; González, José

2018-04-01

We show that, under a strong magnetic field, a 3D nodal-line semimetal is driven into a topological insulating phase in which the electronic transport takes place at the surface of the material. When the magnetic field is perpendicular to the nodal ring, the surface states of the semimetal are transmuted into Landau states which correspond to exceptional points, i.e., branch points in the spectrum of a non-Hermitian Hamiltonian which arise upon the extension to complex values of the momentum. The complex structure of the spectrum then allows us to express the number of zero-energy flat bands in terms of a new topological invariant counting the number of exceptional points. When the magnetic field is parallel to the nodal ring, we find that the bulk states are built from the pairing of surfacelike evanescent waves, giving rise to a 3D quantum Hall effect with a flat level of Landau states residing in parallel 2D slices of the 3D material. The Hall conductance is quantized in either case in units of e2/h , leading in the 3D Hall effect to a number of channels growing linearly with the section of the surface and opening the possibility to observe a macroscopic chiral current at the surface of the material.

Two-stage Electron Acceleration by 3D Collisionless Guide-field Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Buechner, J.; Munoz, P.

2017-12-01

We discuss a two-stage process of electron acceleration near X-lines of 3D collisionless guide-field magnetic reconnection. Non-relativistic electrons are first pre-accelerated by magnetic-field-aligned (parallel) electric fields. At the nonlinear stage of 3D guide-field magnetic reconnection electric and magnetic fields become filamentary structured due to streaming instabilities. This causes an additional curvature-driven electron acceleration in the guide-field direction. The resulting spectrum of the accelerated electrons follows a power law.

Emergent Intelligent Behavior through Integrated Investigation of Embodied Natural Language, Reasoning, Learning, Computer Vision, and Robotic Manipulation

DTIC Science & Technology

2011-10-11

developed a method for determining the structure (component logs and their 3D place- ment) of a LINCOLN LOG assembly from a single image from an uncalibrated...small a class of components. Moreover, we focus on determining the precise pose and structure of an assembly, including the 3D pose of each...medial axes are parallel to the work surface. Thus valid structures Fig. 1. The 3D geometric shape parameters of LINCOLN LOGS. have logs on

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

In vivo verification of particle therapy: how Compton camera configurations affect 3D image quality

NASA Astrophysics Data System (ADS)

Mackin, D.; Draeger, E.; Peterson, S.; Polf, J.; Beddar, S.

2017-05-01

The steep dose gradients enabled by the Bragg peaks of particle therapy beams are a double edged sword. They enable highly conformal dose distributions, but even small deviations from the planned beam range can cause overdosing of healthy tissue or under-dosing of the tumour. To reduce this risk, particle therapy treatment plans include margins large enough to account for all the sources of range uncertainty, which include patient setup errors, patient anatomy changes, and CT number to stopping power ratios. Any system that could verify the beam range in vivo, would allow reduced margins and more conformal dose distributions. Toward our goal developing such a system based on Compton camera (CC) imaging, we studied how three configurations (single camera, parallel opposed, and orthogonal) affect the quality of the 3D images. We found that single CC and parallel opposed configurations produced superior images in 2D. The increase in parallax produced by an orthogonal CC configuration was shown to be beneficial in producing artefact free 3D images.

Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

NASA Astrophysics Data System (ADS)

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

2014-03-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

Studies on complex π-π and T-stacking features of imidazole and phenyl/p-halophenyl units in series of 5-amino-1-(phenyl/p-halophenyl)imidazole-4-carboxamides and their carbonitrile derivatives: Role of halogens in tuning of conformation

NASA Astrophysics Data System (ADS)

Das, Aniruddha

2017-11-01

5-amino-1-(phenyl/p-halophenyl)imidazole-4-carboxamides (N-phenyl AICA) (2a-e) and 5-amino-1-(phenyl/p-halophenyl)imidazole-4-carbonitriles (N-phenyl AICN) (3a-e) had been synthesized. X-ray crystallographic studies of 2a-e and 3a-e had been performed to identify any distinct change in stacking patterns in their crystal lattice. Single crystal X-ray diffraction studies of 2a-e revealed π-π stack formations with both imidazole and phenyl/p-halophenyl units in anti and syn parallel-displaced (PD)-type dispositions. No π-π stacking of imidazole occurred when the halogen substituent is bromo or iodo; π-π stacking in these cases occurred involving phenyl rings only. The presence of an additional T-stacking had been observed in crystal lattices of 3a-e. Vertical π-π stacking distances in anti-parallel PD-type arrangements as well as T-stacking distances had shown stacking distances short enough to impart stabilization whereas syn-parallel stacking arrangements had got much larger π-π stacking distances to belie any syn-parallel stacking stabilization. DFT studies had been pursued for quantifying the π-π stacking and T-stacking stabilization. The plotted curves for anti-parallel and T-stacked moieties had similarities to the 'Morse potential energy curve for diatomic molecule'. The minima of the curves corresponded to the most stable stacking distances and related energy values indicated stacking stabilization. Similar DFT studies on syn-parallel systems of 2b corresponded to no π-π stacking stabilization at all. Halogen-halogen interactions had also been observed to stabilize the compounds 2d, 2e and 3d. Nano-structural behaviour of the series of compounds 2a-e and 3a-e were thoroughly investigated.

Filtrations on Springer fiber cohomology and Kostka polynomials

NASA Astrophysics Data System (ADS)

Bellamy, Gwyn; Schedler, Travis

2018-03-01

We prove a conjecture which expresses the bigraded Poisson-de Rham homology of the nilpotent cone of a semisimple Lie algebra in terms of the generalized (one-variable) Kostka polynomials, via a formula suggested by Lusztig. This allows us to construct a canonical family of filtrations on the flag variety cohomology, and hence on irreducible representations of the Weyl group, whose Hilbert series are given by the generalized Kostka polynomials. We deduce consequences for the cohomology of all Springer fibers. In particular, this computes the grading on the zeroth Poisson homology of all classical finite W-algebras, as well as the filtration on the zeroth Hochschild homology of all quantum finite W-algebras, and we generalize to all homology degrees. As a consequence, we deduce a conjecture of Proudfoot on symplectic duality, relating in type A the Poisson homology of Slodowy slices to the intersection cohomology of nilpotent orbit closures. In the last section, we give an analogue of our main theorem in the setting of mirabolic D-modules.

Pareto genealogies arising from a Poisson branching evolution model with selection.

PubMed

Huillet, Thierry E

2014-02-01

We study a class of coalescents derived from a sampling procedure out of N i.i.d. Pareto(α) random variables, normalized by their sum, including β-size-biasing on total length effects (β < α). Depending on the range of α we derive the large N limit coalescents structure, leading either to a discrete-time Poisson-Dirichlet (α, -β) Ξ-coalescent (α ε[0, 1)), or to a family of continuous-time Beta (2 - α, α - β)Λ-coalescents (α ε[1, 2)), or to the Kingman coalescent (α ≥ 2). We indicate that this class of coalescent processes (and their scaling limits) may be viewed as the genealogical processes of some forward in time evolving branching population models including selection effects. In such constant-size population models, the reproduction step, which is based on a fitness-dependent Poisson Point Process with scaling power-law(α) intensity, is coupled to a selection step consisting of sorting out the N fittest individuals issued from the reproduction step.

A Fast MHD Code for Gravitationally Stratified Media using Graphical Processing Units: SMAUG

NASA Astrophysics Data System (ADS)

Griffiths, M. K.; Fedun, V.; Erdélyi, R.

2015-03-01

Parallelization techniques have been exploited most successfully by the gaming/graphics industry with the adoption of graphical processing units (GPUs), possessing hundreds of processor cores. The opportunity has been recognized by the computational sciences and engineering communities, who have recently harnessed successfully the numerical performance of GPUs. For example, parallel magnetohydrodynamic (MHD) algorithms are important for numerical modelling of highly inhomogeneous solar, astrophysical and geophysical plasmas. Here, we describe the implementation of SMAUG, the Sheffield Magnetohydrodynamics Algorithm Using GPUs. SMAUG is a 1-3D MHD code capable of modelling magnetized and gravitationally stratified plasma. The objective of this paper is to present the numerical methods and techniques used for porting the code to this novel and highly parallel compute architecture. The methods employed are justified by the performance benchmarks and validation results demonstrating that the code successfully simulates the physics for a range of test scenarios including a full 3D realistic model of wave propagation in the solar atmosphere.

Scaled Heavy-Ball Acceleration of the Richardson-Lucy Algorithm for 3D Microscopy Image Restoration.

PubMed

Wang, Hongbin; Miller, Paul C

2014-02-01

The Richardson-Lucy algorithm is one of the most important in image deconvolution. However, a drawback is its slow convergence. A significant acceleration was obtained using the technique proposed by Biggs and Andrews (BA), which is implemented in the deconvlucy function of the image processing MATLAB toolbox. The BA method was developed heuristically with no proof of convergence. In this paper, we introduce the heavy-ball (H-B) method for Poisson data optimization and extend it to a scaled H-B method, which includes the BA method as a special case. The method has a proof of the convergence rate of O(K(-2)), where k is the number of iterations. We demonstrate the superior convergence performance, by a speedup factor of five, of the scaled H-B method on both synthetic and real 3D images.

Signal and noise modeling in confocal laser scanning fluorescence microscopy.

PubMed

Herberich, Gerlind; Windoffer, Reinhard; Leube, Rudolf E; Aach, Til

2012-01-01

Fluorescence confocal laser scanning microscopy (CLSM) has revolutionized imaging of subcellular structures in biomedical research by enabling the acquisition of 3D time-series of fluorescently-tagged proteins in living cells, hence forming the basis for an automated quantification of their morphological and dynamic characteristics. Due to the inherently weak fluorescence, CLSM images exhibit a low SNR. We present a novel model for the transfer of signal and noise in CLSM that is both theoretically sound as well as corroborated by a rigorous analysis of the pixel intensity statistics via measurement of the 3D noise power spectra, signal-dependence and distribution. Our model provides a better fit to the data than previously proposed models. Further, it forms the basis for (i) the simulation of the CLSM imaging process indispensable for the quantitative evaluation of CLSM image analysis algorithms, (ii) the application of Poisson denoising algorithms and (iii) the reconstruction of the fluorescence signal.

Compile-Time Partitioning and Scheduling of Parallel Programs. Extended Summary,

DTIC Science & Technology

1986-01-01

OO-MI70 9PROGRAMS EXTENED, SUMNNRY(U) STANFORD, UNIV CA COMPUTERSYSTEMS LAO V SARKAR ET AL. L986 MDA9S3-SS-C-S432 UNCLASSIFIEDj F/ G 9/2 H El- 1 9 5...9 C M E h h h" E P RIIN N E O UI G O Fh E L i E Eu Iwle ui J l~I-O IWI INW 2-5 1= 13.111 2-2 l o U l1 . A 12- "m ’- - "- m°" m ’o ’ l ’. , " l...J. A. et al. "Parallel Processing: A Smart Compiler and a Dumb Machine". SIGPLAN Notices 19, 6 (June 1984). 8. Gajski , D. D., Padua, D. K. & Kuck, D

Auxetic Mechanical Metamaterials to Enhance Sensitivity of Stretchable Strain Sensors.

PubMed

Jiang, Ying; Liu, Zhiyuan; Matsuhisa, Naoji; Qi, Dianpeng; Leow, Wan Ru; Yang, Hui; Yu, Jiancan; Chen, Geng; Liu, Yaqing; Wan, Changjin; Liu, Zhuangjian; Chen, Xiaodong

2018-03-01

Stretchable strain sensors play a pivotal role in wearable devices, soft robotics, and Internet-of-Things, yet these viable applications, which require subtle strain detection under various strain, are often limited by low sensitivity. This inadequate sensitivity stems from the Poisson effect in conventional strain sensors, where stretched elastomer substrates expand in the longitudinal direction but compress transversely. In stretchable strain sensors, expansion separates the active materials and contributes to the sensitivity, while Poisson compression squeezes active materials together, and thus intrinsically limits the sensitivity. Alternatively, auxetic mechanical metamaterials undergo 2D expansion in both directions, due to their negative structural Poisson's ratio. Herein, it is demonstrated that such auxetic metamaterials can be incorporated into stretchable strain sensors to significantly enhance the sensitivity. Compared to conventional sensors, the sensitivity is greatly elevated with a 24-fold improvement. This sensitivity enhancement is due to the synergistic effect of reduced structural Poisson's ratio and strain concentration. Furthermore, microcracks are elongated as an underlying mechanism, verified by both experiments and numerical simulations. This strategy of employing auxetic metamaterials can be further applied to other stretchable strain sensors with different constituent materials. Moreover, it paves the way for utilizing mechanical metamaterials into a broader library of stretchable electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parallelized CCHE2D flow model with CUDA Fortran on Graphics Process Units

USDA-ARS?s Scientific Manuscript database

This paper presents the CCHE2D implicit flow model parallelized using CUDA Fortran programming technique on Graphics Processing Units (GPUs). A parallelized implicit Alternating Direction Implicit (ADI) solver using Parallel Cyclic Reduction (PCR) algorithm on GPU is developed and tested. This solve...

Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes

NASA Technical Reports Server (NTRS)

Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak

2004-01-01

High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel Benchmarks (NPB). In this paper, we present some interesting performance results of ow OpenMP parallel implementation on different architectures such as the SGI Origin2000, SGI Altix, and Cray MTA-2.

Efficient LIDAR Point Cloud Data Managing and Processing in a Hadoop-Based Distributed Framework

NASA Astrophysics Data System (ADS)

Wang, C.; Hu, F.; Sha, D.; Han, X.

2017-10-01

Light Detection and Ranging (LiDAR) is one of the most promising technologies in surveying and mapping city management, forestry, object recognition, computer vision engineer and others. However, it is challenging to efficiently storage, query and analyze the high-resolution 3D LiDAR data due to its volume and complexity. In order to improve the productivity of Lidar data processing, this study proposes a Hadoop-based framework to efficiently manage and process LiDAR data in a distributed and parallel manner, which takes advantage of Hadoop's storage and computing ability. At the same time, the Point Cloud Library (PCL), an open-source project for 2D/3D image and point cloud processing, is integrated with HDFS and MapReduce to conduct the Lidar data analysis algorithms provided by PCL in a parallel fashion. The experiment results show that the proposed framework can efficiently manage and process big LiDAR data.

3D multiphysics modeling of superconducting cavities with a massively parallel simulation suite

NASA Astrophysics Data System (ADS)

Kononenko, Oleksiy; Adolphsen, Chris; Li, Zenghai; Ng, Cho-Kuen; Rivetta, Claudio

2017-10-01

Radiofrequency cavities based on superconducting technology are widely used in particle accelerators for various applications. The cavities usually have high quality factors and hence narrow bandwidths, so the field stability is sensitive to detuning from the Lorentz force and external loads, including vibrations and helium pressure variations. If not properly controlled, the detuning can result in a serious performance degradation of a superconducting accelerator, so an understanding of the underlying detuning mechanisms can be very helpful. Recent advances in the simulation suite ace3p have enabled realistic multiphysics characterization of such complex accelerator systems on supercomputers. In this paper, we present the new capabilities in ace3p for large-scale 3D multiphysics modeling of superconducting cavities, in particular, a parallel eigensolver for determining mechanical resonances, a parallel harmonic response solver to calculate the response of a cavity to external vibrations, and a numerical procedure to decompose mechanical loads, such as from the Lorentz force or piezoactuators, into the corresponding mechanical modes. These capabilities have been used to do an extensive rf-mechanical analysis of dressed TESLA-type superconducting cavities. The simulation results and their implications for the operational stability of the Linac Coherent Light Source-II are discussed.

A parallel implementation of 3D Zernike moment analysis

NASA Astrophysics Data System (ADS)

Berjón, Daniel; Arnaldo, Sergio; Morán, Francisco

2011-01-01

Zernike polynomials are a well known set of functions that find many applications in image or pattern characterization because they allow to construct shape descriptors that are invariant against translations, rotations or scale changes. The concepts behind them can be extended to higher dimension spaces, making them also fit to describe volumetric data. They have been less used than their properties might suggest due to their high computational cost. We present a parallel implementation of 3D Zernike moments analysis, written in C with CUDA extensions, which makes it practical to employ Zernike descriptors in interactive applications, yielding a performance of several frames per second in voxel datasets about 2003 in size. In our contribution, we describe the challenges of implementing 3D Zernike analysis in a general-purpose GPU. These include how to deal with numerical inaccuracies, due to the high precision demands of the algorithm, or how to deal with the high volume of input data so that it does not become a bottleneck for the system.

Water Selective Imaging and bSSFP Banding Artifact Correction in Humans and Small Animals at 3T and 7T, Respectively

PubMed Central

Ribot, Emeline J.; Wecker, Didier; Trotier, Aurélien J.; Dallaudière, Benjamin; Lefrançois, William; Thiaudière, Eric; Franconi, Jean-Michel; Miraux, Sylvain

2015-01-01

Introduction The purpose of this paper is to develop an easy method to generate both fat signal and banding artifact free 3D balanced Steady State Free Precession (bSSFP) images at high magnetic field. Methods In order to suppress fat signal and bSSFP banding artifacts, two or four images were acquired with the excitation frequency of the water-selective binomial radiofrequency pulse set On Resonance or shifted by a maximum of 3/4TR. Mice and human volunteers were imaged at 7T and 3T, respectively to perform whole-body and musculoskeletal imaging. “Sum-Of-Square” reconstruction was performed and combined or not with parallel imaging. Results The frequency selectivity of 1-2-3-2-1 or 1-3-3-1 binomial pulses was preserved after (3/4TR) frequency shifting. Consequently, whole body small animal 3D imaging was performed at 7T and enabled visualization of small structures within adipose tissue like lymph nodes. In parallel, this method allowed 3D musculoskeletal imaging in humans with high spatial resolution at 3T. The combination with parallel imaging allowed the acquisition of knee images with ~500μm resolution images in less than 2min. In addition, ankles, full head coverage and legs of volunteers were imaged, demonstrating the possible application of the method also for large FOV. Conclusion In conclusion, this robust method can be applied in small animals and humans at high magnetic fields. The high SNR and tissue contrast obtained in short acquisition times allows to prescribe bSSFP sequence for several preclinical and clinical applications. PMID:26426849

Heart Fibrillation and Parallel Supercomputers

NASA Technical Reports Server (NTRS)

Kogan, B. Y.; Karplus, W. J.; Chudin, E. E.

1997-01-01

The Luo and Rudy 3 cardiac cell mathematical model is implemented on the parallel supercomputer CRAY - T3D. The splitting algorithm combined with variable time step and an explicit method of integration provide reasonable solution times and almost perfect scaling for rectilinear wave propagation. The computer simulation makes it possible to observe new phenomena: the break-up of spiral waves caused by intracellular calcium and dynamics and the non-uniformity of the calcium distribution in space during the onset of the spiral wave.

An Investigation of the Flow Physics of Acoustic Liners by Direct Numerical Simulation

NASA Technical Reports Server (NTRS)

Watson, Willie R. (Technical Monitor); Tam, Christopher

2004-01-01

This report concentrates on reporting the effort and status of work done on three dimensional (3-D) simulation of a multi-hole resonator in an impedance tube. This work is coordinated with a parallel experimental effort to be carried out at the NASA Langley Research Center. The outline of this report is as follows : 1. Preliminary consideration. 2. Computation model. 3. Mesh design and parallel computing. 4. Visualization. 5. Status of computer code development. 1. Preliminary Consideration.

Integrable systems with BMS3 Poisson structure and the dynamics of locally flat spacetimes

NASA Astrophysics Data System (ADS)

Fuentealba, Oscar; Matulich, Javier; Pérez, Alfredo; Pino, Miguel; Rodríguez, Pablo; Tempo, David; Troncoso, Ricardo

2018-01-01

We construct a hierarchy of integrable systems whose Poisson structure corresponds to the BMS3 algebra, and then discuss its description in terms of the Riemannian geometry of locally flat spacetimes in three dimensions. The analysis is performed in terms of two-dimensional gauge fields for isl(2,R) , being isomorphic to the Poincaré algebra in 3D. Although the algebra is not semisimple, the formulation can still be carried out à la Drinfeld-Sokolov because it admits a nondegenerate invariant bilinear metric. The hierarchy turns out to be bi-Hamiltonian, labeled by a nonnegative integer k, and defined through a suitable generalization of the Gelfand-Dikii polynomials. The symmetries of the hierarchy are explicitly found. For k ≥ 1, the corresponding conserved charges span an infinite-dimensional Abelian algebra without central extensions, so that they are in involution; while in the case of k = 0, they generate the BMS3 algebra. In the special case of k = 1, by virtue of a suitable field redefinition and time scaling, the field equations are shown to be equivalent to the ones of a specific type of the Hirota-Satsuma coupled KdV systems. For k ≥ 1, the hierarchy also includes the so-called perturbed KdV equations as a particular case. A wide class of analytic solutions is also explicitly constructed for a generic value of k. Remarkably, the dynamics can be fully geometrized so as to describe the evolution of spacelike surfaces embedded in locally flat spacetimes. Indeed, General Relativity in 3D can be endowed with a suitable set of boundary conditions, so that the Einstein equations precisely reduce to the ones of the hierarchy aforementioned. The symmetries of the integrable systems then arise as diffeomorphisms that preserve the asymptotic form of the spacetime metric, and therefore, they become Noetherian. The infinite set of conserved charges is then recovered from the corresponding surface integrals in the canonical approach.

Planned development of a 3D computer based on free-space optical interconnects

NASA Astrophysics Data System (ADS)

Neff, John A.; Guarino, David R.

1994-05-01

Free-space optical interconnection has the potential to provide upwards of a million data channels between planes of electronic circuits. This may result in the planar board and backplane structures of today giving away to 3-D stacks of wafers or multi-chip modules interconnected via channels running perpendicular to the processor planes, thereby eliminating much of the packaging overhead. Three-dimensional packaging is very appealing for tightly coupled fine-grained parallel computing where the need for massive numbers of interconnections is severely taxing the capabilities of the planar structures. This paper describes a coordinated effort by four research organizations to demonstrate an operational fine-grained parallel computer that achieves global connectivity through the use of free space optical interconnects.

Proteus-MOC: A 3D deterministic solver incorporating 2D method of characteristics

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

Marin-Lafleche, A.; Smith, M. A.; Lee, C.

2013-07-01

A new transport solution methodology was developed by combining the two-dimensional method of characteristics with the discontinuous Galerkin method for the treatment of the axial variable. The method, which can be applied to arbitrary extruded geometries, was implemented in PROTEUS-MOC and includes parallelization in group, angle, plane, and space using a top level GMRES linear algebra solver. Verification tests were performed to show accuracy and stability of the method with the increased number of angular directions and mesh elements. Good scalability with parallelism in angle and axial planes is displayed. (authors)

Two-dimensional confinement of 3d{1} electrons in LaTiO_{3}/LaAlO{3} multilayers.

PubMed

Seo, S S A; Han, M J; Hassink, G W J; Choi, W S; Moon, S J; Kim, J S; Susaki, T; Lee, Y S; Yu, J; Bernhard, C; Hwang, H Y; Rijnders, G; Blank, D H A; Keimer, B; Noh, T W

2010-01-22

We report spectroscopic ellipsometry measurements of the anisotropy of the interband transitions parallel and perpendicular to the planes of (LaTiO3)n(LaAlO3)5 multilayers with n=1-3. These provide direct information about the electronic structure of the two-dimensional (2D) 3d{1} state of the Ti ions. In combination with local density approximation, including a Hubbard U calculation, we suggest that 2D confinement in the TiO2 slabs lifts the degeneracy of the t{2g} states leaving only the planar d{xy} orbitals occupied. We outline that these multilayers can serve as a model system for the study of the t{2g} 2D Hubbard model.

Crustal structure of the Transantarctic Mountains, Ellsworth Mountains and Marie Byrd Land, Antarctica: constraints on shear wave velocities, Poisson's ratios and Moho depths

NASA Astrophysics Data System (ADS)

Ramirez, C.; Nyblade, A.; Emry, E. L.; Julià, J.; Sun, X.; Anandakrishnan, S.; Wiens, D. A.; Aster, R. C.; Huerta, A. D.; Winberry, P.; Wilson, T.

2017-12-01

A uniform set of crustal parameters for seismic stations deployed on rock in West Antarctica and the Transantarctic Mountains (TAM) has been obtained to help elucidate similarities and differences in crustal structure within and between several tectonic blocks that make up these regions. P-wave receiver functions have been analysed using the H-κ stacking method to develop estimates of thickness and bulk Poisson's ratio for the crust, and jointly inverted with surface wave dispersion measurements to obtain depth-dependent shear wave velocity models for the crust and uppermost mantle. The results from 33 stations are reported, including three stations for which no previous results were available. The average crustal thickness is 30 ± 5 km along the TAM front, and 38 ± 2 km in the interior of the mountain range. The average Poisson's ratios for these two regions are 0.25 ± 0.03 and 0.26 ± 0.02, respectively, and they have similar average crustal Vs of 3.7 ± 0.1 km s-1. At multiple stations within the TAM, we observe evidence for mafic layering within or at the base of the crust, which may have resulted from the Ferrar magmatic event. The Ellsworth Mountains have an average crustal thickness of 37 ± 2 km, a Poisson's ratio of 0.27, and average crustal Vs of 3.7 ± 0.1 km s-1, similar to the TAM. This similarity is consistent with interpretations of the Ellsworth Mountains as a tectonically rotated TAM block. The Ross Island region has an average Moho depth of 25 ± 1 km, an average crustal Vs of 3.6 ± 0.1 km s-1 and Poisson's ratio of 0.30, consistent with the mafic Cenozoic volcanism found there and its proximity to the Terror Rift. Marie Byrd Land has an average crustal thickness of 30 ± 2 km, Poisson's ratio of 0.25 ± 0.04 and crustal Vs of 3.7 ± 0.1 km s-1. One station (SILY) in Marie Byrd Land is near an area of recent volcanism and deep (25-40 km) seismicity, and has a high Poisson's ratio, consistent with the presence of partial melt in the crust.

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.

Noncommutative gerbes and deformation quantization

NASA Astrophysics Data System (ADS)

Aschieri, Paolo; Baković, Igor; Jurčo, Branislav; Schupp, Peter

2010-11-01

We define noncommutative gerbes using the language of star products. Quantized twisted Poisson structures are discussed as an explicit realization in the sense of deformation quantization. Our motivation is the noncommutative description of D-branes in the presence of topologically non-trivial background fields.

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.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase I is complete for the development of a Computational Fluid Dynamics parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

Research in Parallel Algorithms and Software for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Domel, Neal D.

1996-01-01

Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

First experiments probing the collision of parallel magnetic fields using laser-produced plasmas

DOE PAGES

Rosenberg, M. J.; Li, C. K.; Fox, W.; ...

2015-04-08

Novel experiments to study the strongly-driven collision of parallel magnetic fields in β~10, laser-produced plasmas have been conducted using monoenergetic proton radiography. These experiments were designed to probe the process of magnetic flux pileup, which has been identified in prior laser-plasma experiments as a key physical mechanism in the reconnection of anti-parallel magnetic fields when the reconnection inflow is dominated by strong plasma flows. In the present experiments using colliding plasmas carrying parallel magnetic fields, the magnetic flux is found to be conserved and slightly compressed in the collision region. Two-dimensional (2D) particle-in-cell (PIC) simulations predict a stronger flux compressionmore » and amplification of the magnetic field strength, and this discrepancy is attributed to the three-dimensional (3D) collision geometry. Future experiments may drive a stronger collision and further explore flux pileup in the context of the strongly-driven interaction of magnetic fields.« less

Implementation of a 3D mixing layer code on parallel computers

NASA Technical Reports Server (NTRS)

Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.

1995-01-01

This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations

NASA Astrophysics Data System (ADS)

Tzoupis, Haralambos; Leonis, Georgios; Durdagi, Serdar; Mouchlis, Varnavas; Mavromoustakos, Thomas; Papadopoulos, Manthos G.

2011-10-01

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein-ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.

Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains.

PubMed

Jha, Ashwani; Flurchick, K M; Bikdash, Marwan; Kc, Dukka B

2016-01-01

Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10-15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry. In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers. The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors. Scaling is better for proteins with a larger number of residues. For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors.

Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains

PubMed Central

Jha, Ashwani; Flurchick, K. M.; Bikdash, Marwan

2016-01-01

Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10–15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry. In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers. The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors. Scaling is better for proteins with a larger number of residues. For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors. PMID:27747230

A numerical code for a three-dimensional magnetospheric MHD equilibrium model

NASA Technical Reports Server (NTRS)

Voigt, G.-H.

1992-01-01

Two dimensional and three dimensional MHD equilibrium models were begun for Earth's magnetosphere. The original proposal was motivated by realizing that global, purely data based models of Earth's magnetosphere are inadequate for studying the underlying plasma physical principles according to which the magnetosphere evolves on the quasi-static convection time scale. Complex numerical grid generation schemes were established for a 3-D Poisson solver, and a robust Grad-Shafranov solver was coded for high beta MHD equilibria. Thus, the effects were calculated of both the magnetopause geometry and boundary conditions on the magnetotail current distribution.

Exploiting Data Similarity to Reduce Memory Footprints

DTIC Science & Technology

2011-01-01

leslie3d Fortran Computational Fluid Dynamics (CFD) application 122. tachyon C Parallel Ray Tracing application 128.GAPgeofem C and Fortran Simulates...benefits most from SBLLmalloc; LAMMPS, which shows moderate similarity from primarily zero pages; and 122. tachyon , a parallel ray- tracing application...similarity across MPI tasks. They primarily are zero- pages although a small fraction (≈10%) are non-zero pages. 122. tachyon is an image rendering

Partial-Interval Estimation of Count: Uncorrected and Poisson-Corrected Error Levels

ERIC Educational Resources Information Center

Yoder, Paul J.; Ledford, Jennifer R.; Harbison, Amy L.; Tapp, Jon T.

2018-01-01

A simulation study that used 3,000 computer-generated event streams with known behavior rates, interval durations, and session durations was conducted to test whether the main and interaction effects of true rate and interval duration affect the error level of uncorrected and Poisson-transformed (i.e., "corrected") count as estimated by…

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.

Vitamin D3 Supplementation and Childhood Diarrhea: A Randomized Controlled Trial

PubMed Central

Maroof, Zabihullah; Chandramohan, Daniel; Bruce, Jane; Mughal, M. Zulf; Bhutta, Zulfiqar; Walraven, Gijs; Masher, Mohammad I.; Ensink, Jeroen H.J.; Manaseki-Holland, Semira

2013-01-01

OBJECTIVE: To investigate the effect of vitamin D3 supplementation on the incidence and risk for first and recurrent diarrheal illnesses among children in Kabul, Afghanistan. METHODS: This double-blind placebo-controlled trial randomized 3046 high-risk 1- to 11-month-old infants to receive 6 quarterly doses of oral vitamin D3 (cholecalciferol 100 000 IU) or placebo in inner city Kabul. Data on diarrheal episodes (≥3 loose/liquid stools in 24 hours) was gathered through active and passive surveillance over 18 months of follow-up. Time to first diarrheal illness was analyzed by using Kaplan-Meier plots. Incidence rates and hazard ratios (HRs) were calculated by using recurrent event Poisson regression models. RESULTS: No significant difference existed in survival time to first diarrheal illness (log rank P = .55). The incidences of diarrheal episodes were 3.43 (95% confidence interval [CI], 3.28–3.59) and 3.59 per child-year (95% CI, 3.44–3.76) in the placebo and intervention arms, respectively. Vitamin D3 supplementation was found to have no effect on the risk for recurrent diarrheal disease in either intention-to-treat (HR, 1.05; 95% CI, 0.98–1.17; P = .15) or per protocol (HR, 1.05; 95% CI, 0.98–1.12; P = .14) analyses. The lack of preventive benefit remained when the randomized population was stratified by age groups, nutritional status, and seasons. CONCLUSIONS: Quarterly supplementation with vitamin D3 conferred no reduction on time to first illness or on the risk for recurrent diarrheal disease in this study. Similar supplementation to comparable populations is not recommended. Additional research in alternative settings may be helpful in elucidating the role of vitamin D3 supplementation for prevention of diarrheal diseases. PMID:24019420

Parallel 3D Multi-Stage Simulation of a Turbofan Engine

NASA Technical Reports Server (NTRS)

Turner, Mark G.; Topp, David A.

1998-01-01

A 3D multistage simulation of each component of a modern GE Turbofan engine has been made. An axisymmetric view of this engine is presented in the document. This includes a fan, booster rig, high pressure compressor rig, high pressure turbine rig and a low pressure turbine rig. In the near future, all components will be run in a single calculation for a solution of 49 blade rows. The simulation exploits the use of parallel computations by using two levels of parallelism. Each blade row is run in parallel and each blade row grid is decomposed into several domains and run in parallel. 20 processors are used for the 4 blade row analysis. The average passage approach developed by John Adamczyk at NASA Lewis Research Center has been further developed and parallelized. This is APNASA Version A. It is a Navier-Stokes solver using a 4-stage explicit Runge-Kutta time marching scheme with variable time steps and residual smoothing for convergence acceleration. It has an implicit K-E turbulence model which uses an ADI solver to factor the matrix. Between 50 and 100 explicit time steps are solved before a blade row body force is calculated and exchanged with the other blade rows. This outer iteration has been coined a "flip." Efforts have been made to make the solver linearly scaleable with the number of blade rows. Enough flips are run (between 50 and 200) so the solution in the entire machine is not changing. The K-E equations are generally solved every other explicit time step. One of the key requirements in the development of the parallel code was to make the parallel solution exactly (bit for bit) match the serial solution. This has helped isolate many small parallel bugs and guarantee the parallelization was done correctly. The domain decomposition is done only in the axial direction since the number of points axially is much larger than the other two directions. This code uses MPI for message passing. The parallel speed up of the solver portion (no 1/0 or body force calculation) for a grid which has 227 points axially.

FoxP2 is a Parvocellular-Specific Transcription Factor in the Visual Thalamus of Monkeys and Ferrets

PubMed Central

Iwai, Lena; Ohashi, Yohei; van der List, Deborah; Usrey, William Martin; Miyashita, Yasushi; Kawasaki, Hiroshi

2013-01-01

Although the parallel visual pathways are a fundamental basis of visual processing, our knowledge of their molecular properties is still limited. Here, we uncovered a parvocellular-specific molecule in the dorsal lateral geniculate nucleus (dLGN) of higher mammals. We found that FoxP2 transcription factor was specifically expressed in X cells of the adult ferret dLGN. Interestingly, FoxP2 was also specifically expressed in parvocellular layers 3–6 of the dLGN of adult old world monkeys, providing new evidence for a homology between X cells in the ferret dLGN and parvocellular cells in the monkey dLGN. Furthermore, this expression pattern was established as early as gestation day 140 in the embryonic monkey dLGN, suggesting that parvocellular specification has already occurred when the cytoarchitectonic dLGN layers are formed. Our results should help in gaining a fundamental understanding of the development, evolution, and function of the parallel visual pathways, which are especially prominent in higher mammals. PMID:22791804

Evaluation of Tensile Young's Modulus and Poisson's Ratio of a Bi-modular Rock from the Displacement Measurements in a Brazilian Test

NASA Astrophysics Data System (ADS)

Patel, Shantanu; Martin, C. Derek

2018-02-01

Unlike metals, rocks show bi-modularity (different Young's moduli and Poisson's ratios in compression and tension). Displacements monitored during the Brazilian test are used in this study to obtain the Young's modulus and Poisson's ratio in tension. New equations for the displacements in a Brazilian test are derived considering the bi-modularity in the stress-strain relations. The digital image correlation technique was used to monitor the displacements of the Brazilian disk flat surface. To validate the Young's modulus and Poisson's ratio obtained from the Brazilian test, the results were compared with the values from the direct tension tests. The results obtained from the Brazilian test were repetitive and within 3.5% of the value obtained from the direct tension test for the rock tested.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

2016-11-02

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

Monitoring the Deterioration of Stone at Mindener MUSEUM'S Lapidarium

NASA Astrophysics Data System (ADS)

Pomaska, G.

2013-07-01

Mindener Museum's Lapidarium incorporates a collection of stone work like reliefs, sculptures and inscriptions from different time epochs as advices of the city's history. These gems must be protected against environmental influences and deterioration. In advance of the measures a 3D reconstruction and detailed documentation has to be taken. The framework to establish hard- and software must match the museum's infrastructure. Two major question will be answered. Are low-cost scanning devices like depth cameras and digital of the shelf cameras suitable for the data acquisition? Does the functionality of open source and freeware covers the demand on investigation and analysis in this application? The working chain described in this contribution covers the structure from motion method and the reconstruction with RGB-D cameras. Mesh processing such as cleaning, smoothing, poisson surface reconstruction and texturing will be accomplished with MeshLab. Data acquisition and modelling continues in structure analysis. Therefore the focus lies as well on latest software developments related to 3D printing technologies. Repairing and finishing of meshes is a task for MeshMixer. Netfabb as a tool for positioning, dimensioning and slicing enables virtual handling of the items. On the Sketchfab web site one can publish and share 3D objects with integration into web pages supported by WebGL. Finally if a prototype is needed, the mesh can be uploaded to a 3D printing device provided by an online service.

Improving Bed Management at Wright-Patterson Medical Center

DTIC Science & Technology

1989-09-01

arrival distributions are Poisson, as in Sim2, then interarrival times are distributed exponentially (Budnick, Mcleavey , and Mojena, 1988:770). While... McLeavey , D. and Mojena R., Principles of Operations Research for Management (second edition). Homewood IL: Irwin, 1988. Cannoodt, L. J. and

Enhanced electron mixing and heating in 3-D asymmetric reconnection at the Earth's magnetopause

DOE PAGES

Le, Ari Yitzchak; Daughton, William Scott; Chen, Li -Jen; ...

2017-03-01

Here, electron heating and mixing during asymmetric reconnection are studied with a 3-D kinetic simulation that matches plasma parameters from Magnetospheric Multiscale (MMS) spacecraft observations of a magnetopause diffusion region. The mixing and heating are strongly enhanced across the magnetospheric separatrix compared to a 2-D simulation. The transport of particles across the separatrix in 3-D is attributed to lower hybrid drift turbulence excited at the steep density gradient near the magnetopause. In the 3-D simulation (and not the 2-D simulation), the electron temperature parallel to the magnetic field within the mixing layer is significantly higher than its upstream value inmore » agreement with the MMS observations.« less

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.

Wave Turning and Flow Angle in the E-Region Ionosphere

NASA Astrophysics Data System (ADS)

Young, M.; Oppenheim, M. M.; Dimant, Y. S.

2016-12-01

This work presents results of particle-in-cell (PIC) simulations of Farley-Buneman (FB) turbulence at various altitudes in the high-latitude E-region ionosphere. In that region, the FB instability regularly produces meter-scale plasma irregularities. VHF radars observe coherent echoes via Bragg scatter from wave fronts parallel or anti-parallel to the radar line of sight (LoS) but do not necessarily measure the mean direction of wave propagation. Haldoupis (1984) conducted a study of diffuse radar aurora and found that the spectral width of back-scattered power depends critically on the angle between the radar LoS and the true flow direction, called the flow angle. Knowledge of the flow angle will allow researchers to better interpret observations of coherent back-scatter. Experiments designed to observe meter-scale irregularities in the E-region ionosphere created by the FB instability typically assume that the predominant flow direction is the E×B direction. However, linear theory of Dimant and Oppenheim (2004) showed that FB waves should turn away from E×B and particle-in-cell simulations by Oppenheim and Dimant (2013) support the theory. The present study comprises a quantitative analysis of the dependence of back-scattered power, flow velocity, and spectral width as functions of the flow angle. It also demonstrates that the mean direction of meter-scale wave propagation may differ from the E×B direction by tens of degrees. The analysis includes 2-D and 3-D simulations at a range of altitudes in the auroral ionosphere. Comparison between 2-D and 3-D simulations illustrates the relative importance to the irregularity spectrum of a small but finite component in the direction parallel to B. Previous work has shown this small parallel component to be important to turbulent electron heating and nonlinear transport.

Automated Generation of Message-Passing Programs: An Evaluation Using CAPTools

NASA Technical Reports Server (NTRS)

Hribar, Michelle R.; Jin, Haoqiang; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

1998-01-01

Scientists at NASA Ames Research Center have been developing computational aeroscience applications on highly parallel architectures over the past ten years. During that same time period, a steady transition of hardware and system software also occurred, forcing us to expend great efforts into migrating and re-coding our applications. As applications and machine architectures become increasingly complex, the cost and time required for this process will become prohibitive. In this paper, we present the first set of results in our evaluation of interactive parallelization tools. In particular, we evaluate CAPTool's ability to parallelize computational aeroscience applications. CAPTools was tested on serial versions of the NAS Parallel Benchmarks and ARC3D, a computational fluid dynamics application, on two platforms: the SGI Origin 2000 and the Cray T3E. This evaluation includes performance, amount of user interaction required, limitations and portability. Based on these results, a discussion on the feasibility of computer aided parallelization of aerospace applications is presented along with suggestions for future work.

Existence and uniqueness, attraction for stochastic age-structured population systems with diffusion and Poisson jump

NASA Astrophysics Data System (ADS)

Chen, Huabin

2013-08-01

In this paper, the problems about the existence and uniqueness, attraction for strong solution of stochastic age-structured population systems with diffusion and Poisson jump are considered. Under the non-Lipschitz condition with the Lipschitz condition being considered as a special case, the existence and uniqueness for such systems is firstly proved by using the Burkholder-Davis-Gundy inequality (B-D-G inequality) and Itô's formula. And then by using a novel inequality technique, some sufficient conditions ensuring the existence for the domain of attraction are established. As another by-product, the exponential stability in mean square moment of strong solution for such systems can be also discussed.

Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

PubMed Central

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

2013-01-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803

Analyzing hospitalization data: potential limitations of Poisson regression.

PubMed

Weaver, Colin G; Ravani, Pietro; Oliver, Matthew J; Austin, Peter C; Quinn, Robert R

2015-08-01

Poisson regression is commonly used to analyze hospitalization data when outcomes are expressed as counts (e.g. number of days in hospital). However, data often violate the assumptions on which Poisson regression is based. More appropriate extensions of this model, while available, are rarely used. We compared hospitalization data between 206 patients treated with hemodialysis (HD) and 107 treated with peritoneal dialysis (PD) using Poisson regression and compared results from standard Poisson regression with those obtained using three other approaches for modeling count data: negative binomial (NB) regression, zero-inflated Poisson (ZIP) regression and zero-inflated negative binomial (ZINB) regression. We examined the appropriateness of each model and compared the results obtained with each approach. During a mean 1.9 years of follow-up, 183 of 313 patients (58%) were never hospitalized (indicating an excess of 'zeros'). The data also displayed overdispersion (variance greater than mean), violating another assumption of the Poisson model. Using four criteria, we determined that the NB and ZINB models performed best. According to these two models, patients treated with HD experienced similar hospitalization rates as those receiving PD {NB rate ratio (RR): 1.04 [bootstrapped 95% confidence interval (CI): 0.49-2.20]; ZINB summary RR: 1.21 (bootstrapped 95% CI 0.60-2.46)}. Poisson and ZIP models fit the data poorly and had much larger point estimates than the NB and ZINB models [Poisson RR: 1.93 (bootstrapped 95% CI 0.88-4.23); ZIP summary RR: 1.84 (bootstrapped 95% CI 0.88-3.84)]. We found substantially different results when modeling hospitalization data, depending on the approach used. Our results argue strongly for a sound model selection process and improved reporting around statistical methods used for modeling count data. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

A Survey of Parallel Computing

DTIC Science & Technology

1988-07-01

Evaluating Two Massively Parallel Machines. Communications of the ACM .9, , , 176 BIBLIOGRAPHY 29, 8 (August), pp. 752-758. Gajski , D.D., Padua, D.A., Kuck...Computer Architecture, edited by Gajski , D. D., Milutinovic, V. M. Siegel, H. J. and Furht, B. P. IEEE Computer Society Press, Washington, D.C., pp. 387-407

Ordering transitions of weakly anisotropic hard rods in narrow slitlike pores.

PubMed

Aliabadi, Roohollah; Gurin, Péter; Velasco, Enrique; Varga, Szabolcs

2018-01-01

The effect of strong confinement on the positional and orientational ordering is examined in a system of hard rectangular rods with length L and diameter D (L>D) using the Parsons-Lee modification of the second virial density-functional theory. The rods are nonmesogenic (L/D<3) and confined between two parallel hard walls, where the width of the pore (H) is chosen in such a way that both planar (particle's long axis parallel to the walls) and homeotropic (particle's long axis perpendicular to the walls) orderings are possible and a maximum of two layers is allowed to form in the pore. In the extreme confinement limit of H≤2D, where only one-layer structures appear, we observe a structural transition from a planar to a homeotropic fluid layer with increasing density, which becomes sharper as L→H. In wider pores (2D

An Australian and New Zealand Scoping Study on the Use of 3D Immersive Virtual Worlds in Higher Education

ERIC Educational Resources Information Center

Dalgarno, Barney; Lee, Mark J. W.; Carlson, Lauren; Gregory, Sue; Tynan, Belinda

2011-01-01

This article describes the research design of, and reports selected findings from, a scoping study aimed at examining current and planned applications of 3D immersive virtual worlds at higher education institutions across Australia and New Zealand. The scoping study is the first of its kind in the region, intended to parallel and complement a…

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.

Treatment of singularities in cracked bodies

NASA Technical Reports Server (NTRS)

Shivakumar, K. N.; Raju, I. S.

1990-01-01

Three-dimensional finite-element analyses of middle-crack tension (M-T) and bend specimens subjected to mode I loadings were performed to study the stress singularity along the crack front. The specimen was modeled using 20-node isoparametric elements. The displacements and stresses from the analysis were used to estimate the power of singularities using a log-log regression analysis along the crack front. The analyses showed that finite-sized cracked bodies have two singular stress fields of the form rho = C sub o (theta, z) r to the -1/2 power + D sub o (theta, phi) R to the lambda rho power. The first term is the cylindrical singularity with the power -1/2 and is dominant over the middle 96 pct (for Poisson's ratio = 0.3) of the crack front and becomes nearly zero at the free surface. The second singularity is a vertex singularity with the vertex point located at the intersection of the crack front and the free surface. The second term is dominant at the free surface and becomes nearly zero away from the boundary layer. The thickness of the boundary layer depends on Poisson's ratio of the material and is independent of the specimen type. The thickness of the boundary layer varied from 0 pct to about 5 pct of the total specimen thickness as Poisson's ratio varied from 0.0 to 0.45. Because there are two singular stress fields near the free surface, the strain energy release rate (G) is an appropriate parameter to measure the severity of the crack.

Treatment of singularities in cracked bodies

NASA Technical Reports Server (NTRS)

Shivakumar, K. N.; Raju, I. S.

1989-01-01

Three-dimensional finite-element analyses of middle-crack tension (M-T) and bend specimens subjected to mode I loadings were performed to study the stress singularity along the crack front. The specimen was modeled using 20-node isoparametric elements. The displacements and stresses from the analysis were used to estimate the power of singularities using a log-log regression analysis along the crack front. The analyses showed that finite-sized cracked bodies have two singular stress fields of the form rho = C sub o (theta, z) r to the -1/2 power + D sub o (theta, phi) R to the lambda rho power. The first term is the cylindrical singularity with the power -1/2 and is dominant over the middle 96 pct (for Poisson's ratio = 0.3) of the crack front and becomes nearly zero at the free surface. The second singularity is a vertex singularity with the vertex point located at the intersection of the crack front and the free surface. The second term is dominant at the free surface and becomes nearly zero away from the the boundary layer. The thickness of the boundary layer depends on Poisson's ratio of the material and is independent of the specimen type. The thickness of the boundary layer varied from 0 pct to about 5 pct of the total specimen thickness as Poisson's ratio varied from 0.0 to 0.45. Because there are two singular stress fields near the free surface, the strain energy release rate (G) is an appropriate parameter to measure the severity of the crack.

3D and 4D magnetic susceptibility tomography based on complex MR images

DOEpatents

Chen, Zikuan; Calhoun, Vince D

2014-11-11

Magnetic susceptibility is the physical property for T2*-weighted magnetic resonance imaging (T2*MRI). The invention relates to methods for reconstructing an internal distribution (3D map) of magnetic susceptibility values, .chi. (x,y,z), of an object, from 3D T2*MRI phase images, by using Computed Inverse Magnetic Resonance Imaging (CIMRI) tomography. The CIMRI technique solves the inverse problem of the 3D convolution by executing a 3D Total Variation (TV) regularized iterative convolution scheme, using a split Bregman iteration algorithm. The reconstruction of .chi. (x,y,z) can be designed for low-pass, band-pass, and high-pass features by using a convolution kernel that is modified from the standard dipole kernel. Multiple reconstructions can be implemented in parallel, and averaging the reconstructions can suppress noise. 4D dynamic magnetic susceptibility tomography can be implemented by reconstructing a 3D susceptibility volume from a 3D phase volume by performing 3D CIMRI magnetic susceptibility tomography at each snapshot time.

Self-Assembly of Coherently Dynamic, Auxetic Two-Dimensional Protein Crystals

PubMed Central

Suzuki, Yuta; Cardone, Giovanni; Restrepo, David; Zavattieri, Pablo D.; Baker, Timothy S.; Tezcan, F. Akif

2016-01-01

Two-dimensional (2D) crystalline materials possess unique structural, mechanical, and electronic properties1,2, which have rendered them highly attractive in many applications3-5. Although there have been advances in preparing 2D materials that consist of one or few atomic/molecular layers6,7, bottom-up assembly of 2D crystalline materials remains a considerable challenge and an active area of development8-10. Even more challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamicity in porous 3D crystalline solids has been exploited for stimuli-responsive functions and adaptive behavior11-13. As in the case of such 3D materials, integrating flexibility/adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns through a readily accessible design strategy. Three single- or double-point mutants of the C4 symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single disulfide, double disulfide and metal coordination) into crystalline 2D arrays. Owing to the flexibility of the single disulfide interactions, the lattices of one of the variants (C98RhuA) are essentially defect-free and undergo substantial but fully correlated changes in molecular arrangement, giving coherently dynamic 2D molecular lattices. Notably, C98RhuA lattices possess a Poisson's ratio of −1, the lowest thermodynamically possible value for an isotropic material. PMID:27135928

Direct Machining of Low-Loss THz Waveguide Components With an RF Choke.

PubMed

Lewis, Samantha M; Nanni, Emilio A; Temkin, Richard J

2014-12-01

We present results for the successful fabrication of low-loss THz metallic waveguide components using direct machining with a CNC end mill. The approach uses a split-block machining process with the addition of an RF choke running parallel to the waveguide. The choke greatly reduces coupling to the parasitic mode of the parallel-plate waveguide produced by the split-block. This method has demonstrated loss as low as 0.2 dB/cm at 280 GHz for a copper WR-3 waveguide. It has also been used in the fabrication of 3 and 10 dB directional couplers in brass, demonstrating excellent agreement with design simulations from 240-260 GHz. The method may be adapted to structures with features on the order of 200 μm.

MAP Reconstruction for Fourier Rebinned TOF-PET Data

PubMed Central

Bai, Bing; Lin, Yanguang; Zhu, Wentao; Ren, Ran; Li, Quanzheng; Dahlbom, Magnus; DiFilippo, Frank; Leahy, Richard M.

2014-01-01

Time-of-flight (TOF) information improves signal to noise ratio in Positron Emission Tomography (PET). Computation cost in processing TOF-PET sinograms is substantially higher than for nonTOF data because the data in each line of response is divided among multiple time of flight bins. This additional cost has motivated research into methods for rebinning TOF data into lower dimensional representations that exploit redundancies inherent in TOF data. We have previously developed approximate Fourier methods that rebin TOF data into either 3D nonTOF or 2D nonTOF formats. We refer to these methods respectively as FORET-3D and FORET-2D. Here we describe maximum a posteriori (MAP) estimators for use with FORET rebinned data. We first derive approximate expressions for the variance of the rebinned data. We then use these results to rescale the data so that the variance and mean are approximately equal allowing us to use the Poisson likelihood model for MAP reconstruction. MAP reconstruction from these rebinned data uses a system matrix in which the detector response model accounts for the effects of rebinning. Using these methods we compare performance of FORET-2D and 3D with TOF and nonTOF reconstructions using phantom and clinical data. Our phantom results show a small loss in contrast recovery at matched noise levels using FORET compared to reconstruction from the original TOF data. Clinical examples show FORET images that are qualitatively similar to those obtained from the original TOF-PET data but a small increase in variance at matched resolution. Reconstruction time is reduced by a factor of 5 and 30 using FORET3D+MAP and FORET2D+MAP respectively compared to 3D TOF MAP, which makes these methods attractive for clinical applications. PMID:24504374

Parallel algorithms for modeling flow in permeable media. Annual report, February 15, 1995 - February 14, 1996

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

G.A. Pope; K. Sephernoori; D.C. McKinney

1996-03-15

This report describes the application of distributed-memory parallel programming techniques to a compositional simulator called UTCHEM. The University of Texas Chemical Flooding reservoir simulator (UTCHEM) is a general-purpose vectorized chemical flooding simulator that models the transport of chemical species in three-dimensional, multiphase flow through permeable media. The parallel version of UTCHEM addresses solving large-scale problems by reducing the amount of time that is required to obtain the solution as well as providing a flexible and portable programming environment. In this work, the original parallel version of UTCHEM was modified and ported to CRAY T3D and CRAY T3E, distributed-memory, multiprocessor computersmore » using CRAY-PVM as the interprocessor communication library. Also, the data communication routines were modified such that the portability of the original code across different computer architectures was mad possible.« less

Culture et Gestion d'Etangs a Poissons d'Eau Douce (Freshwater Fish Pond Culture and Management). Appropriate Technologies for Development. Manual Series--M37.

ERIC Educational Resources Information Center

Chakroff, Marilyn; Druben, Laurel, Ed.

This is the French translation of a "how-to" manual, designed as a working and teaching tool for extension agents as they establish and/or maintain local fish pond operations. The manual presents information to facilitate technology transfer and to provide a clear guide for warm water fish pond construction and management. Major topic…

Obstructions for twist star products

NASA Astrophysics Data System (ADS)

Bieliavsky, Pierre; Esposito, Chiara; Waldmann, Stefan; Weber, Thomas

2018-05-01

In this short note, we point out that not every star product is induced by a Drinfel'd twist by showing that not every Poisson structure is induced by a classical r-matrix. Examples include the higher genus symplectic Pretzel surfaces and the symplectic sphere S^2.

Exact Dynamics via Poisson Process: a unifying Monte Carlo paradigm

NASA Astrophysics Data System (ADS)

Gubernatis, James

2014-03-01

A common computational task is solving a set of ordinary differential equations (o.d.e.'s). A little known theorem says that the solution of any set of o.d.e.'s is exactly solved by the expectation value over a set of arbitary Poisson processes of a particular function of the elements of the matrix that defines the o.d.e.'s. The theorem thus provides a new starting point to develop real and imaginary-time continous-time solvers for quantum Monte Carlo algorithms, and several simple observations enable various quantum Monte Carlo techniques and variance reduction methods to transfer to a new context. I will state the theorem, note a transformation to a very simple computational scheme, and illustrate the use of some techniques from the directed-loop algorithm in context of the wavefunction Monte Carlo method that is used to solve the Lindblad master equation for the dynamics of open quantum systems. I will end by noting that as the theorem does not depend on the source of the o.d.e.'s coming from quantum mechanics, it also enables the transfer of continuous-time methods from quantum Monte Carlo to the simulation of various classical equations of motion heretofore only solved deterministically.

Updating a preoperative surface model with information from real-time tracked 2D ultrasound using a Poisson surface reconstruction algorithm

NASA Astrophysics Data System (ADS)

Sun, Deyu; Rettmann, Maryam E.; Holmes, David R.; Linte, Cristian A.; Packer, Douglas; Robb, Richard A.

2014-03-01

In this work, we propose a method for intraoperative reconstruction of a left atrial surface model for the application of cardiac ablation therapy. In this approach, the intraoperative point cloud is acquired by a tracked, 2D freehand intra-cardiac echocardiography device, which is registered and merged with a preoperative, high resolution left atrial surface model built from computed tomography data. For the surface reconstruction, we introduce a novel method to estimate the normal vector of the point cloud from the preoperative left atrial model, which is required for the Poisson Equation Reconstruction algorithm. In the current work, the algorithm is evaluated using a preoperative surface model from patient computed tomography data and simulated intraoperative ultrasound data. Factors such as intraoperative deformation of the left atrium, proportion of the left atrial surface sampled by the ultrasound, sampling resolution, sampling noise, and registration error were considered through a series of simulation experiments.